Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	validation_status	validation_method	validation_tumor_sample	validation_alt_allele
Unknown	0	broad.mit.edu	37	1	847050	847050	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:847050delG	uc001abu.1	+											Homo sapiens cDNA FLJ31924 fis, clone NT2RP7005468.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	993468	993468	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:993468delA	uc009vjs.1	+						uc001acl.1_5'Flank					Homo sapiens cDNA, FLJ17392.																														---	---	---	---
TTLL10	254173	broad.mit.edu	37	1	1108387	1108388	+	5'Flank	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1108387_1108388delAA	uc001acy.2	+						TTLL10_uc010nyg.1_5'Flank	NM_001130045	NP_001123517			tubulin tyrosine ligase-like family, member 10						protein modification process		ATP binding|tubulin-tyrosine ligase activity			large_intestine(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;4.75e-36)|OV - Ovarian serous cystadenocarcinoma(86;5.82e-22)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)														---	---	---	---
UBE2J2	118424	broad.mit.edu	37	1	1207530	1207531	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1207530_1207531delAA	uc001adn.2	-						UBE2J2_uc001ado.2_Intron|UBE2J2_uc001adp.2_Intron|UBE2J2_uc001adq.2_Intron|UBE2J2_uc001adr.2_Intron|UBE2J2_uc001ads.2_Intron	NM_194458	NP_919440			ubiquitin conjugating enzyme E2, J2 isoform 3						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)														---	---	---	---
ATAD3A	55210	broad.mit.edu	37	1	1469613	1469614	+	3'UTR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1469613_1469614insC	uc001afz.1	+	16					ATAD3A_uc001aga.1_3'UTR|ATAD3A_uc001agb.1_3'UTR|ATAD3A_uc001agc.1_RNA	NM_018188	NP_060658			ATPase family, AAA domain containing 3A								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)														---	---	---	---
GNB1	2782	broad.mit.edu	37	1	1814360	1814361	+	Intron	DEL	AA	-	-	rs75877253		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1814360_1814361delAA	uc001aif.2	-						GNB1_uc009vky.2_Intron	NM_002074	NP_002065			guanine nucleotide-binding protein, beta-1						cellular response to glucagon stimulus|energy reserve metabolic process|muscarinic acetylcholine receptor signaling pathway|platelet activation|Ras protein signal transduction|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|GTPase binding|signal transducer activity				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)														---	---	---	---
PRKCZ	5590	broad.mit.edu	37	1	2038182	2038183	+	Intron	INS	-	T	T	rs142626853	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2038182_2038183insT	uc001aiq.2	+						PRKCZ_uc001air.2_Intron|PRKCZ_uc010nyw.1_Intron|PRKCZ_uc001ais.2_Intron	NM_002744	NP_002735			protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)														---	---	---	---
PRKCZ	5590	broad.mit.edu	37	1	2077359	2077359	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2077359delA	uc001aiq.2	+						PRKCZ_uc001air.2_Intron|PRKCZ_uc010nyw.1_Intron|PRKCZ_uc001ais.2_Intron|PRKCZ_uc009vla.2_Intron|PRKCZ_uc010nyx.1_Intron|PRKCZ_uc009vlb.2_Intron	NM_002744	NP_002735			protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)														---	---	---	---
PRKCZ	5590	broad.mit.edu	37	1	2078048	2078049	+	Intron	INS	-	AG	AG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2078048_2078049insAG	uc001aiq.2	+						PRKCZ_uc001air.2_Intron|PRKCZ_uc010nyw.1_Intron|PRKCZ_uc001ais.2_Intron|PRKCZ_uc009vla.2_Intron|PRKCZ_uc010nyx.1_Intron|PRKCZ_uc009vlb.2_Intron	NM_002744	NP_002735			protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)														---	---	---	---
PRKCZ	5590	broad.mit.edu	37	1	2104603	2104603	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2104603delT	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_Intron	NM_002744	NP_002735			protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	2689314	2689314	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2689314delT								MMEL1 (124833 upstream) : ACTRT2 (248732 downstream)																																			---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3043679	3043680	+	Intron	INS	-	AG	AG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3043679_3043680insAG	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron|hsa-mir-4251|MI0015861_5'Flank	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	4669228	4669228	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4669228delA								LOC284661 (184484 upstream) : AJAP1 (45877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5082559	5082570	+	IGR	DEL	ACACACACACAC	-	-	rs111915896		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5082559_5082570delACACACACACAC								AJAP1 (238709 upstream) : NPHP4 (840300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5342964	5342965	+	IGR	INS	-	G	G	rs145826888	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5342964_5342965insG								AJAP1 (499114 upstream) : NPHP4 (579905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5655487	5655490	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5655487_5655490delAAAA	uc001alp.1	-											Homo sapiens cDNA FLJ43088 fis, clone BRTHA3025826.																														---	---	---	---
KCNAB2	8514	broad.mit.edu	37	1	6090839	6090846	+	Intron	DEL	TGTGTGTA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6090839_6090846delTGTGTGTA	uc009vlv.1	+						KCNAB2_uc001alv.1_Intron|KCNAB2_uc001alw.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	6457320	6457321	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6457320_6457321delAA								ACOT7 (3494 upstream) : HES2 (15179 downstream)																																			---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7311934	7311935	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7311934_7311935delTG	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	7327767	7327767	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7327767delT	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	7419046	7419046	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7419046delT	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	7637623	7637624	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7637623_7637624delTT	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)												OREG0013054	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	8065713	8065714	+	IGR	DEL	TT	-	-	rs71567341		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8065713_8065714delTT								PARK7 (20372 upstream) : ERRFI1 (6066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	8100605	8100605	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8100605delA								ERRFI1 (14212 upstream) : SLC45A1 (283785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	8331970	8331970	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8331970delT								ERRFI1 (245577 upstream) : SLC45A1 (52420 downstream)																																			---	---	---	---
RERE	473	broad.mit.edu	37	1	8812264	8812264	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8812264delA	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc001aph.1_Intron	NM_012102	NP_036234			atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)														---	---	---	---
CA6	765	broad.mit.edu	37	1	9011280	9011281	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9011280_9011281delAA	uc001apm.2	+						CA6_uc009vmn.2_Intron	NM_001215	NP_001206			carbonic anhydrase VI precursor						one-carbon metabolic process	extracellular region	carbonate dehydratase activity|zinc ion binding			ovary(2)	2	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|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;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SLC2A7	155184	broad.mit.edu	37	1	9080733	9080736	+	Intron	DEL	TCTT	-	-	rs813983	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9080733_9080736delTCTT	uc009vmo.1	-							NM_207420	NP_997303			intestinal facilitative glucose transporter 7							integral to membrane|plasma membrane	sugar transmembrane transporter activity				0	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;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-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	9102465	9102466	+	Intron	DEL	TA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9102465_9102466delTA	uc001apo.2	-						SLC2A5_uc010nzy.1_Intron|SLC2A5_uc010nzz.1_Intron|SLC2A5_uc010oaa.1_Intron|SLC2A5_uc010oab.1_Intron|SLC2A5_uc010oac.1_Intron|SLC2A5_uc001app.3_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	9275141	9275141	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9275141delA								MIR34A (63305 upstream) : H6PD (19722 downstream)																																			---	---	---	---
SPSB1	80176	broad.mit.edu	37	1	9381718	9381718	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9381718delA	uc010oae.1	+							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)														---	---	---	---
SPSB1	80176	broad.mit.edu	37	1	9400342	9400342	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9400342delG	uc010oae.1	+							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)														---	---	---	---
SPSB1	80176	broad.mit.edu	37	1	9416314	9416315	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9416314_9416315insC	uc010oae.1	+	2	703_704	c.364_365insC	c.(364-366)GCCfs	p.A122fs	SPSB1_uc001apv.2_Frame_Shift_Ins_p.A122fs	NM_025106	NP_079382	Q96BD6	SPSB1_HUMAN	splA/ryanodine receptor domain and SOCS box	122	B30.2/SPRY.				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)														---	---	---	---
TMEM201	199953	broad.mit.edu	37	1	9674450	9674450	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9674450delT	uc001apz.2	+	10						NM_001130924	NP_001124396			transmembrane protein 201 isoform 1							integral to membrane|nuclear inner membrane					0	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
CLSTN1	22883	broad.mit.edu	37	1	9839914	9839914	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9839914delT	uc001aqh.2	-						CLSTN1_uc001aqi.2_Intron|CLSTN1_uc010oag.1_Intron	NM_001009566	NP_001009566			calsyntenin 1 isoform 1						homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
NMNAT1	64802	broad.mit.edu	37	1	10037927	10037927	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10037927delA	uc001aqp.2	+							NM_022787	NP_073624			nicotinamide mononucleotide adenylyltransferase						water-soluble vitamin metabolic process	nucleoplasm	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity|protein binding				0		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.31e-08)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(185;0.00028)|BRCA - Breast invasive adenocarcinoma(304;0.00032)|KIRC - Kidney renal clear cell carcinoma(229;0.00101)|STAD - Stomach adenocarcinoma(132;0.00908)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
RBP7	116362	broad.mit.edu	37	1	10068112	10068113	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10068112_10068113delAA	uc001aqq.2	+						RBP7_uc009vms.2_Intron	NM_052960	NP_443192			retinol binding protein 7, cellular							cytoplasm	retinal binding|retinol binding|transporter activity				0		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|BRCA - Breast invasive adenocarcinoma(304;0.000302)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00856)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)													---	---	---	---
RBP7	116362	broad.mit.edu	37	1	10074068	10074068	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10074068delA	uc001aqq.2	+						RBP7_uc009vms.2_Intron	NM_052960	NP_443192			retinol binding protein 7, cellular							cytoplasm	retinal binding|retinol binding|transporter activity				0		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|BRCA - Breast invasive adenocarcinoma(304;0.000302)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00856)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)													---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10287867	10287867	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10287867delA	uc001aqx.3	+						KIF1B_uc001aqv.3_Intron|KIF1B_uc001aqw.3_Intron|KIF1B_uc009vmt.2_Intron	NM_015074	NP_055889			kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10344920	10344920	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10344920delA	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	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)														---	---	---	---
DFFA	1676	broad.mit.edu	37	1	10527572	10527575	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10527572_10527575delTTTT	uc001arj.2	-						DFFA_uc001ark.2_Intron	NM_004401	NP_004392			DNA fragmentation factor, 45kDa, alpha						DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction|negative regulation of apoptosis	cytosol|mitochondrion|nucleoplasm|plasma membrane	deoxyribonuclease activity|identical protein binding				0	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)														---	---	---	---
CASZ1	54897	broad.mit.edu	37	1	10781350	10781350	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10781350delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	10956104	10956105	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10956104_10956105insT								CASZ1 (99397 upstream) : C1orf127 (50428 downstream)																																			---	---	---	---
TARDBP	23435	broad.mit.edu	37	1	11079629	11079629	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11079629delT	uc001art.2	+						TARDBP_uc010oap.1_Intron	NM_007375	NP_031401			TAR DNA binding protein						3'-UTR-mediated mRNA stabilization|cell death|mRNA processing|negative regulation by host of viral transcription|RNA splicing|transcription from RNA polymerase II promoter	nucleus	double-stranded DNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0578)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.37e-07)|COAD - Colon adenocarcinoma(227;7.38e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)														---	---	---	---
MASP2	10747	broad.mit.edu	37	1	11088275	11088275	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11088275delA	uc001aru.2	-							NM_006610	NP_006601			mannan-binding lectin serine protease 2 isoform						complement activation, classical pathway|complement activation, lectin pathway|proteolysis	extracellular region	calcium ion binding|calcium-dependent protein binding|serine-type endopeptidase activity			ovary(2)|pancreas(1)|skin(1)	4	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)														---	---	---	---
SRM	6723	broad.mit.edu	37	1	11116944	11116944	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11116944delT	uc001arz.1	-						SRM_uc001ary.1_5'Flank	NM_003132	NP_003123			spermidine synthase						spermidine biosynthetic process	cytosol	protein homodimerization activity|spermidine synthase activity				0	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)	STAD - Stomach adenocarcinoma(5;0.228)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)	S-Adenosylmethionine(DB00118)|Spermine(DB00127)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	11485720	11485731	+	IGR	DEL	TTGTGATTACTG	-	-	rs57124099		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11485720_11485731delTTGTGATTACTG								UBIAD1 (137230 upstream) : PTCHD2 (53564 downstream)																																			---	---	---	---
PTCHD2	57540	broad.mit.edu	37	1	11592056	11592057	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11592056_11592057delTC	uc001ash.3	+							NM_020780	NP_065831			patched domain containing 2						cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	11832102	11832103	+	5'Flank	INS	-	CT	CT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11832102_11832103insCT	uc001asz.2	+											RecName: Full=Uncharacterized protein C1orf167;																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	12104257	12104257	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12104257delA								MIIP (12151 upstream) : TNFRSF8 (19177 downstream)																																			---	---	---	---
TNFRSF8	943	broad.mit.edu	37	1	12131666	12131666	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12131666delT	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	12150752	12150752	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12150752delG	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	12198204	12198204	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12198204delA	uc001atq.2	+						TNFRSF8_uc010obc.1_Intron|TNFRSF8_uc001atr.2_Intron|TNFRSF8_uc001ats.2_Intron	NM_001243	NP_001234			tumor necrosis factor receptor superfamily,						cellular response to mechanical stimulus|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of TRAIL biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	cytoplasm|integral to membrane|plasma membrane				skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	5	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	12620646	12620648	+	IGR	DEL	CTT	-	-	rs6669325	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12620646_12620648delCTT								VPS13D (48550 upstream) : DHRS3 (7292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	12730529	12730529	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12730529delT								AADACL4 (3433 upstream) : AADACL3 (45589 downstream)																																			---	---	---	---
PRAMEF11	440560	broad.mit.edu	37	1	12890087	12890087	+	Intron	DEL	C	-	-	rs138946496	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12890087delC	uc001auk.2	-							NM_001146344	NP_001139816			PRAME family member 11												0																		---	---	---	---
PDPN	10630	broad.mit.edu	37	1	13917446	13917446	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13917446delT	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)														---	---	---	---
PRDM2	7799	broad.mit.edu	37	1	14107246	14107246	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14107246delC	uc001avi.2	+	8	3812	c.2956delC	c.(2956-2958)CCCfs	p.P986fs	PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Frame_Shift_Del_p.P986fs|PRDM2_uc001avj.2_Intron|PRDM2_uc001avk.2_Frame_Shift_Del_p.P785fs|PRDM2_uc009voe.2_Intron|PRDM2_uc009vof.2_Intron	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger	986	Pro-rich.|SH3-binding (Potential).					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)														---	---	---	---
PRDM2	7799	broad.mit.edu	37	1	14107892	14107893	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14107892_14107893insT	uc001avi.2	+	8	4458_4459	c.3602_3603insT	c.(3601-3603)GCTfs	p.A1201fs	PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Frame_Shift_Ins_p.A1201fs|PRDM2_uc001avj.2_Intron|PRDM2_uc001avk.2_Frame_Shift_Ins_p.A1000fs|PRDM2_uc009voe.2_Intron|PRDM2_uc009vof.2_Intron	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger	1201	C2H2-type 6.					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)														---	---	---	---
PRDM2	7799	broad.mit.edu	37	1	14150514	14150514	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14150514delA	uc001avi.2	+	10					PRDM2_uc001avg.2_3'UTR|PRDM2_uc009voe.2_RNA|PRDM2_uc009vof.2_RNA	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	14279154	14279155	+	IGR	INS	-	T	T	rs139609810	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14279154_14279155insT								PRDM2 (127582 upstream) : KAZ (646058 downstream)																																			---	---	---	---
KAZ	23254	broad.mit.edu	37	1	15231268	15231269	+	Intron	INS	-	T	T	rs4661545		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15231268_15231269insT	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	15344301	15344302	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15344301_15344302delAA	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																		---	---	---	---
KAZ	23254	broad.mit.edu	37	1	15359517	15359517	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15359517delT	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																		---	---	---	---
KAZ	23254	broad.mit.edu	37	1	15392332	15392332	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15392332delG	uc001avm.3	+						KAZ_uc009vog.1_3'UTR|KAZ_uc010obj.1_3'UTR|KAZ_uc001avo.2_3'UTR|KAZ_uc001avp.2_3'UTR|KAZ_uc001avq.2_3'UTR|KAZ_uc001avr.2_3'UTR	NM_201628	NP_963922			kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0																		---	---	---	---
C1orf126	200197	broad.mit.edu	37	1	15446039	15446039	+	Intron	DEL	T	-	-	rs77933605		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15446039delT	uc001avv.3	-						C1orf126_uc009voh.2_Intron	NR_027136				Homo sapiens cDNA FLJ23703 fis, clone HEP10820.												0																		---	---	---	---
FHAD1	114827	broad.mit.edu	37	1	15720104	15720105	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15720104_15720105delTT	uc001awb.2	+						FHAD1_uc010obl.1_Intron|FHAD1_uc001awe.1_Intron|FHAD1_uc001awg.2_Intron	NM_052929	NP_443161			forkhead-associated (FHA) phosphopeptide binding											skin(1)	1																		---	---	---	---
DNAJC16	23341	broad.mit.edu	37	1	15888980	15888981	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15888980_15888981delTT	uc001aws.2	+						DNAJC16_uc001awr.1_Intron|DNAJC16_uc001awt.2_Intron|DNAJC16_uc001awu.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)														---	---	---	---
DNAJC16	23341	broad.mit.edu	37	1	15898140	15898140	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15898140delT	uc001aws.2	+	15					DNAJC16_uc001awt.2_3'UTR|DNAJC16_uc001awu.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	16248729	16248729	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16248729delT	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	16456618	16456619	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16456618_16456619insC	uc001aya.1	-							NM_004431	NP_004422			ephrin receptor EphA2 precursor						activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus	focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane	ATP binding|ephrin receptor activity|protein binding			lung(3)|central_nervous_system(3)|stomach(2)|ovary(2)	10		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)													---	---	---	---
NBPF1	55672	broad.mit.edu	37	1	16937527	16937528	+	Intron	DEL	AA	-	-	rs71247398		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16937527_16937528delAA	uc009vos.1	-						NBPF1_uc001aza.3_Intron|NBPF1_uc001azb.1_Intron|NBPF1_uc001azc.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)														---	---	---	---
CROCCL1	84809	broad.mit.edu	37	1	16961526	16961526	+	Intron	DEL	T	-	-	rs1762955		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16961526delT	uc001azg.1	-						CROCCL1_uc001azf.2_5'Flank|CROCCL1_uc001azi.1_Intron|uc001azj.1_RNA					Homo sapiens mRNA for FLJ00313 protein.												0																		---	---	---	---
CROCCL1	84809	broad.mit.edu	37	1	16964050	16964050	+	Intron	DEL	A	-	-	rs71224330		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16964050delA	uc001azg.1	-						CROCCL1_uc001azi.1_Intron|uc001azj.1_Intron					Homo sapiens mRNA for FLJ00313 protein.												0																		---	---	---	---
ESPNP	284729	broad.mit.edu	37	1	17019432	17019433	+	Intron	INS	-	GC	GC	rs138548890	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17019432_17019433insGC	uc001azn.1	-							NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0																		---	---	---	---
ESPNP	284729	broad.mit.edu	37	1	17034125	17034126	+	Frame_Shift_Ins	INS	-	AGCT	AGCT	rs141324796	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17034125_17034126insAGCT	uc001azn.1	-	3	478_479	c.364_365insAGCT	c.(364-366)TGGfs	p.W122fs	ESPNP_uc010ocj.1_Frame_Shift_Ins_p.W52fs	NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0																		---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17208381	17208382	+	Intron	INS	-	G	G	rs67937751		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17208381_17208382insG	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	17240120	17240120	+	Intron	DEL	A	-	-	rs71962187		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17240120delA	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	17259963	17259963	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17259963delA	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	17299013	17299014	+	3'UTR	DEL	CA	-	-	rs6661019	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17299013_17299014delCA	uc001azt.2	+	37					CROCC_uc001azu.2_3'UTR|CROCC_uc001azv.2_3'UTR	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)														---	---	---	---
PADI6	353238	broad.mit.edu	37	1	17707289	17707289	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17707289delC	uc001bak.1	+							NM_207421	NP_997304			peptidylarginine deiminase type 6						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)													---	---	---	---
ARHGEF10L	55160	broad.mit.edu	37	1	17983222	17983222	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17983222delG	uc001ban.2	+						ARHGEF10L_uc009vpe.1_Intron|ARHGEF10L_uc001bao.2_Intron|ARHGEF10L_uc001bap.2_Intron|ARHGEF10L_uc001baq.2_Intron|ARHGEF10L_uc010ocs.1_Intron|ARHGEF10L_uc001bar.2_Intron|ARHGEF10L_uc009vpf.2_Intron	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	18027425	18027425	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18027425delG								ARHGEF10L (3056 upstream) : ACTL8 (54383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	18058869	18058869	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18058869delA								ARHGEF10L (34500 upstream) : ACTL8 (22939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	18074881	18074881	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18074881delT								ARHGEF10L (50512 upstream) : ACTL8 (6927 downstream)																																			---	---	---	---
ACTL8	81569	broad.mit.edu	37	1	18125956	18125956	+	Intron	DEL	T	-	-	rs144331230		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18125956delT	uc001bat.2	+							NM_030812	NP_110439			actin-like 8							cytoplasm|cytoskeleton				ovary(4)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00186)|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;0.00583)|BRCA - Breast invasive adenocarcinoma(304;6.43e-06)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.00652)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	18251837	18251837	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18251837delG								ACTL8 (98281 upstream) : IGSF21 (182403 downstream)																																			---	---	---	---
IGSF21	84966	broad.mit.edu	37	1	18432075	18432075	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18432075delC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	18717330	18717331	+	IGR	DEL	GG	-	-	rs112150540		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18717330_18717331delGG								IGSF21 (12354 upstream) : KLHDC7A (90093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	18774151	18774152	+	IGR	INS	-	ACAC	ACAC	rs147080604	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18774151_18774152insACAC								IGSF21 (69175 upstream) : KLHDC7A (33272 downstream)																																			---	---	---	---
IFFO2	126917	broad.mit.edu	37	1	19264450	19264451	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19264450_19264451insC	uc001bbd.2	-							NM_001136265	NP_001129737			intermediate filament family orphan 2												0																		---	---	---	---
IFFO2	126917	broad.mit.edu	37	1	19269874	19269874	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19269874delA	uc001bbd.2	-							NM_001136265	NP_001129737			intermediate filament family orphan 2												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	19308528	19308529	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19308528_19308529delAG								IFFO2 (25702 upstream) : UBR4 (90075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	19340080	19340080	+	IGR	DEL	A	-	-	rs113047860		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19340080delA								IFFO2 (57254 upstream) : UBR4 (58524 downstream)																																			---	---	---	---
KIAA0090	23065	broad.mit.edu	37	1	19557063	19557064	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19557063_19557064insA	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	19590022	19590022	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19590022delT								MRTO4 (3401 upstream) : AKR7L (2454 downstream)																																			---	---	---	---
AKR7A2	8574	broad.mit.edu	37	1	19631484	19631484	+	Intron	DEL	T	-	-	rs112155249		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19631484delT	uc001bbw.2	-						AKR7A2_uc001bbx.2_Intron	NM_003689	NP_003680			aldo-keto reductase family 7, member A2						carbohydrate metabolic process|cellular aldehyde metabolic process	Golgi apparatus	alditol:NADP+ 1-oxidoreductase activity|electron carrier activity			central_nervous_system(1)	1		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;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	19894600	19894600	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19894600delA								CAPZB (82608 upstream) : C1orf151 (28867 downstream)																																			---	---	---	---
TMCO4	255104	broad.mit.edu	37	1	20030050	20030050	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20030050delT	uc001bcn.2	-						TMCO4_uc001bcm.2_Intron|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron	NM_181719	NP_859070			transmembrane and coiled-coil domains 4							integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)														---	---	---	---
TMCO4	255104	broad.mit.edu	37	1	20121667	20121667	+	Intron	DEL	A	-	-	rs111532754		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20121667delA	uc001bcn.2	-						TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron|TMCO4_uc009vpn.1_Intron|TMCO4_uc001bcq.1_Intron	NM_181719	NP_859070			transmembrane and coiled-coil domains 4							integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)														---	---	---	---
PLA2G5	5322	broad.mit.edu	37	1	20400362	20400363	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20400362_20400363delAA	uc001bcy.2	+						PLA2G5_uc001bcw.2_Intron|PLA2G5_uc001bcx.2_Intron	NM_000929	NP_000920			phospholipase A2, group V precursor						lipid catabolic process	extracellular region	calcium ion binding|calcium-dependent phospholipase A2 activity			skin(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)														---	---	---	---
PLA2G2F	64600	broad.mit.edu	37	1	20474908	20474909	+	3'UTR	INS	-	GA	GA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20474908_20474909insGA	uc009vpp.1	+	5						NM_022819	NP_073730			phospholipase A2, group IIF						lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|phospholipase A2 activity			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	20505705	20505706	+	IGR	INS	-	TG	TG	rs139820513	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20505705_20505706insTG								PLA2G2C (4018 upstream) : UBXN10 (6872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	20547663	20547664	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20547663_20547664delAA								UBXN10 (27722 upstream) : VWA5B1 (69748 downstream)																																			---	---	---	---
VWA5B1	127731	broad.mit.edu	37	1	20618698	20618698	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20618698delT	uc009vps.2	+						VWA5B1_uc001bdd.2_Intron|VWA5B1_uc010odc.1_Intron	NM_001039500	NP_001034589			von Willebrand factor A domain containing 5B1							extracellular region					0																		---	---	---	---
CDA	978	broad.mit.edu	37	1	20920926	20920926	+	Intron	DEL	A	-	-	rs140203894	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20920926delA	uc001bdk.2	+						CDA_uc001bdl.2_Intron|CDA_uc009vpv.2_Intron	NM_001785	NP_001776			cytidine deaminase						cell surface receptor linked signaling pathway|cytosine metabolic process|negative regulation of cell growth|negative regulation of nucleotide metabolic process|protein homotetramerization|pyrimidine nucleoside salvage	cytosol|extracellular region	cytidine deaminase activity|nucleoside binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)													---	---	---	---
KIF17	57576	broad.mit.edu	37	1	21014538	21014538	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21014538delT	uc001bdr.3	-						KIF17_uc001bdp.3_5'Flank|KIF17_uc001bdq.3_5'Flank|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)														---	---	---	---
KIF17	57576	broad.mit.edu	37	1	21034256	21034256	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21034256delA	uc001bdr.3	-						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)														---	---	---	---
SH2D5	400745	broad.mit.edu	37	1	21059410	21059411	+	5'Flank	INS	-	C	C	rs142324139	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21059410_21059411insC	uc001bdt.1	-						SH2D5_uc009vpy.1_5'Flank|SH2D5_uc001bdu.1_5'Flank	NM_001103160	NP_001096630			SH2 domain containing 5 isoform 2												0		Colorectal(325;3.46e-05)|all_lung(284;5.32e-05)|Lung NSC(340;5.51e-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;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|GBM - Glioblastoma multiforme(114;0.000465)|Kidney(64;0.000476)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(64;0.00634)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
HP1BP3	50809	broad.mit.edu	37	1	21088901	21088902	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21088901_21088902insA	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	21175886	21175886	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21175886delT	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	21351941	21351941	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21351941delA	uc001bec.2	-						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)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21553520	21553520	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	21689372	21689372	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21689372delT								ECE1 (17338 upstream) : NBPF3 (77259 downstream)																																			---	---	---	---
ALPL	249	broad.mit.edu	37	1	21883601	21883601	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21883601delT	uc001bet.2	+						ALPL_uc010odn.1_Intron|ALPL_uc010odo.1_Intron|ALPL_uc010odp.1_Intron|ALPL_uc001beu.3_Intron	NM_000478	NP_000469			tissue-nonspecific alkaline phosphatase						response to vitamin D|skeletal system development	anchored to membrane|cytoplasm|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)													---	---	---	---
RAP1GAP	5909	broad.mit.edu	37	1	21959879	21959880	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21959879_21959880insC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	22270445	22270445	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22270445delA								HSPG2 (6695 upstream) : CELA3B (32973 downstream)																																			---	---	---	---
CDC42	998	broad.mit.edu	37	1	22410099	22410100	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22410099_22410100delAA	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	22594113	22594114	+	IGR	DEL	GT	-	-	rs72339369		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22594113_22594114delGT								WNT4 (123728 upstream) : ZBTB40 (184230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22646224	22646224	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22646224delA								WNT4 (175839 upstream) : ZBTB40 (132120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22741950	22741950	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22741950delA								WNT4 (271565 upstream) : ZBTB40 (36394 downstream)																																			---	---	---	---
C1QB	713	broad.mit.edu	37	1	22985391	22985426	+	Intron	DEL	GATGGATGGATGGATGCAGGGATGGAGGGGTAGAGA	-	-	rs72301775	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22985391_22985426delGATGGATGGATGGATGCAGGGATGGAGGGGTAGAGA	uc001bgd.2	+							NM_000491	NP_000482			complement component 1, q subcomponent, B chain						complement activation, classical pathway|innate immune response	collagen|complement component C1 complex				breast(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.06e-27)|Colorectal(126;1.58e-07)|GBM - Glioblastoma multiforme(114;6.72e-06)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000551)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)													---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23104498	23104499	+	Intron	INS	-	GTTT	GTTT	rs140306701	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23104498_23104499insGTTT	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	23107812	23107816	+	Intron	DEL	AAAAA	-	-	rs143757031		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23107812_23107816delAAAAA	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				---	---	---	---
Unknown	0	broad.mit.edu	37	1	23259645	23259645	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23259645delT								EPHB2 (17823 upstream) : KDM1A (86296 downstream)																																			---	---	---	---
KDM1A	23028	broad.mit.edu	37	1	23352890	23352891	+	Intron	INS	-	G	G	rs35806585		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23352890_23352891insG	uc001bgi.2	+						KDM1A_uc001bgj.2_Intron	NM_015013	NP_055828			lysine-specific histone demethylase 1 isoform b						blood coagulation|muscle cell development|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of protein binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin	androgen receptor binding|chromatin binding|enzyme binding|flavin adenine dinucleotide binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-K9 specific)|ligand-dependent nuclear receptor transcription coactivator activity|MyoD binding|oxidoreductase activity|p53 binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2																		---	---	---	---
HNRNPR	10236	broad.mit.edu	37	1	23650294	23650295	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23650294_23650295delTT	uc001bgr.3	-						HNRNPR_uc001bgp.3_Intron|HNRNPR_uc009vqk.2_Intron|HNRNPR_uc001bgs.3_Intron|HNRNPR_uc010odw.1_Intron|HNRNPR_uc010odx.1_Intron|HNRNPR_uc009vql.2_Intron	NM_005826	NP_005817			heterogeneous nuclear ribonucleoprotein R							catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)														---	---	---	---
HNRNPR	10236	broad.mit.edu	37	1	23660416	23660416	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23660416delT	uc001bgr.3	-						HNRNPR_uc001bgp.3_Intron|HNRNPR_uc009vqk.2_Intron|HNRNPR_uc001bgs.3_Intron|HNRNPR_uc010odw.1_Intron|HNRNPR_uc010odx.1_Intron|HNRNPR_uc009vql.2_Intron	NM_005826	NP_005817			heterogeneous nuclear ribonucleoprotein R							catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	24024718	24024718	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24024718delG								RPL11 (1805 upstream) : TCEB3 (45138 downstream)																																			---	---	---	---
LYPLA2	11313	broad.mit.edu	37	1	24119502	24119502	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24119502delT	uc001bht.2	+	3	204	c.83delT	c.(82-84)ATTfs	p.I28fs	LYPLA2_uc001bhr.2_Frame_Shift_Del_p.I23fs|LYPLA2_uc001bhs.1_Frame_Shift_Del_p.I23fs|LYPLA2_uc001bhu.2_Intron	NM_007260	NP_009191	O95372	LYPA2_HUMAN	lysophospholipase II	28					fatty acid metabolic process	cytoplasm	hydrolase activity			ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;1.79e-24)|Colorectal(126;4.8e-08)|COAD - Colon adenocarcinoma(152;2.83e-06)|GBM - Glioblastoma multiforme(114;4.22e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0827)|LUSC - Lung squamous cell carcinoma(448;0.184)														---	---	---	---
MYOM3	127294	broad.mit.edu	37	1	24382908	24382908	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24382908delT	uc001bin.3	-	37					MYOM3_uc001bil.3_3'UTR|MYOM3_uc001bim.3_3'UTR	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)														---	---	---	---
MYOM3	127294	broad.mit.edu	37	1	24395007	24395007	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24395007delC	uc001bin.3	-						MYOM3_uc001bil.3_5'Flank|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)														---	---	---	---
LOC284632	284632	broad.mit.edu	37	1	24533556	24533557	+	Intron	DEL	AC	-	-	rs5773079		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24533556_24533557delAC	uc010oei.1	+							NR_027087				Homo sapiens hypothetical protein LOC284632, mRNA (cDNA clone IMAGE:4826835).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	24945203	24945205	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24945203_24945205delAAA								C1orf130 (9387 upstream) : SRRM1 (24389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25033979	25033980	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25033979_25033980delAA								SRRM1 (34208 upstream) : CLIC4 (37780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25053719	25053720	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25053719_25053720delCT								SRRM1 (53948 upstream) : CLIC4 (18040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25346274	25346275	+	IGR	INS	-	CA	CA	rs144846778	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25346274_25346275insCA								RUNX3 (54662 upstream) : SYF2 (202492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25380969	25380970	+	IGR	INS	-	CCTT	CCTT	rs56362360	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25380969_25380970insCCTT								RUNX3 (89357 upstream) : SYF2 (167797 downstream)																																			---	---	---	---
C1orf63	57035	broad.mit.edu	37	1	25571795	25571796	+	Intron	DEL	AA	-	-	rs113744649		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25571795_25571796delAA	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)														---	---	---	---
TMEM57	55219	broad.mit.edu	37	1	25800739	25800739	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25800739delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	25900890	25900891	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25900890_25900891delAG								LDLRAP1 (5515 upstream) : MAN1C1 (43068 downstream)																																			---	---	---	---
MAN1C1	57134	broad.mit.edu	37	1	25977450	25977450	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25977450delT	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)														---	---	---	---
PAQR7	164091	broad.mit.edu	37	1	26195624	26195624	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26195624delA	uc001bkx.2	-							NM_178422	NP_848509			progestin and adipoQ receptor family member VII						cell differentiation|multicellular organismal development|oogenesis	integral to membrane|plasma membrane	receptor activity|steroid binding			breast(3)	3		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.16e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000724)|BRCA - Breast invasive adenocarcinoma(304;0.000965)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0136)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PAFAH2	5051	broad.mit.edu	37	1	26314634	26314634	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26314634delT	uc001bld.3	-						PAFAH2_uc001ble.3_Intron	NM_000437	NP_000428			platelet-activating factor acetylhydrolase 2						lipid catabolic process	cytoplasm	1-alkyl-2-acetylglycerophosphocholine esterase activity|phospholipid binding			ovary(2)	2		Colorectal(325;3.47e-05)|Lung NSC(340;6.23e-05)|all_lung(284;9.48e-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;3.84e-25)|Colorectal(126;3.57e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00717)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	26533504	26533504	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26533504delA								CATSPER4 (4472 upstream) : CCDC21 (27189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	26549595	26549596	+	5'Flank	INS	-	A	A	rs111819835		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26549595_26549596insA	uc001blq.2	+											Homo sapiens cDNA clone IMAGE:4813089.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	26687259	26687259	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26687259delC								AIM1L (16816 upstream) : ZNF683 (866 downstream)																																			---	---	---	---
DHDDS	79947	broad.mit.edu	37	1	26782238	26782238	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26782238delA	uc001bml.2	+						DHDDS_uc001bmk.2_Intron|DHDDS_uc001bmm.2_Intron|DHDDS_uc001bmn.2_Intron|DHDDS_uc010ofd.1_Intron	NM_205861	NP_995583			dehydrodolichyl diphosphate synthase isoform b								protein binding|transferase activity, transferring alkyl or aryl (other than methyl) groups			breast(3)	3		all_cancers(24;2.04e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)														---	---	---	---
RPS6KA1	6195	broad.mit.edu	37	1	26900923	26900923	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26900923delT	uc001bmr.1	+	22					RPS6KA1_uc010ofe.1_3'UTR|RPS6KA1_uc001bms.1_3'UTR|RPS6KA1_uc009vsl.1_3'UTR	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	27105931	27105931	+	Frame_Shift_Del	DEL	G	-	-	rs140055856		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27105931delG	uc001bmv.1	+	20	5915	c.5542delG	c.(5542-5544)GGGfs	p.G1848fs	ARID1A_uc001bmu.1_Frame_Shift_Del_p.G1631fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.G694fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.G176fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.G90fs	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1848					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	p.G1848fs*6(3)		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								---	---	---	---
ZDHHC18	84243	broad.mit.edu	37	1	27170541	27170542	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27170541_27170542insT	uc001bnb.2	+						ZDHHC18_uc010ofh.1_Intron	NM_032283	NP_115659			zinc finger, DHHC-type containing 18							integral to membrane	zinc ion binding				0		all_cancers(24;5.82e-22)|all_epithelial(13;9.91e-20)|Colorectal(325;0.000147)|Breast(348;0.000706)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;5.71e-53)|Epithelial(14;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(117;1.53e-29)|Colorectal(126;1.9e-09)|COAD - Colon adenocarcinoma(152;4.2e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000548)|STAD - Stomach adenocarcinoma(196;0.00065)|KIRC - Kidney renal clear cell carcinoma(1967;0.000779)|GBM - Glioblastoma multiforme(114;0.0265)|READ - Rectum adenocarcinoma(331;0.0455)|Lung(427;0.163)|LUSC - Lung squamous cell carcinoma(448;0.237)														---	---	---	---
GPN2	54707	broad.mit.edu	37	1	27215784	27215784	+	Intron	DEL	C	-	-	rs910048	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27215784delC	uc001bnd.1	-							NM_018066	NP_060536			ATP binding domain 1 family, member B								GTP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	27377673	27377673	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27377673delA								FAM46B (38340 upstream) : SLC9A1 (47628 downstream)																																			---	---	---	---
MAP3K6	9064	broad.mit.edu	37	1	27687696	27687696	+	Frame_Shift_Del	DEL	G	-	-	rs139401154		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27687696delG	uc001bny.1	-	13	2033	c.1784delC	c.(1783-1785)CCGfs	p.P595fs	MAP3K6_uc009vsw.1_Frame_Shift_Del_p.P587fs|MAP3K6_uc001bnz.1_Frame_Shift_Del_p.P118fs	NM_004672	NP_004663	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase	595					activation of JUN kinase activity		ATP binding|magnesium ion binding|MAP kinase kinase kinase activity			breast(4)|lung(3)|ovary(1)|central_nervous_system(1)	9		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
WASF2	10163	broad.mit.edu	37	1	27755557	27755557	+	Intron	DEL	A	-	-	rs74061798	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27755557delA	uc001bof.1	-						WASF2_uc010ofl.1_Intron	NM_006990	NP_008921			WAS protein family, member 2						actin cytoskeleton organization|G-protein signaling, coupled to cAMP nucleotide second messenger	actin cytoskeleton|lamellipodium	actin binding			skin(2)|ovary(1)	3		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)														---	---	---	---
WASF2	10163	broad.mit.edu	37	1	27756286	27756286	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27756286delA	uc001bof.1	-						WASF2_uc010ofl.1_Intron	NM_006990	NP_008921			WAS protein family, member 2						actin cytoskeleton organization|G-protein signaling, coupled to cAMP nucleotide second messenger	actin cytoskeleton|lamellipodium	actin binding			skin(2)|ovary(1)	3		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)														---	---	---	---
AHDC1	27245	broad.mit.edu	37	1	27890799	27890799	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27890799delG	uc009vsy.2	-						AHDC1_uc009vsz.1_Intron|AHDC1_uc001boh.1_Intron	NM_001029882	NP_001025053			AT hook, DNA binding motif, containing 1								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)														---	---	---	---
EYA3	2140	broad.mit.edu	37	1	28329328	28329328	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28329328delA	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)														---	---	---	---
SESN2	83667	broad.mit.edu	37	1	28595177	28595177	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28743548	28743548	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28743548delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	28923519	28923523	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28923519_28923523delTTTTT								RAB42 (2433 upstream) : TAF12 (6088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	28984872	28984872	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28984872delA								RNU11 (9626 upstream) : GMEB1 (10372 downstream)																																			---	---	---	---
GMEB1	10691	broad.mit.edu	37	1	29003766	29003766	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29003766delT	uc001bra.2	+						GMEB1_uc001bqz.2_Intron|GMEB1_uc001brb.2_Intron	NM_006582	NP_006573			glucocorticoid modulatory element binding						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|metal ion binding|transcription coactivator activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	29041386	29041387	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29041386_29041387delAA								GMEB1 (1 upstream) : YTHDF2 (21749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	29051735	29051735	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29051735delT								GMEB1 (10350 upstream) : YTHDF2 (11401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	29515132	29515132	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29515132delT								SFRS4 (6495 upstream) : MECR (4253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	29852431	29852432	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29852431_29852432delTT								PTPRU (199116 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30172282	30172282	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30172282delT								PTPRU (518967 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30216750	30216751	+	IGR	DEL	GG	-	-	rs72458042		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30216750_30216751delGG								PTPRU (563435 upstream) : MATN1 (967375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30357964	30357964	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30357964delC								PTPRU (704649 upstream) : MATN1 (826162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30503947	30503947	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30503947delA	uc001bry.3	-											Homo sapiens cDNA clone IMAGE:4830073.																														---	---	---	---
PUM1	9698	broad.mit.edu	37	1	31484012	31484017	+	Intron	DEL	ACACAC	-	-	rs71964070		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31484012_31484017delACACAC	uc001bsi.1	-						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)														---	---	---	---
ZCCHC17	51538	broad.mit.edu	37	1	31791934	31791934	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31791934delT	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	31915369	31915369	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31915369delA								SERINC2 (7845 upstream) : LOC284551 (68667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	31971702	31971702	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31971702delC	uc001bsw.1	+						uc001bsx.2_5'Flank					Homo sapiens hypothetical protein LOC149086, mRNA (cDNA clone IMAGE:5171562), with apparent retained intron.																														---	---	---	---
TINAGL1	64129	broad.mit.edu	37	1	32011995	32011998	+	5'Flank	DEL	CATC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32011995_32011998delCATC	uc001bsz.2	+							NM_022164	NP_071447			tubulointerstitial nephritis antigen-like 1						endosome transport|immune response|proteolysis	extracellular region	cysteine-type endopeptidase activity|extracellular matrix structural constituent|polysaccharide binding|scavenger receptor activity				0		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)														---	---	---	---
HCRTR1	3061	broad.mit.edu	37	1	32081721	32081722	+	5'Flank	DEL	CA	-	-	rs10563217		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32081721_32081722delCA	uc009vtx.2	+						HCRTR1_uc001btb.2_5'Flank|HCRTR1_uc001btc.3_5'Flank|HCRTR1_uc001btd.2_5'Flank|HCRTR1_uc010ogl.1_5'Flank	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)														---	---	---	---
COL16A1	1307	broad.mit.edu	37	1	32131296	32131296	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32131296delG	uc001btk.1	-						COL16A1_uc001bti.1_Intron|COL16A1_uc001btj.1_Intron	NM_001856	NP_001847			alpha 1 type XVI collagen precursor						cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)														---	---	---	---
PTP4A2	8073	broad.mit.edu	37	1	32375887	32375887	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32375887delT	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)																---	---	---	---
KHDRBS1	10657	broad.mit.edu	37	1	32519675	32519676	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32519675_32519676insA	uc001buc.1	+							NM_006559				KH domain containing, RNA binding, signal						cell cycle arrest|cell proliferation|cell surface receptor linked signaling pathway|G2/M transition of mitotic cell cycle|mRNA processing|negative regulation of transcription, DNA-dependent|regulation of RNA export from nucleus|transcription, DNA-dependent	membrane|nucleus	DNA binding|RNA binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(1)	1		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	32813956	32813956	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32813956delT								MARCKSL1 (12122 upstream) : TSSK3 (13906 downstream)																																			---	---	---	---
ZBTB8B	728116	broad.mit.edu	37	1	32938907	32938908	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32938907_32938908delAA	uc001bvl.3	+						ZBTB8A_uc001bvk.2_Intron	NM_001145720	NP_001139192			zinc finger and BTB domain containing 8B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
SYNC	81493	broad.mit.edu	37	1	33146114	33146114	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
SYNC	81493	broad.mit.edu	37	1	33162058	33162058	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33162058delT	uc001bvt.2	-						SYNC_uc010ohl.1_Intron	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	33171518	33171518	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33171518delT								SYNC (3157 upstream) : KIAA1522 (35994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	33201095	33201096	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33201095_33201096insT								SYNC (32734 upstream) : KIAA1522 (6416 downstream)																																			---	---	---	---
S100PBP	64766	broad.mit.edu	37	1	33296681	33296682	+	Intron	DEL	AA	-	-	rs71727205		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33296681_33296682delAA	uc001bvz.2	+						S100PBP_uc001bwa.1_Intron|S100PBP_uc001bwb.1_Intron|S100PBP_uc001bwc.2_Intron|S100PBP_uc001bwd.2_Intron	NM_022753	NP_073590			S100P binding protein isoform a							nucleus	calcium-dependent protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)																---	---	---	---
RNF19B	127544	broad.mit.edu	37	1	33415573	33415573	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34624930	34624930	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34624930delC	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128			CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	34816045	34816045	+	IGR	DEL	T	-	-	rs2177621	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34816045delT								C1orf94 (131316 upstream) : MIR552 (319155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	35018403	35018403	+	IGR	DEL	A	-	-	rs79965030		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35018403delA								C1orf94 (333674 upstream) : MIR552 (116797 downstream)																																			---	---	---	---
DLGAP3	58512	broad.mit.edu	37	1	35369544	35369545	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35369544_35369545delCT	uc001byc.2	-							NM_001080418	NP_001073887			discs, large (Drosophila) homolog-associated						cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)																---	---	---	---
ZMYM6	9204	broad.mit.edu	37	1	35458647	35458647	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35458647delA	uc001byh.2	-						ZMYM6_uc001byf.1_Intron|ZMYM6_uc010oht.1_Intron|ZMYM6_uc009vup.2_Intron|ZMYM6_uc009vuq.1_Intron	NM_007167	NP_009098			zinc finger protein 258						multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)																---	---	---	---
ZMYM1	79830	broad.mit.edu	37	1	35542222	35542222	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35542222delA	uc001bym.2	+						ZMYM1_uc001byl.1_5'Flank|ZMYM1_uc009vus.1_5'Flank|ZMYM1_uc001byn.2_5'Flank|ZMYM1_uc010ohu.1_5'Flank|ZMYM1_uc001byo.2_5'Flank|ZMYM1_uc009vut.2_5'Flank	NM_024772	NP_079048			zinc finger, MYM domain containing 1							nucleus	nucleic acid binding|protein dimerization activity|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
ZMYM1	79830	broad.mit.edu	37	1	35561402	35561402	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35561402delT	uc001bym.2	+						ZMYM1_uc001byl.1_Intron|ZMYM1_uc009vus.1_Intron|ZMYM1_uc001byn.2_Intron|ZMYM1_uc010ohu.1_Intron|ZMYM1_uc001byo.2_Intron|ZMYM1_uc009vut.2_Intron	NM_024772	NP_079048			zinc finger, MYM domain containing 1							nucleus	nucleic acid binding|protein dimerization activity|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	35613783	35613783	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35613783delT								ZMYM1 (32329 upstream) : SFPQ (28199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	36033867	36033867	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36033867delT								NCDN (1489 upstream) : PSMB2 (1546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	36252158	36252159	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36252158_36252159delAA								CLSPN (16607 upstream) : EIF2C4 (21669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	37028623	37028624	+	IGR	DEL	TC	-	-	rs72173554		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37028623_37028624delTC								CSF3R (80114 upstream) : GRIK3 (232504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	37659557	37659558	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37659557_37659558delTT								GRIK3 (159713 upstream) : ZC3H12A (280561 downstream)																																			---	---	---	---
MEAF6	64769	broad.mit.edu	37	1	37959772	37959772	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37959772delA	uc001cbg.1	-						MEAF6_uc001cbd.1_Intron|MEAF6_uc001cbe.1_Intron|MEAF6_uc009vvd.1_Intron|MEAF6_uc001cbf.1_Intron	NM_022756	NP_073593			MYST/Esa1-associated factor 6						histone H2A acetylation|histone H3-K14 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|NuA4 histone acetyltransferase complex|nucleolus	protein binding				0																		---	---	---	---
CDCA8	55143	broad.mit.edu	37	1	38164439	38164439	+	Intron	DEL	C	-	-	rs3842536		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38164439delC	uc001cbr.2	+						CDCA8_uc001cbs.2_Intron|CDCA8_uc010oih.1_Intron	NM_018101	NP_060571			cell division cycle associated 8						cell division|chromosome organization|mitotic metaphase|mitotic prometaphase	chromosome passenger complex|chromosome, centromeric region|cytosol|nucleolus|spindle	protein binding			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
CDCA8	55143	broad.mit.edu	37	1	38170966	38170966	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38170966delT	uc001cbr.2	+						CDCA8_uc001cbs.2_Intron|CDCA8_uc010oih.1_Intron	NM_018101	NP_060571			cell division cycle associated 8						cell division|chromosome organization|mitotic metaphase|mitotic prometaphase	chromosome passenger complex|chromosome, centromeric region|cytosol|nucleolus|spindle	protein binding			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
INPP5B	3633	broad.mit.edu	37	1	38340948	38340949	+	Intron	INS	-	T	T	rs146816630	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38340948_38340949insT	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)																---	---	---	---
INPP5B	3633	broad.mit.edu	37	1	38408584	38408585	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38408584_38408585delAG	uc001ccg.1	-						INPP5B_uc009vvk.1_Intron|INPP5B_uc001cch.2_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)																---	---	---	---
FHL3	2275	broad.mit.edu	37	1	38462977	38462977	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38462977delT	uc001ccj.2	-	6					FHL3_uc001cck.2_3'UTR|FHL3_uc001ccl.2_Frame_Shift_Del_p.K313fs|FHL3_uc001ccm.2_3'UTR	NM_004468	NP_004459			four and a half LIM domains 3						muscle organ development		zinc ion binding				0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	38534479	38534480	+	IGR	DEL	GT	-	-	rs11801495	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38534479_38534480delGT								POU3F1 (22029 upstream) : RRAGC (770535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38716698	38716699	+	IGR	INS	-	TG	TG	rs144252081	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38716698_38716699insTG								POU3F1 (204248 upstream) : RRAGC (588316 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39182917	39182918	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39182917_39182918insT								POU3F1 (670467 upstream) : RRAGC (122097 downstream)																																			---	---	---	---
RRAGC	64121	broad.mit.edu	37	1	39313233	39313233	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39313233delT	uc001ccq.2	-						RRAGC_uc010oim.1_Intron|RRAGC_uc001ccr.2_Intron	NM_022157	NP_071440			Ras-related GTP binding C						apoptosis|cell growth|cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade|RNA splicing|small GTPase mediated signal transduction|transcription, DNA-dependent	lysosome|nucleus	GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein heterodimerization activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)																---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39572859	39572859	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39572859delA	uc010ois.1	+							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	39573722	39573724	+	Intron	DEL	TTT	-	-	rs140005907		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39573722_39573724delTTT	uc010ois.1	+							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	39906884	39906884	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39906884delT	uc010oiu.1	+						MACF1_uc010ois.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	39950262	39950262	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39950262delT	uc010oiu.1	+						MACF1_uc010ois.1_Intron|MACF1_uc001cde.1_Intron|MACF1_uc001cdf.1_Intron|MACF1_uc001cdg.2_Intron|MACF1_uc001cdh.2_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	40120618	40120618	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40120618delT								HEYL (15270 upstream) : NT5C1A (4175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	40398949	40398949	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40398949delA								MYCL1 (31262 upstream) : MFSD2A (21835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	40409723	40409723	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40409723delT								MYCL1 (42036 upstream) : MFSD2A (11061 downstream)																																			---	---	---	---
MFSD2A	84879	broad.mit.edu	37	1	40430369	40430370	+	Intron	INS	-	GT	GT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40430369_40430370insGT	uc001cev.2	+						MFSD2A_uc010ojb.1_Intron|MFSD2A_uc001ceu.2_Intron|MFSD2A_uc010ojc.1_Intron|MFSD2A_uc009vvy.2_Intron|MFSD2A_uc001cex.2_5'Flank	NM_001136493	NP_001129965			major facilitator superfamily domain containing						transmembrane transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)|pancreas(1)	2																		---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42354704	42354705	+	Intron	INS	-	AC	AC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42354704_42354705insAC	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron|HIVEP3_uc001chb.1_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)																---	---	---	---
FOXJ3	22887	broad.mit.edu	37	1	42654673	42654673	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42654673delT	uc001che.2	-						FOXJ3_uc001chf.2_Intron|FOXJ3_uc001chg.2_Intron	NM_014947	NP_055762			forkhead box J3						embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
RIMKLA	284716	broad.mit.edu	37	1	42879374	42879374	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42879374delT	uc001chi.2	+							NM_173642	NP_775913			ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
CCDC30	728621	broad.mit.edu	37	1	43021760	43021760	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
CCDC30	728621	broad.mit.edu	37	1	43063536	43063536	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43063536delA	uc009vwk.1	+						CCDC30_uc001chm.2_Intron|CCDC30_uc001chn.2_Intron	NM_001080850	NP_001074319			coiled-coil domain containing 30												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	43242778	43242778	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43242778delT								C1orf50 (1364 upstream) : CCDC23 (29945 downstream)																																			---	---	---	---
TIE1	7075	broad.mit.edu	37	1	43770692	43770692	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43770692delC	uc001ciu.2	+	2	308	c.229delC	c.(229-231)CCCfs	p.P77fs	TIE1_uc010okd.1_Frame_Shift_Del_p.P77fs|TIE1_uc010oke.1_Frame_Shift_Del_p.P32fs|TIE1_uc009vwq.2_Frame_Shift_Del_p.P77fs|TIE1_uc010okf.1_5'UTR|TIE1_uc010okg.1_5'Flank|TIE1_uc010oka.1_Frame_Shift_Del_p.P77fs|TIE1_uc010okb.1_Frame_Shift_Del_p.P77fs|TIE1_uc010okc.1_Frame_Shift_Del_p.P77fs	NM_005424	NP_005415	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and	77	Extracellular (Potential).|Ig-like C2-type 1.				mesoderm development	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	43847417	43847417	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43847417delA								ELOVL1 (13718 upstream) : MED8 (2171 downstream)																																			---	---	---	---
KIAA0467	23334	broad.mit.edu	37	1	43895161	43895161	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43895161delA	uc001cjk.1	+							NM_015284	NP_056099			hypothetical protein LOC23334							peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
RNF220	55182	broad.mit.edu	37	1	44940749	44940749	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44940749delA	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620			ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
RNF220	55182	broad.mit.edu	37	1	45063122	45063125	+	Intron	DEL	TCTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45063122_45063125delTCTC	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620			ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
TMEM53	79639	broad.mit.edu	37	1	45124824	45124825	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45124824_45124825insT	uc001cmc.2	-						TMEM53_uc001cmb.1_Intron|TMEM53_uc001cmd.2_Intron|TMEM53_uc009vxh.1_Intron|TMEM53_uc010ola.1_Intron	NM_024587	NP_078863			transmembrane protein 53							integral to membrane				ovary(2)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
TMEM53	79639	broad.mit.edu	37	1	45138443	45138444	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45138443_45138444delAA	uc001cmc.2	-						TMEM53_uc001cmb.1_Intron|TMEM53_uc001cmd.2_Intron|TMEM53_uc009vxh.1_Intron|C1orf228_uc001cmf.2_5'Flank	NM_024587	NP_078863			transmembrane protein 53							integral to membrane				ovary(2)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
C1orf228	339541	broad.mit.edu	37	1	45181818	45181818	+	Intron	DEL	T	-	-	rs67697786		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45181818delT	uc001cmf.2	+							NM_001145636	NP_001139108			hypothetical protein LOC339541								binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	45245791	45245791	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45245791delT								RPS8 (1380 upstream) : BEST4 (3468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	45245946	45245946	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45245946delT								RPS8 (1535 upstream) : BEST4 (3313 downstream)																																			---	---	---	---
ZSWIM5	57643	broad.mit.edu	37	1	45486714	45486715	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45486714_45486715delTT	uc001cnd.2	-							NM_020883	NP_065934			zinc finger, SWIM domain containing 5								zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
MUTYH	4595	broad.mit.edu	37	1	45796007	45796007	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45796007delT	uc001cnm.2	-						MUTYH_uc009vxn.2_Intron|MUTYH_uc001cnf.2_Intron|MUTYH_uc009vxo.2_Intron|MUTYH_uc001cng.2_Intron|MUTYH_uc001cnj.2_Intron|MUTYH_uc001cni.2_Intron|MUTYH_uc001cnh.2_Intron|MUTYH_uc001cno.2_Intron|MUTYH_uc001cnk.2_Intron|MUTYH_uc010oll.1_Intron|MUTYH_uc001cnl.2_Intron|MUTYH_uc009vxp.2_Intron|MUTYH_uc001cnn.2_Intron	NM_012222	NP_036354			mutY homolog isoform 1						depurination|mismatch repair	nucleoplasm	4 iron, 4 sulfur cluster binding|DNA N-glycosylase activity|endonuclease activity|metal ion binding|MutSalpha complex binding				0	Acute lymphoblastic leukemia(166;0.155)							Mis			colorectal		BER_DNA_glycosylases	MUTYH-associated_polyposis				---	---	---	---
TESK2	10420	broad.mit.edu	37	1	45882463	45882464	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45882463_45882464delTT	uc001cns.1	-						TESK2_uc009vxr.1_Intron|TESK2_uc010olo.1_Intron|TESK2_uc009vxs.1_Intron|TESK2_uc010olp.1_Intron	NM_007170	NP_009101			testis-specific protein kinase 2						actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
PIK3R3	8503	broad.mit.edu	37	1	46511446	46511446	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46511446delT	uc001cpb.3	-						PIK3R3_uc009vyb.2_Intron|PIK3R3_uc009vyc.2_Intron|PIK3R3_uc001cpc.3_Intron|PIK3R3_uc010olw.1_Intron|PIK3R3_uc010olv.1_Intron	NM_003629	NP_003620			phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
POMGNT1	55624	broad.mit.edu	37	1	46673217	46673217	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46673217delT	uc001cpg.2	-						POMGNT1_uc001cpf.2_Intron|C1orf190_uc010oma.1_Intron	NR_024332				SubName: Full=Protein O-linked mannose beta1,2-N-acetylglucosaminyltransferase;						protein N-linked glycosylation|protein O-linked glycosylation	Golgi membrane|integral to membrane|microsome	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
LRRC41	10489	broad.mit.edu	37	1	46752493	46752493	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46752493delT	uc001cpn.2	-						LRRC41_uc010omb.1_Intron|LRRC41_uc001cpo.1_Intron	NM_006369	NP_006360			MUF1 protein											ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
NSUN4	387338	broad.mit.edu	37	1	46818124	46818124	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46818124delA	uc001cpr.1	+						NSUN4_uc010omc.1_Intron|NSUN4_uc009vyf.1_Intron|NSUN4_uc009vyg.1_Intron|NSUN4_uc001cpt.1_Intron|NSUN4_uc001cps.1_Intron	NM_199044	NP_950245			NOL1/NOP2/Sun domain family 4 protein								methyltransferase activity				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	46945307	46945307	+	IGR	DEL	G	-	-	rs60864579	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46945307delG								FAAH (65787 upstream) : DMBX1 (27361 downstream)																																			---	---	---	---
CYP4Z2P	163720	broad.mit.edu	37	1	47353700	47353701	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47353700_47353701delTC	uc001cqo.1	-						CYP4Z2P_uc009vyn.1_Intron	NR_002788				Homo sapiens cDNA FLJ40054 fis, clone TBAES2000315, weakly similar to CYTOCHROME P450 4A1 (EC 1.14.15.3).												0																		---	---	---	---
CYP4Z1	199974	broad.mit.edu	37	1	47581140	47581141	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47581140_47581141delAA	uc001cqu.1	+							NM_178134	NP_835235			cytochrome P450 4Z1							endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	48332939	48332939	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48332939delA								FOXD2 (426577 upstream) : SKINTL (234448 downstream)																																			---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49194046	49194046	+	Intron	DEL	T	-	-	rs11344354		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49194046delT	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron|BEND5_uc001crx.3_Intron|BEND5_uc001crw.3_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	49246884	49246885	+	Intron	DEL	AG	-	-	rs113548415		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49246884_49246885delAG	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	49745239	49745239	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49745239delT	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	49961908	49961909	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49961908_49961909insT	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	50202492	50202493	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50202492_50202493delAA	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	50416746	50416746	+	Intron	DEL	G	-	-	rs146339683	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50416746delG	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)														---	---	---	---
FAF1	11124	broad.mit.edu	37	1	50965036	50965040	+	Intron	DEL	TTTTT	-	-	rs72898956		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50965036_50965040delTTTTT	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	p.0?(1)		ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)														---	---	---	---
FAF1	11124	broad.mit.edu	37	1	51275052	51275052	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51275052delA	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?(1)		ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	51509622	51509622	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51509622delT								CDKN2C (69315 upstream) : C1orf185 (58284 downstream)														p.0?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	1	51643001	51643002	+	IGR	INS	-	TATG	TATG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51643001_51643002insTATG								C1orf185 (29249 upstream) : RNF11 (58943 downstream)																																			---	---	---	---
RNF11	26994	broad.mit.edu	37	1	51716222	51716222	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51716222delT	uc001csi.3	+							NM_014372	NP_055187			ring finger protein 11						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	DNA binding|protein binding|zinc ion binding				0																		---	---	---	---
TTC39A	22996	broad.mit.edu	37	1	51757478	51757478	+	Intron	DEL	A	-	-	rs112294762		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51757478delA	uc001csl.2	-						TTC39A_uc001csk.2_Intron|TTC39A_uc010ond.1_Intron|TTC39A_uc010one.1_Intron|TTC39A_uc010onf.1_Intron|TTC39A_uc001csj.2_Intron	NM_001080494	NP_001073963			tetratricopeptide repeat domain 39A isoform 2								binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	51815994	51815994	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51815994delT								TTC39A (5209 upstream) : EPS15 (3941 downstream)																																			---	---	---	---
EPS15	2060	broad.mit.edu	37	1	51868089	51868089	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51868089delA	uc001csq.1	-						EPS15_uc009vyz.1_Intron|EPS15_uc001csp.3_Intron	NM_001981	NP_001972			epidermal growth factor receptor pathway						cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2								T	MLL	ALL								---	---	---	---
EPS15	2060	broad.mit.edu	37	1	51978516	51978524	+	Intron	DEL	TTTTTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51978516_51978524delTTTTTTTTT	uc001csq.1	-						EPS15_uc009vyz.1_Intron|EPS15_uc001csr.1_Intron	NM_001981	NP_001972			epidermal growth factor receptor pathway						cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2								T	MLL	ALL								---	---	---	---
OSBPL9	114883	broad.mit.edu	37	1	52092975	52092975	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52092975delT	uc001cst.2	+						OSBPL9_uc001css.2_Intron|OSBPL9_uc001csx.2_Intron|OSBPL9_uc009vza.2_Intron|OSBPL9_uc001csu.2_Intron|OSBPL9_uc001csv.2_Intron|OSBPL9_uc001csw.2_Intron	NM_024586	NP_078862			oxysterol binding protein-like 9 isoform e						lipid transport		lipid binding			central_nervous_system(1)	1																		---	---	---	---
OSBPL9	114883	broad.mit.edu	37	1	52122289	52122289	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52122289delT	uc001cst.2	+						OSBPL9_uc001css.2_Intron|OSBPL9_uc001csx.2_Intron|OSBPL9_uc009vza.2_Intron|OSBPL9_uc001csu.2_Intron|OSBPL9_uc001csv.2_Intron|OSBPL9_uc001csw.2_Intron	NM_024586	NP_078862			oxysterol binding protein-like 9 isoform e						lipid transport		lipid binding			central_nervous_system(1)	1																		---	---	---	---
NRD1	4898	broad.mit.edu	37	1	52301764	52301764	+	Intron	DEL	A	-	-	rs115629064	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52301764delA	uc001ctc.3	-						NRD1_uc009vzb.2_Intron|NRD1_uc001ctd.3_Intron|NRD1_uc001cte.2_Intron|NRD1_uc001ctf.2_Intron|NRD1_uc010ong.1_Intron|NRD1_uc009vzc.1_Intron	NM_002525	NP_002516			nardilysin isoform a						cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity	cell surface|cytosol	epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	52602629	52602631	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52602629_52602631delAAA								BTF3L4 (48539 upstream) : ZFYVE9 (5415 downstream)																																			---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52716699	52716701	+	Intron	DEL	TTG	-	-	rs111747771		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52716699_52716701delTTG	uc001cto.2	+						ZFYVE9_uc001ctn.2_Intron|ZFYVE9_uc001ctp.2_Intron	NM_004799	NP_004790			zinc finger, FYVE domain containing 9 isoform 3						endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity			ovary(2)|lung(2)|central_nervous_system(2)|skin(2)	8																		---	---	---	---
ZYG11B	79699	broad.mit.edu	37	1	53255588	53255589	+	Intron	DEL	TT	-	-	rs67389144		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53255588_53255589delTT	uc001cuj.2	+						ZYG11B_uc009vzg.2_Intron|ZYG11B_uc010onj.1_Intron	NM_024646	NP_078922			zyg-11 homolog B								protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
ZYG11B	79699	broad.mit.edu	37	1	53279194	53279194	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53279194delT	uc001cuj.2	+						ZYG11B_uc009vzg.2_Intron|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																		---	---	---	---
SCP2	6342	broad.mit.edu	37	1	53509737	53509738	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53509737_53509738delTT	uc001cur.1	+						SCP2_uc001cus.1_Intron|SCP2_uc010ono.1_Intron|SCP2_uc010onp.1_Intron|SCP2_uc009vzi.1_Intron|SCP2_uc010onq.1_Intron|SCP2_uc001cut.1_Intron|SCP2_uc001cuu.1_Intron	NM_002979	NP_002970			sterol carrier protein 2 isoform 1 proprotein						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|lipid transport	mitochondrion|nucleus|peroxisomal matrix	propanoyl-CoA C-acyltransferase activity|propionyl-CoA C2-trimethyltridecanoyltransferase activity|protein binding|sterol binding			breast(1)	1																		---	---	---	---
SLC1A7	6512	broad.mit.edu	37	1	53606139	53606139	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53606139delA	uc001cuy.2	-						SLC1A7_uc001cuz.3_Intron	NM_006671	NP_006662			solute carrier family 1 (glutamate transporter),							integral to membrane|plasma membrane	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|large_intestine(1)	3				Colorectal(1306;0.234)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	53955011	53955012	+	IGR	INS	-	TT	TT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53955011_53955012insTT								DMRTB1 (21853 upstream) : GLIS1 (16894 downstream)																																			---	---	---	---
GLIS1	148979	broad.mit.edu	37	1	54064208	54064208	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54064208delA	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																		---	---	---	---
ACOT11	26027	broad.mit.edu	37	1	55088935	55088935	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55088935delG	uc001cxm.1	+						FAM151A_uc001cxn.2_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																		---	---	---	---
TTC22	55001	broad.mit.edu	37	1	55247528	55247528	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55247528delA	uc009vzt.1	-							NM_001114108	NP_001107580			tetratricopeptide repeat domain 22 isoform 1								binding				0																		---	---	---	---
C1orf177	163747	broad.mit.edu	37	1	55278815	55278816	+	Intron	DEL	TT	-	-	rs11308288		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55278815_55278816delTT	uc001cyb.3	+						C1orf177_uc001cya.3_Intron	NM_001110533	NP_001104003			hypothetical protein LOC163747 isoform 2												0																		---	---	---	---
USP24	23358	broad.mit.edu	37	1	55573113	55573113	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55573113delA	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	55770373	55770374	+	IGR	INS	-	C	C	rs140167832	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55770373_55770374insC								USP24 (89611 upstream) : None (None downstream)																																			---	---	---	---
PPAP2B	8613	broad.mit.edu	37	1	56962089	56962089	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56962089delT	uc001cyj.1	-	7						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	57002826	57002826	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57002826delA	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																		---	---	---	---
C1orf168	199920	broad.mit.edu	37	1	57284868	57284868	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57284868delT	uc001cym.3	-						C1orf168_uc009vzu.1_Intron|C1orf168_uc009vzv.1_Intron	NM_001004303	NP_001004303			hypothetical protein LOC199920											ovary(3)|skin(2)	5																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57619297	57619297	+	Intron	DEL	T	-	-	rs71734245		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57619297delT	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57769344	57769345	+	Intron	INS	-	A	A	rs149398650	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57769344_57769345insA	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57910308	57910309	+	Intron	INS	-	AC	AC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57910308_57910309insAC	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	58345781	58345781	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58345781delC	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	59004990	59004990	+	Intron	DEL	A	-	-	rs79348154		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59004990delA	uc001cyt.1	-						OMA1_uc001cyx.1_5'Flank|OMA1_uc001cyy.2_Intron|OMA1_uc009vzz.2_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	59676814	59676816	+	IGR	DEL	TGA	-	-	rs331632	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59676814_59676816delTGA								LOC729467 (64335 upstream) : FGGY (85809 downstream)																																			---	---	---	---
FGGY	55277	broad.mit.edu	37	1	59812017	59812017	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59812017delG	uc001czi.3	+	4	624	c.412delG	c.(412-414)GGGfs	p.G138fs	FGGY_uc001czg.2_Frame_Shift_Del_p.G26fs|FGGY_uc001czh.2_RNA|FGGY_uc009wac.2_Frame_Shift_Del_p.G138fs|FGGY_uc001czj.3_Frame_Shift_Del_p.G138fs|FGGY_uc001czk.3_Frame_Shift_Del_p.G26fs|FGGY_uc001czl.3_Intron	NM_018291	NP_060761	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	138					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	60272171	60272171	+	IGR	DEL	T	-	-	rs138191130		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60272171delT								FGGY (43771 upstream) : HOOK1 (8292 downstream)																																			---	---	---	---
C1orf87	127795	broad.mit.edu	37	1	60493394	60493394	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60493394delA	uc001czs.1	-							NM_152377	NP_689590			hypothetical protein LOC127795								calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	60636885	60636885	+	IGR	DEL	A	-	-	rs113919366		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60636885delA								C1orf87 (97459 upstream) : NFIA (906061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	61033750	61033750	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61033750delA								C1orf87 (494324 upstream) : NFIA (509196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	61482436	61482436	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61482436delC								C1orf87 (943010 upstream) : NFIA (60510 downstream)																																			---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61860961	61860964	+	Intron	DEL	TTTT	-	-	rs77381718		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61860961_61860964delTTTT	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron	NM_001134673	NP_001128145			nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62231063	62231064	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62231063_62231064delTT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62232379	62232379	+	Intron	DEL	A	-	-	rs10889254	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62232379delA	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62237397	62237397	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62237397delT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62264562	62264563	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62264562_62264563delAA	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62267609	62267610	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62267609_62267610delTT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
KANK4	163782	broad.mit.edu	37	1	62744912	62744915	+	Intron	DEL	ACAG	-	-	rs71702540		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62744912_62744915delACAG	uc001dah.3	-						KANK4_uc001dai.3_Intron	NM_181712	NP_859063			ankyrin repeat domain 38											ovary(3)|skin(2)|lung(1)	6																		---	---	---	---
KANK4	163782	broad.mit.edu	37	1	62777079	62777079	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	62817699	62817699	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62817699delT								KANK4 (32616 upstream) : USP1 (84276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	63339135	63339135	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63339135delA								ATG4C (9086 upstream) : FOXD3 (449595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	63811417	63811417	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63811417delT								FOXD3 (20620 upstream) : ALG6 (21844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	63825424	63825425	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63825424_63825425delCT								FOXD3 (34627 upstream) : ALG6 (7836 downstream)																																			---	---	---	---
EFCAB7	84455	broad.mit.edu	37	1	64016784	64016784	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64016784delT	uc001dbf.2	+							NM_032437	NP_115813			EF-hand calcium binding domain 7								calcium ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	64162681	64162681	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64162681delT								PGM1 (36767 upstream) : ROR1 (77009 downstream)																																			---	---	---	---
ROR1	4919	broad.mit.edu	37	1	64299637	64299637	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64299637delT	uc001dbj.2	+						ROR1_uc001dbi.3_Intron	NM_005012	NP_005003			receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19																		---	---	---	---
ROR1	4919	broad.mit.edu	37	1	64537273	64537274	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64537273_64537274delAC	uc001dbj.2	+						ROR1_uc001dbi.3_Intron	NM_005012	NP_005003			receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19																		---	---	---	---
ROR1	4919	broad.mit.edu	37	1	64573744	64573745	+	Intron	DEL	TG	-	-	rs3084945		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64573744_64573745delTG	uc001dbj.2	+						ROR1_uc001dbi.3_Intron|uc001dbl.2_Intron|uc001dbk.2_Intron	NM_005012	NP_005003			receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19																		---	---	---	---
ROR1	4919	broad.mit.edu	37	1	64576678	64576678	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64576678delA	uc001dbj.2	+						ROR1_uc001dbi.3_Intron|uc001dbl.2_Intron|uc001dbk.2_Intron	NM_005012	NP_005003			receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19																		---	---	---	---
CACHD1	57685	broad.mit.edu	37	1	65154801	65154802	+	Intron	DEL	AT	-	-	rs61230054		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65154801_65154802delAT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	65170288	65170288	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65170288delA								CACHD1 (11547 upstream) : RAVER2 (40490 downstream)																																			---	---	---	---
JAK1	3716	broad.mit.edu	37	1	65310329	65310329	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65310329delA	uc001dbu.1	-						JAK1_uc009wam.1_Intron|JAK1_uc009wal.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								---	---	---	---
JAK1	3716	broad.mit.edu	37	1	65351779	65351779	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65351779delT	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								---	---	---	---
JAK1	3716	broad.mit.edu	37	1	65360471	65360471	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65360471delA	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								---	---	---	---
Unknown	0	broad.mit.edu	37	1	65488670	65488670	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65488670delT								JAK1 (56051 upstream) : MIR101-1 (35447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	65695219	65695220	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65695219_65695220delAA								AK3L1 (2046 upstream) : DNAJC6 (24928 downstream)																																			---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66728184	66728184	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66728184delG	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	66799151	66799152	+	Intron	DEL	AC	-	-	rs78012721		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66799151_66799152delAC	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.2_Intron|PDE4B_uc001dcp.2_Intron|PDE4B_uc001dcq.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)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	67538430	67538431	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67538430_67538431delCT								SLC35D1 (18350 upstream) : C1orf141 (19428 downstream)																																			---	---	---	---
C1orf141	400757	broad.mit.edu	37	1	67568176	67568176	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67568176delT	uc001ddl.1	-						C1orf141_uc001ddm.1_Intron|C1orf141_uc001ddn.1_Intron	NM_001013674	NP_001013696			hypothetical protein LOC400757											ovary(1)	1																		---	---	---	---
IL23R	149233	broad.mit.edu	37	1	67672004	67672004	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67672004delT	uc001ddo.2	+						IL23R_uc009waz.2_Intron|IL23R_uc001ddp.2_Intron|IL23R_uc010opi.1_Intron|IL23R_uc010opj.1_Intron|IL23R_uc010opk.1_Intron|IL23R_uc010opl.1_Intron|IL23R_uc010opm.1_Intron|IL23R_uc001ddq.2_Intron|IL23R_uc010opn.1_Intron|IL23R_uc001ddr.2_Intron|IL23R_uc010opo.1_Intron|IL23R_uc010opp.1_Intron|IL23R_uc010opq.1_Intron|IL23R_uc010opr.1_Intron|IL23R_uc010ops.1_Intron|IL23R_uc010opt.1_Intron|IL23R_uc010opu.1_Intron|IL23R_uc010opv.1_Intron|IL23R_uc010opw.1_Intron|IL23R_uc010opx.1_Intron|IL23R_uc010opy.1_Intron|IL23R_uc010opz.1_Intron|IL23R_uc010oqa.1_Intron|IL23R_uc010oqb.1_Intron|IL23R_uc010oqc.1_Intron|IL23R_uc010oqd.1_Intron|IL23R_uc010oqe.1_Intron|IL23R_uc010oqf.1_Intron|IL23R_uc010oqg.1_Intron|IL23R_uc010oqh.1_Intron|IL23R_uc001dds.2_5'Flank|IL23R_uc001ddt.2_5'Flank	NM_144701	NP_653302			interleukin 23 receptor precursor						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																		---	---	---	---
SERBP1	26135	broad.mit.edu	37	1	67889712	67889712	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67889712delA	uc001ddv.2	-						SERBP1_uc001ddx.2_Intron|SERBP1_uc001ddy.2_Intron|SERBP1_uc001ddw.2_Intron	NM_001018067	NP_001018077			SERPINE1 mRNA binding protein 1 isoform 1						regulation of mRNA stability	nucleus|perinuclear region of cytoplasm	mRNA 3'-UTR binding|protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	67933043	67933044	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67933043_67933044delGT								SERBP1 (36920 upstream) : GADD45A (217839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	67943873	67943873	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67943873delA								SERBP1 (47750 upstream) : GADD45A (207010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	68044033	68044034	+	IGR	INS	-	TG	TG	rs76397557		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68044033_68044034insTG								SERBP1 (147910 upstream) : GADD45A (106849 downstream)																																			---	---	---	---
GNG12	55970	broad.mit.edu	37	1	68174556	68174556	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68174556delT	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	68203294	68203294	+	Intron	DEL	T	-	-	rs75611844		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68203294delT	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	68301812	68301812	+	5'Flank	DEL	T	-	-	rs76771403		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68301812delT	uc001dea.1	-						uc001deb.1_Intron|uc001dec.1_Intron	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	68314315	68314315	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68314315delT	uc001deb.1	+						uc001dec.1_Intron					Homo sapiens cDNA FLJ38762 fis, clone KIDNE2013801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	69349719	69349720	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69349719_69349720delGA								DEPDC1 (386920 upstream) : LRRC7 (683148 downstream)																																			---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70144021	70144021	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70144021delA	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																		---	---	---	---
ANKRD13C	81573	broad.mit.edu	37	1	70742533	70742533	+	Intron	DEL	A	-	-	rs79912084		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70742533delA	uc001dex.3	-						ANKRD13C_uc009wbk.2_Intron	NM_030816	NP_110443			ankyrin repeat domain 13C						protein retention in ER lumen|regulation of anoikis|regulation of receptor biosynthetic process	endoplasmic reticulum membrane|perinuclear region of cytoplasm	receptor binding				0																		---	---	---	---
ANKRD13C	81573	broad.mit.edu	37	1	70747260	70747260	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70747260delT	uc001dex.3	-						ANKRD13C_uc009wbk.2_Intron	NM_030816	NP_110443			ankyrin repeat domain 13C						protein retention in ER lumen|regulation of anoikis|regulation of receptor biosynthetic process	endoplasmic reticulum membrane|perinuclear region of cytoplasm	receptor binding				0																		---	---	---	---
ANKRD13C	81573	broad.mit.edu	37	1	70758274	70758274	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70758274delA	uc001dex.3	-						ANKRD13C_uc009wbk.2_Intron	NM_030816	NP_110443			ankyrin repeat domain 13C						protein retention in ER lumen|regulation of anoikis|regulation of receptor biosynthetic process	endoplasmic reticulum membrane|perinuclear region of cytoplasm	receptor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	70854696	70854696	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70854696delC								HHLA3 (20993 upstream) : CTH (22259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	71220470	71220471	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71220470_71220471insT	uc001dff.2	+											Homo sapiens cDNA clone IMAGE:5167131, partial cds.																														---	---	---	---
PTGER3	5733	broad.mit.edu	37	1	71483945	71483945	+	Intron	DEL	T	-	-	rs67355521		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71483945delT	uc001dfg.1	-						PTGER3_uc001dfh.1_Intron|PTGER3_uc001dfi.1_Intron|PTGER3_uc001dfj.1_Intron|PTGER3_uc001dfk.1_Intron|PTGER3_uc001dfl.1_Intron|PTGER3_uc009wbm.1_Intron|PTGER3_uc001dfm.1_Intron|PTGER3_uc001dfn.2_Intron|PTGER3_uc009wbn.1_Intron|PTGER3_uc009wbo.2_Intron|PTGER3_uc001dfo.2_Intron|PTGER3_uc001dfp.1_Intron|PTGER3_uc001dfq.2_Intron	NM_198714	NP_942007			prostaglandin E receptor 3, subtype EP3 isoform						cell death|positive regulation of fever generation|transcription, DNA-dependent	integral to plasma membrane|nuclear envelope	ligand-dependent nuclear receptor activity|prostaglandin E receptor activity			pancreas(1)|lung(1)|skin(1)	3					Bimatoprost(DB00905)													---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72269411	72269411	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72269411delA	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169			neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	72902942	72902942	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72902942delT								NEGR1 (154537 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	72963682	72963683	+	IGR	INS	-	ATAG	ATAG	rs146419234	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72963682_72963683insATAG								NEGR1 (215277 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	73682261	73682261	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73682261delT								NEGR1 (933856 upstream) : LRRIQ3 (809443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	74066673	74066674	+	IGR	INS	-	A	A	rs142649482	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74066673_74066674insA								None (None upstream) : LRRIQ3 (425030 downstream)																																			---	---	---	---
TNNI3K	51086	broad.mit.edu	37	1	74968575	74968576	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74968575_74968576delCT	uc001dgf.1	+						TNNI3K_uc001dge.1_Intron	NM_015978	NP_057062			TNNI3 interacting kinase isoform b							cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10																		---	---	---	---
C1orf173	127254	broad.mit.edu	37	1	75105589	75105589	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75105589delA	uc001dgg.2	-							NM_001002912	NP_001002912			hypothetical protein LOC127254											ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5																		---	---	---	---
C1orf173	127254	broad.mit.edu	37	1	75108652	75108652	+	Intron	DEL	T	-	-	rs75412273	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75108652delT	uc001dgg.2	-							NM_001002912	NP_001002912			hypothetical protein LOC127254											ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5																		---	---	---	---
CRYZ	1429	broad.mit.edu	37	1	75182917	75182917	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75182917delA	uc001dgk.2	-						CRYZ_uc001dgj.2_Intron|CRYZ_uc001dgl.2_Intron|CRYZ_uc001dgm.2_Intron	NM_001130042	NP_001123514			crystallin, zeta isoform a						protein homotetramerization|visual perception|xenobiotic catabolic process	cytosol|Golgi apparatus	mRNA 3'-UTR binding|NADPH binding|NADPH:quinone reductase activity|zinc ion binding				0					Dicumarol(DB00266)													---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75685359	75685359	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75685359delA	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910			solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	76242691	76242692	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76242691_76242692delCT								ACADM (13338 upstream) : RABGGTB (9194 downstream)																																			---	---	---	---
ST6GALNAC3	256435	broad.mit.edu	37	1	76666741	76666741	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76666741delA	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																		---	---	---	---
AK5	26289	broad.mit.edu	37	1	77920069	77920070	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77920069_77920070delTC	uc001dhn.2	+						AK5_uc001dho.2_Intron	NM_174858	NP_777283			adenylate kinase 5 isoform 1						ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1																		---	---	---	---
USP33	23032	broad.mit.edu	37	1	78188043	78188044	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78188043_78188044insA	uc001dht.2	-						USP33_uc001dhs.2_Intron|USP33_uc001dhu.2_Intron|USP33_uc001dhv.2_Intron|USP33_uc001dhw.2_Intron	NM_015017	NP_055832			ubiquitin specific protease 33 isoform 1						axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3																		---	---	---	---
USP33	23032	broad.mit.edu	37	1	78221964	78221965	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78221964_78221965delTT	uc001dht.2	-						USP33_uc001dhu.2_Intron|USP33_uc001dhw.2_Intron	NM_015017	NP_055832			ubiquitin specific protease 33 isoform 1						axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	78239446	78239446	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78239446delA								USP33 (13909 upstream) : FAM73A (5863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	78240627	78240627	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78240627delT								USP33 (15090 upstream) : FAM73A (4682 downstream)																																			---	---	---	---
MGC27382	149047	broad.mit.edu	37	1	78713434	78713435	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78713434_78713435delTG	uc001dil.1	+						MGC27382_uc009wcc.2_Intron					Homo sapiens cDNA FLJ34438 fis, clone HLUNG2001144.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	80004072	80004073	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80004072_80004073insG								ELTD1 (531577 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	80102616	80102617	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80102616_80102617insT								ELTD1 (630121 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	80953814	80953815	+	IGR	DEL	CG	-	-	rs12044148		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80953814_80953815delCG								None (None upstream) : LPHN2 (818030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	81080675	81080676	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81080675_81080676delTT								None (None upstream) : LPHN2 (691169 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	81467785	81467785	+	IGR	DEL	C	-	-	rs76332244		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81467785delC								None (None upstream) : LPHN2 (304060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	81500784	81500784	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81500784delA								None (None upstream) : LPHN2 (271061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	81609035	81609035	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81609035delA								None (None upstream) : LPHN2 (162810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	81674934	81674934	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81674934delA								None (None upstream) : LPHN2 (96911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	82890894	82890894	+	IGR	DEL	G	-	-	rs72154029		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82890894delG								LPHN2 (432788 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83016491	83016491	+	IGR	DEL	G	-	-	rs66518962		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83016491delG								LPHN2 (558385 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83381850	83381850	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83381850delA								LPHN2 (923744 upstream) : TTLL7 (953209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83532628	83532629	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83532628_83532629delGA								None (None upstream) : TTLL7 (802430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83726886	83726886	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83726886delT								None (None upstream) : TTLL7 (608173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	84259638	84259638	+	Intron	DEL	A	-	-	rs111685871		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84259638delA	uc001diz.3	-											Homo sapiens cDNA clone IMAGE:4815396.																														---	---	---	---
PRKACB	5567	broad.mit.edu	37	1	84582718	84582718	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84582718delT	uc001djj.2	+						PRKACB_uc001dji.2_Intron	NM_002731	NP_002722			cAMP-dependent protein kinase catalytic subunit						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein signaling, coupled to cAMP nucleotide second messenger|gluconeogenesis|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|regulation of insulin secretion|synaptic transmission|transmembrane transport|triglyceride catabolic process|water transport	cAMP-dependent protein kinase complex|centrosome|cytosol|nucleoplasm|plasma membrane	ATP binding|cAMP-dependent protein kinase activity|magnesium ion binding|protein binding			lung(2)|ovary(1)	3				all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	85264403	85264403	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85264403delA								SSX2IP (107963 upstream) : LPAR3 (14683 downstream)																																			---	---	---	---
MCOLN2	255231	broad.mit.edu	37	1	85403851	85403851	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85403851delA	uc001dkm.2	-						MCOLN2_uc001dkn.2_Intron	NM_153259	NP_694991			mucolipin 2							integral to membrane	ion channel activity			ovary(3)|upper_aerodigestive_tract(1)	4				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)														---	---	---	---
SYDE2	84144	broad.mit.edu	37	1	85624415	85624415	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	85816886	85816886	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85816886delT	uc001dlb.2	-						DDAH1_uc001dlc.2_Intron|uc001dla.1_Intron|DDAH1_uc010osb.1_Intron|DDAH1_uc009wco.2_Intron	NM_012137	NP_036269			dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)													---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	85825203	85825204	+	Intron	INS	-	CA	CA	rs150537414	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85825203_85825204insCA	uc001dlb.2	-						DDAH1_uc001dlc.2_Intron|uc001dla.1_Intron|DDAH1_uc010osb.1_Intron|DDAH1_uc009wco.2_Intron	NM_012137	NP_036269			dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)													---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	85993017	85993018	+	Intron	DEL	TG	-	-	rs10597768		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85993017_85993018delTG	uc001dlc.2	-							NM_001134445	NP_001127917			dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)													---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	86003581	86003581	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86003581delA	uc001dlc.2	-							NM_001134445	NP_001127917			dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)													---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86206802	86206803	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86206802_86206803delAA	uc001dlj.2	-						COL24A1_uc001dli.2_Intron|COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850			collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)														---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86356740	86356740	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86356740delT	uc001dlj.2	-						COL24A1_uc001dli.2_Intron|COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850			collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)														---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86444261	86444262	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86444261_86444262insA	uc001dlj.2	-						COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850			collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)														---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86567769	86567769	+	Intron	DEL	G	-	-	rs76755199		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86567769delG	uc001dlj.2	-						COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron|COL24A1_uc009wcq.2_Intron	NM_152890	NP_690850			collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)														---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86588882	86588882	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86588882delA	uc001dlj.2	-						COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron|COL24A1_uc009wcq.2_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	86715715	86715715	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86715715delA								COL24A1 (93269 upstream) : ODF2L (98697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	86752519	86752520	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86752519_86752520delTT								COL24A1 (130073 upstream) : ODF2L (61892 downstream)																																			---	---	---	---
ODF2L	57489	broad.mit.edu	37	1	86848553	86848553	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86848553delA	uc001dll.1	-						ODF2L_uc001dlm.1_Intron|ODF2L_uc001dln.2_Intron|ODF2L_uc001dlo.2_Intron|ODF2L_uc001dlp.2_Intron|ODF2L_uc010osg.1_Intron|ODF2L_uc001dlq.1_Intron|ODF2L_uc009wcr.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	86928377	86928378	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86928377_86928378delGT								CLCA2 (6139 upstream) : CLCA1 (6017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	87074967	87074968	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87074967_87074968insC								CLCA4 (28537 upstream) : CLCA3P (24991 downstream)																																			---	---	---	---
SH3GLB1	51100	broad.mit.edu	37	1	87200203	87200203	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87200203delT	uc001dlw.2	+						SH3GLB1_uc001dlx.2_Intron|SH3GLB1_uc001dly.2_Intron|SH3GLB1_uc001dlz.2_Intron	NM_016009	NP_057093			SH3-containing protein SH3GLB1						anti-apoptosis|filopodium assembly|signal transduction	Golgi membrane|mitochondrial outer membrane	cytoskeletal adaptor activity|protein homodimerization activity|SH3 domain binding				0		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)														---	---	---	---
SH3GLB1	51100	broad.mit.edu	37	1	87200981	87200982	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87200981_87200982insT	uc001dlw.2	+						SH3GLB1_uc001dlx.2_Intron|SH3GLB1_uc001dly.2_Intron|SH3GLB1_uc001dlz.2_Intron	NM_016009	NP_057093			SH3-containing protein SH3GLB1						anti-apoptosis|filopodium assembly|signal transduction	Golgi membrane|mitochondrial outer membrane	cytoskeletal adaptor activity|protein homodimerization activity|SH3 domain binding				0		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)														---	---	---	---
LMO4	8543	broad.mit.edu	37	1	87806074	87806074	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87806074delA	uc001dmi.2	+						LMO4_uc001dmj.2_Intron	NM_006769	NP_006760			LIM domain only 4						neural tube closure|transcription from RNA polymerase II promoter	transcription factor complex	sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding				0		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	87921025	87921025	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87921025delT								LMO4 (106422 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88085503	88085503	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88085503delA								LMO4 (270900 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88135470	88135470	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88135470delT								LMO4 (320867 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	89047023	89047023	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89047023delA								None (None upstream) : PKN2 (102899 downstream)																																			---	---	---	---
CCBL2	56267	broad.mit.edu	37	1	89418562	89418562	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89418562delA	uc001dmp.2	-						CCBL2_uc001dmq.2_Intron|CCBL2_uc001dmr.2_Intron	NM_001008661	NP_001008661			kynurenine aminotransferase III isoform 1						biosynthetic process|kynurenine metabolic process|tryptophan catabolic process		cysteine-S-conjugate beta-lyase activity|kynurenine-glyoxylate transaminase activity|kynurenine-oxoglutarate transaminase activity|pyridoxal phosphate binding			ovary(1)	1		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	89538468	89538468	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89538468delA								GBP1 (7425 upstream) : GBP2 (33375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	89755340	89755340	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89755340delA								GBP5 (16796 upstream) : GBP6 (74096 downstream)																																			---	---	---	---
LRRC8D	55144	broad.mit.edu	37	1	90329218	90329219	+	Intron	INS	-	G	G	rs139636769	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90329218_90329219insG	uc001dnm.2	+						LRRC8D_uc001dnn.2_Intron	NM_001134479	NP_001127951			leucine rich repeat containing 8 family, member							integral to membrane	protein binding			ovary(2)	2		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	90866210	90866211	+	IGR	INS	-	TG	TG	rs143344951	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90866210_90866211insTG								ZNF326 (372116 upstream) : BARHL2 (311369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	92095635	92095635	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92095635delA								CDC7 (104315 upstream) : HSP90B3P (4933 downstream)																																			---	---	---	---
TGFBR3	7049	broad.mit.edu	37	1	92253501	92253503	+	Intron	DEL	AAA	-	-	rs111981257		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92253501_92253503delAAA	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)														---	---	---	---
KIAA1107	23285	broad.mit.edu	37	1	92647504	92647505	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92647504_92647505insA	uc010otd.1	+	8	3048_3049	c.2950_2951insA	c.(2950-2952)GAAfs	p.E984fs	KIAA1107_uc001dop.2_Frame_Shift_Ins_p.E909fs	NM_015237	NP_056052	Q9UPP5	K1107_HUMAN	hypothetical protein LOC23285	1039											0																		---	---	---	---
RPAP2	79871	broad.mit.edu	37	1	92765881	92765882	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	92837288	92837288	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92837288delA	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	92905541	92905541	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92905541delT								RPAP2 (51809 upstream) : GFI1 (34778 downstream)																																			---	---	---	---
EVI5	7813	broad.mit.edu	37	1	93170032	93170032	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93170032delT	uc001dox.2	-						EVI5_uc010otf.1_Intron	NM_005665	NP_005656			ecotropic viral integration site 5						cell cycle|cell division|cell proliferation|multicellular organismal development	microtubule organizing center|nucleus|spindle	protein binding|Rab GTPase activator activity			ovary(1)|breast(1)	2		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)														---	---	---	---
EVI5	7813	broad.mit.edu	37	1	93198614	93198615	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93198614_93198615delAA	uc001dox.2	-						EVI5_uc010otf.1_Intron	NM_005665	NP_005656			ecotropic viral integration site 5						cell cycle|cell division|cell proliferation|multicellular organismal development	microtubule organizing center|nucleus|spindle	protein binding|Rab GTPase activator activity			ovary(1)|breast(1)	2		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)														---	---	---	---
EVI5	7813	broad.mit.edu	37	1	93201874	93201874	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93201874delA	uc001dox.2	-						EVI5_uc010otf.1_Intron	NM_005665	NP_005656			ecotropic viral integration site 5						cell cycle|cell division|cell proliferation|multicellular organismal development	microtubule organizing center|nucleus|spindle	protein binding|Rab GTPase activator activity			ovary(1)|breast(1)	2		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)														---	---	---	---
FAM69A	388650	broad.mit.edu	37	1	93388484	93388485	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93388484_93388485delTT	uc001dpg.2	-						FAM69A_uc001dpc.2_Intron	NM_001006605	NP_001006606			family with sequence similarity 69, member A							endoplasmic reticulum membrane|integral to membrane					0		all_lung(203;0.00265)|Lung NSC(277;0.00562)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000563)|all cancers(265;0.000751)|Epithelial(280;0.127)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	93779932	93779933	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93779932_93779933delTT	uc001dps.2	-						uc001dpt.1_Intron					Homo sapiens cDNA FLJ42965 fis, clone BRSTN2014751.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	94025117	94025117	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94025117delT								FNBP1L (4901 upstream) : BCAR3 (2234 downstream)																																			---	---	---	---
BCAR3	8412	broad.mit.edu	37	1	94102108	94102109	+	Intron	INS	-	AA	AA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94102108_94102109insAA	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)														---	---	---	---
BCAR3	8412	broad.mit.edu	37	1	94174585	94174585	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94174585delA	uc001dqb.2	-							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)														---	---	---	---
BCAR3	8412	broad.mit.edu	37	1	94284627	94284629	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94284627_94284629delTTT	uc001dqb.2	-							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)														---	---	---	---
F3	2152	broad.mit.edu	37	1	95001871	95001871	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95001871delT	uc001dqr.2	-						F3_uc001dqp.2_Intron|F3_uc001dqq.2_Intron|F3_uc001dqs.2_Intron	NM_001993	NP_001984			coagulation factor III precursor						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)													---	---	---	---
TMEM56	148534	broad.mit.edu	37	1	95580386	95580386	+	5'Flank	DEL	A	-	-	rs74833855		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95580386delA	uc001drb.2	+						TMEM56_uc001drc.2_5'Flank	NM_152487	NP_689700			transmembrane protein 56							integral to membrane					0		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.133)														---	---	---	---
RWDD3	25950	broad.mit.edu	37	1	95709927	95709928	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95709927_95709928delTG	uc009wdu.2	+	2	322_323	c.246_247delTG	c.(244-249)ACTGTGfs	p.T82fs	RWDD3_uc001drd.3_3'UTR|RWDD3_uc010oty.1_Frame_Shift_Del_p.T67fs|RWDD3_uc009wdt.2_Frame_Shift_Del_p.T82fs|RWDD3_uc001drf.3_Frame_Shift_Del_p.T82fs|RWDD3_uc001drh.3_Frame_Shift_Del_p.T67fs|RWDD3_uc009wdv.2_Intron|RWDD3_uc001drg.3_RNA|RWDD3_uc001dri.3_Frame_Shift_Del_p.T82fs	NM_015485	NP_056300	Q9Y3V2	RWDD3_HUMAN	RWD domain containing 3 isoform a	82_83	RWD.					cytoplasm|nucleus	protein binding			ovary(1)	1		all_epithelial(167;5.99e-05)|all_lung(203;0.00168)|Lung NSC(277;0.00769)		all cancers(265;0.112)|Epithelial(280;0.229)														---	---	---	---
PTBP2	58155	broad.mit.edu	37	1	97213993	97213993	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97213993delT	uc001drq.2	+						PTBP2_uc001drn.2_Intron|PTBP2_uc001dro.2_Intron|PTBP2_uc010otz.1_Intron|PTBP2_uc001drp.2_Intron|PTBP2_uc009wdw.2_Intron|PTBP2_uc001drr.2_Intron|PTBP2_uc010oua.1_Intron|PTBP2_uc001dru.2_Intron|PTBP2_uc001drm.2_Intron	NM_021190	NP_067013			polypyrimidine tract binding protein 2								nucleotide binding				0		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)														---	---	---	---
DPYD	1806	broad.mit.edu	37	1	97824814	97824814	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97824814delA	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	98060470	98060470	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98060470delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	98454392	98454392	+	RNA	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98454392delA	uc001drx.1	-	5		c.1545delT								Homo sapiens cDNA FLJ37288 fis, clone BRAMY2014205.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	98523979	98523979	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98523979delT								MIR137 (12252 upstream) : SNX7 (603257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	98524711	98524711	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98524711delA								MIR137 (12984 upstream) : SNX7 (602525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	99122471	99122471	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99122471delT								MIR137 (610744 upstream) : SNX7 (4765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	99474094	99474097	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99474094_99474097delAAAA	uc001dsd.1	+											Homo sapiens cDNA FLJ38225 fis, clone FCBBF2003528.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	99967946	99967946	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99967946delT								LPPR4 (192810 upstream) : PALMD (143485 downstream)																																			---	---	---	---
AGL	178	broad.mit.edu	37	1	100365494	100365495	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100365494_100365495insT	uc001dsi.1	+						AGL_uc001dsj.1_Intron|AGL_uc001dsk.1_Intron|AGL_uc001dsl.1_Intron|AGL_uc001dsm.1_Intron|AGL_uc001dsn.1_Intron	NM_000642	NP_000633			amylo-1,6-glucosidase,						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)														---	---	---	---
HIAT1	64645	broad.mit.edu	37	1	100534122	100534123	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100534122_100534123delTT	uc001dst.2	+	7	799_800	c.799_800delTT	c.(799-801)TTTfs	p.F267fs		NM_033055	NP_149044	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	267	Cytoplasmic (Potential).				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)														---	---	---	---
RTCD1	8634	broad.mit.edu	37	1	100733960	100733961	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100733960_100733961delTT	uc001dtc.2	+						RTCD1_uc010ouh.1_Intron|RTCD1_uc001dtd.2_Intron	NM_003729	NP_003720			RNA terminal phosphate cyclase domain 1 isoform						RNA processing	mitochondrion|nucleoplasm	ATP binding|protein binding|RNA binding|RNA-3'-phosphate cyclase activity				0		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.0513)|all cancers(265;0.0902)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)														---	---	---	---
CDC14A	8556	broad.mit.edu	37	1	100950184	100950185	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100950184_100950185delAA	uc001dtg.3	+						CDC14A_uc009web.2_Intron|CDC14A_uc010oui.1_Intron|CDC14A_uc001dte.3_3'UTR|CDC14A_uc001dtf.2_Intron|CDC14A_uc009wed.1_Intron|CDC14A_uc009wee.2_Intron	NM_003672	NP_003663			CDC14 homolog A isoform 1						cell cycle|cell division|cell proliferation	centrosome|nucleus|spindle	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			large_intestine(1)	1		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	101084303	101084303	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101084303delT								GPR88 (76721 upstream) : VCAM1 (100994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	101663723	101663723	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101663723delT								DPH5 (172079 upstream) : S1PR1 (38582 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	102196381	102196382	+	IGR	INS	-	TA	TA	rs145755813		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102196381_102196382insTA								S1PR1 (489305 upstream) : OLFM3 (71745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	102225505	102225505	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102225505delT								S1PR1 (518429 upstream) : OLFM3 (42622 downstream)																																			---	---	---	---
OLFM3	118427	broad.mit.edu	37	1	102371742	102371742	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102371742delT	uc001dug.2	-						OLFM3_uc001duh.2_Intron|OLFM3_uc001dui.2_Intron|OLFM3_uc001duj.2_Intron	NM_058170	NP_477518			olfactomedin 3							extracellular region				ovary(2)|skin(1)	3		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	103060983	103060984	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103060983_103060984insT								OLFM3 (598193 upstream) : COL11A1 (281040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	103617402	103617406	+	IGR	DEL	TGAAA	-	-	rs141067231		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103617402_103617406delTGAAA								COL11A1 (43350 upstream) : RNPC3 (451172 downstream)																																			---	---	---	---
AMY2B	280	broad.mit.edu	37	1	104120335	104120335	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104120335delT	uc001duq.2	+						AMY2B_uc010ouo.1_Intron|LOC648740_uc001dur.2_Intron|AMY2B_uc001dus.1_Intron	NM_020978	NP_066188			amylase, pancreatic, alpha-2B precursor						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	104435617	104435617	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104435617delA								AMY1A (228445 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	104820103	104820104	+	IGR	DEL	GG	-	-	rs72328157		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104820103_104820104delGG								AMY1A (612931 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105475072	105475073	+	IGR	INS	-	C	C	rs143377462	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105475072_105475073insC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105661002	105661002	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105661002delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	106239575	106239578	+	IGR	DEL	CCTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106239575_106239578delCCTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	107334278	107334278	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107334278delT								None (None upstream) : PRMT6 (264989 downstream)																																			---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	107682675	107682675	+	5'UTR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107682675delG	uc001dvh.3	+	1					NTNG1_uc001dvf.3_5'UTR|NTNG1_uc010out.1_5'UTR|NTNG1_uc001dvc.3_5'Flank|NTNG1_uc001dvd.1_5'Flank	NM_001113226	NP_001106697			netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)														---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	107738235	107738236	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107738235_107738236delAC	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_Intron	NM_001113226	NP_001106697			netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)														---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	107850635	107850635	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107850635delT	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_Intron	NM_001113226	NP_001106697			netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)														---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	108012493	108012493	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108012493delT	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvi.2_Intron|NTNG1_uc001dve.2_Intron|NTNG1_uc009wek.2_Intron|NTNG1_uc001dvg.2_Intron|NTNG1_uc009wem.2_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)														---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108212234	108212235	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108212234_108212235insT	uc001dvk.1	-						VAV3_uc010ouu.1_Intron|VAV3_uc001dvj.1_Intron|VAV3_uc010ouv.1_Intron|VAV3_uc010ouw.1_Intron|VAV3_uc001dvl.1_Intron|VAV3_uc010oux.1_Intron	NM_006113	NP_006104			vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)														---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108297607	108297607	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108297607delT	uc001dvk.1	-						VAV3_uc010ouw.1_Intron|VAV3_uc001dvl.1_Intron|VAV3_uc010oux.1_Intron	NM_006113	NP_006104			vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)														---	---	---	---
SLC25A24	29957	broad.mit.edu	37	1	108721435	108721435	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108721435delA	uc001dvn.3	-						SLC25A24_uc001dvm.2_Intron	NM_013386	NP_037518			solute carrier family 25 member 24 isoform 1						transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding			ovary(1)	1		all_epithelial(167;3.72e-05)|all_lung(203;0.000567)|Lung NSC(277;0.0011)|Melanoma(281;0.211)		Colorectal(144;0.0345)|Lung(183;0.0971)|COAD - Colon adenocarcinoma(174;0.127)|Epithelial(280;0.134)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	108748676	108748677	+	IGR	DEL	TT	-	-	rs140132352		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108748676_108748677delTT								SLC25A24 (5702 upstream) : NBPF4 (17286 downstream)																																			---	---	---	---
FAM102B	284611	broad.mit.edu	37	1	109156228	109156228	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109156228delA	uc010ouy.1	+							NM_001010883	NP_001010883			hypothetical protein LOC284611											large_intestine(1)	1		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)														---	---	---	---
AKNAD1	254268	broad.mit.edu	37	1	109390070	109390070	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109390070delA	uc001dwa.2	-						AKNAD1_uc010ovb.1_Intron|AKNAD1_uc001dwb.2_Intron	NM_152763	NP_689976			hypothetical protein LOC254268											ovary(3)	3																		---	---	---	---
WDR47	22911	broad.mit.edu	37	1	109535490	109535490	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109535490delA	uc001dwj.2	-						WDR47_uc001dwl.2_Intron|WDR47_uc001dwi.2_Intron|WDR47_uc001dwk.2_Intron|WDR47_uc010ovf.1_Intron	NM_001142551	NP_001136023			WD repeat domain 47 isoform 3											ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)														---	---	---	---
WDR47	22911	broad.mit.edu	37	1	109560141	109560141	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109560141delT	uc001dwj.2	-	3	617	c.241delA	c.(241-243)AGGfs	p.R81fs	WDR47_uc001dwl.2_Frame_Shift_Del_p.R81fs|WDR47_uc001dwi.2_Frame_Shift_Del_p.R81fs|WDR47_uc001dwk.2_Intron|WDR47_uc010ovf.1_Frame_Shift_Del_p.R8fs	NM_001142551	NP_001136023	O94967	WDR47_HUMAN	WD repeat domain 47 isoform 3	81	CTLH.									ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	109596809	109596809	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109596809delA								WDR47 (11959 upstream) : TAF13 (10189 downstream)																																			---	---	---	---
TAF13	6884	broad.mit.edu	37	1	109617756	109617756	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109617756delT	uc001dwm.1	-							NM_005645	NP_005636			TBP-associated factor 13						transcription elongation from RNA polymerase II promoter|viral reproduction	transcription factor TFIID complex	protein C-terminus binding|sequence-specific DNA binding transcription factor activity				0		all_epithelial(167;0.000102)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0138)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.166)|all cancers(265;0.191)|LUSC - Lung squamous cell carcinoma(189;0.228)														---	---	---	---
KIAA1324	57535	broad.mit.edu	37	1	109726109	109726111	+	Intron	DEL	AGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109726109_109726111delAGG	uc001dwq.2	+						KIAA1324_uc009wex.1_Intron|KIAA1324_uc009wey.2_Intron|KIAA1324_uc010ovg.1_Intron	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)														---	---	---	---
MYBPHL	343263	broad.mit.edu	37	1	109836686	109836686	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109836686delA	uc001dxk.1	-						MYBPHL_uc010ovh.1_Intron|MYBPHL_uc001dxl.2_Intron	NM_001010985	NP_001010985			myosin binding protein H-like											ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(203;0.00519)|all_epithelial(167;0.00575)|Lung NSC(277;0.00822)		Colorectal(144;0.0306)|Lung(183;0.0681)|COAD - Colon adenocarcinoma(174;0.117)|Epithelial(280;0.197)|all cancers(265;0.225)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	109998765	109998765	+	IGR	DEL	A	-	-	rs116777117	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109998765delA								PSMA5 (29728 upstream) : SYPL2 (10335 downstream)																																			---	---	---	---
GNAI3	2773	broad.mit.edu	37	1	110129583	110129583	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110129583delT	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)														---	---	---	---
AHCYL1	10768	broad.mit.edu	37	1	110558746	110558746	+	Intron	DEL	T	-	-	rs145081118		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110558746delT	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)														---	---	---	---
AHCYL1	10768	broad.mit.edu	37	1	110564356	110564356	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110564356delT	uc001dyx.2	+	17					AHCYL1_uc010ovw.1_3'UTR|AHCYL1_uc001dyy.2_3'UTR|AHCYL1_uc010ovx.1_3'UTR	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)														---	---	---	---
SLC6A17	388662	broad.mit.edu	37	1	110696859	110696859	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110696859delA	uc009wfq.2	+							NM_001010898	NP_001010898			solute carrier family 6, member 17						alanine transport|glycine transport|leucine transport|proline transport	cell junction|integral to plasma membrane|synaptic vesicle membrane	neurotransmitter:sodium symporter activity			ovary(1)|pancreas(1)	2		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	110750071	110750071	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110750071delG								SLC6A17 (5250 upstream) : KCNC4 (3994 downstream)																																	OREG0013654	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	111360068	111360068	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111360068delT								KCNA3 (142413 upstream) : CD53 (53753 downstream)																																			---	---	---	---
CHI3L2	1117	broad.mit.edu	37	1	111772303	111772304	+	Intron	INS	-	AAAAAAA	AAAAAAA	rs61237890		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111772303_111772304insAAAAAAA	uc001eam.2	+						CHI3L2_uc001ean.2_Intron|CHI3L2_uc001eao.2_5'Flank|CHI3L2_uc009wga.2_5'Flank	NM_004000	NP_003991			chitinase 3-like 2 isoform a						chitin catabolic process	extracellular space	cation binding|chitinase activity			central_nervous_system(1)	1		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)														---	---	---	---
RAP1A	5906	broad.mit.edu	37	1	112232301	112232301	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112232301delT	uc001ebi.2	+						RAP1A_uc001ebk.2_Intron|RAP1A_uc001ebl.2_Intron|RAP1A_uc001ebm.2_Intron	NM_002884	NP_002875			RAP1A, member of RAS oncogene family precursor						activation of MAPKK activity|blood coagulation|energy reserve metabolic process|nerve growth factor receptor signaling pathway|regulation of insulin secretion	cytosol|plasma membrane	GTP binding|GTPase activity				0		all_cancers(81;6.79e-06)|all_epithelial(167;2.42e-05)|all_lung(203;0.000105)|Lung NSC(277;0.00021)		Lung(183;0.0183)|Colorectal(144;0.0418)|LUSC - Lung squamous cell carcinoma(189;0.0966)|all cancers(265;0.098)|Epithelial(280;0.0981)|COAD - Colon adenocarcinoma(174;0.141)														---	---	---	---
KCND3	3752	broad.mit.edu	37	1	112321943	112321943	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112321943delA	uc001ebu.1	-						KCND3_uc001ebv.1_Intron	NM_004980	NP_004971			potassium voltage-gated channel, Shal-related							sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)														---	---	---	---
KCND3	3752	broad.mit.edu	37	1	112472157	112472157	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112472157delT	uc001ebu.1	-						KCND3_uc001ebv.1_Intron	NM_004980	NP_004971			potassium voltage-gated channel, Shal-related							sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	112828763	112828764	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112828763_112828764insA								KCND3 (296986 upstream) : CTTNBP2NL (110036 downstream)																																			---	---	---	---
ST7L	54879	broad.mit.edu	37	1	113126864	113126865	+	Intron	DEL	AA	-	-	rs76579294		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113126864_113126865delAA	uc001ecd.2	-						ST7L_uc009wgh.2_Intron|ST7L_uc001ecc.2_Intron|ST7L_uc010owg.1_Intron|ST7L_uc010owh.1_Intron|ST7L_uc001ece.2_Intron|ST7L_uc001ecf.2_Intron|ST7L_uc001ecg.2_Intron|ST7L_uc010owi.1_Intron|ST7L_uc001ech.2_Intron|ST7L_uc001eci.2_Intron|ST7L_uc009wgi.1_Intron|ST7L_uc010owj.1_Intron	NM_017744	NP_060214			suppression of tumorigenicity 7-like isoform 1						negative regulation of cell growth	integral to membrane	binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
ST7L	54879	broad.mit.edu	37	1	113144188	113144188	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113144188delA	uc001ecd.2	-						ST7L_uc009wgh.2_Intron|ST7L_uc001ecc.2_Intron|ST7L_uc010owg.1_Intron|ST7L_uc010owh.1_Intron|ST7L_uc001ece.2_Intron|ST7L_uc001ecf.2_Intron|ST7L_uc001ecg.2_Intron|ST7L_uc010owi.1_Intron|ST7L_uc001ech.2_Intron|ST7L_uc001eci.2_Intron|ST7L_uc009wgi.1_Intron|ST7L_uc010owj.1_Intron	NM_017744	NP_060214			suppression of tumorigenicity 7-like isoform 1						negative regulation of cell growth	integral to membrane	binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
CAPZA1	829	broad.mit.edu	37	1	113192225	113192225	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113192225delT	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)														---	---	---	---
CAPZA1	829	broad.mit.edu	37	1	113202197	113202198	+	Intron	DEL	TC	-	-	rs113906793		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113202197_113202198delTC	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	113347051	113347052	+	IGR	INS	-	G	G	rs142845088	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113347051_113347052insG								FAM19A3 (77197 upstream) : SLC16A1 (107420 downstream)																																	OREG0013682	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	113450751	113450752	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113450751_113450752delTT								FAM19A3 (180897 upstream) : SLC16A1 (3720 downstream)																																			---	---	---	---
LRIG2	9860	broad.mit.edu	37	1	113635953	113635953	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113635953delT	uc001edf.1	+						LRIG2_uc009wgn.1_Intron	NM_014813	NP_055628			leucine-rich repeats and immunoglobulin-like							cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)														---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	113957133	113957133	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113957133delT	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	114380072	114380073	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114380072_114380073delAA	uc001eds.2	-						PTPN22_uc009wgq.2_Intron|PTPN22_uc010owo.1_Intron|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Intron|PTPN22_uc009wgs.2_Intron|PTPN22_uc001edu.2_Intron	NM_015967	NP_057051			protein tyrosine phosphatase, non-receptor type						negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
PTPN22	26191	broad.mit.edu	37	1	114414022	114414022	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114414022delT	uc001eds.2	-						uc001edv.1_Intron|PTPN22_uc009wgq.2_Intron|PTPN22_uc010owo.1_Intron|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Intron|PTPN22_uc009wgs.2_Intron|PTPN22_uc001edu.2_Intron	NM_015967	NP_057051			protein tyrosine phosphatase, non-receptor type						negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
HIPK1	204851	broad.mit.edu	37	1	114480911	114480912	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114480911_114480912delTT	uc001eem.2	+						HIPK1_uc001eel.2_Intron|HIPK1_uc001een.2_Intron	NM_198268	NP_938009			homeodomain-interacting protein kinase 1 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(4)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
CSDE1	7812	broad.mit.edu	37	1	115279333	115279333	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115279333delA	uc001efk.2	-						CSDE1_uc001efi.2_Intron|CSDE1_uc001efj.2_Intron|CSDE1_uc001efl.2_Intron|CSDE1_uc001efm.2_Intron|CSDE1_uc009wgv.2_Intron|CSDE1_uc001efn.2_Intron	NM_001007553	NP_001007554			upstream of NRAS isoform 1						male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
CSDE1	7812	broad.mit.edu	37	1	115282611	115282611	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115282611delA	uc001efk.2	-						CSDE1_uc001efi.2_Intron|CSDE1_uc001efj.2_Intron|CSDE1_uc001efl.2_Intron|CSDE1_uc001efm.2_Intron|CSDE1_uc009wgv.2_Intron|CSDE1_uc001efn.2_Intron	NM_001007553	NP_001007554			upstream of NRAS isoform 1						male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
VANGL1	81839	broad.mit.edu	37	1	116211330	116211330	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116211330delT	uc001efv.1	+						VANGL1_uc009wgy.1_Intron	NM_138959	NP_620409			vang-like 1						multicellular organismal development	integral to membrane	protein binding			central_nervous_system(1)	1	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	116869492	116869492	+	IGR	DEL	A	-	-	rs150668532		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116869492delA								C1orf161 (191631 upstream) : ATP1A1 (45512 downstream)																																			---	---	---	---
IGSF3	3321	broad.mit.edu	37	1	117126818	117126818	+	Intron	DEL	A	-	-	rs141377961		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117126818delA	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	117639956	117639957	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117639956_117639957delTG	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)														---	---	---	---
VTCN1	79679	broad.mit.edu	37	1	117688571	117688571	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117688571delA	uc001ehb.2	-						VTCN1_uc001ehc.2_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	117756602	117756602	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117756602delT								VTCN1 (3053 upstream) : MAN1A2 (153483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118081647	118081648	+	IGR	INS	-	A	A	rs144202021	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118081647_118081648insA								MAN1A2 (13327 upstream) : FAM46C (66956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118301105	118301105	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118301105delA								FAM46C (130095 upstream) : GDAP2 (105003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118397912	118397912	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118397912delA								FAM46C (226902 upstream) : GDAP2 (8196 downstream)																																			---	---	---	---
GDAP2	54834	broad.mit.edu	37	1	118413299	118413300	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118413299_118413300insA	uc001ehf.2	-							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	118474542	118474542	+	Intron	DEL	G	-	-	rs112949200		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118474542delG	uc010oxe.1	+						WDR3_uc001ehi.2_Intron|GDAP2_uc001ehf.2_5'Flank|GDAP2_uc001ehg.2_5'Flank|WDR3_uc001ehh.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	119394625	119394632	+	IGR	DEL	AAGAAAGA	-	-	rs28533475		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119394625_119394632delAAGAAAGA								SPAG17 (666777 upstream) : TBX15 (31034 downstream)																																			---	---	---	---
TBX15	6913	broad.mit.edu	37	1	119451543	119451544	+	Intron	INS	-	CA	CA	rs146145670	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119451543_119451544insCA	uc001ehl.1	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	119729281	119729281	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119729281delT	uc001ehp.1	+											Homo sapiens cDNA FLJ43771 fis, clone TESTI2049553.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	119864543	119864544	+	IGR	INS	-	GT	GT	rs147332746	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119864543_119864544insGT								WARS2 (181248 upstream) : HAO2 (46858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	120004263	120004263	+	IGR	DEL	A	-	-	rs145355901		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120004263delA								HSD3B2 (15143 upstream) : HSD3B1 (45563 downstream)																																			---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120560538	120560538	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120560538delA	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				---	---	---	---
Unknown	0	broad.mit.edu	37	1	120619558	120619559	+	IGR	DEL	CT	-	-	rs3862256		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120619558_120619559delCT								NOTCH2 (7282 upstream) : FAM72B (219446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	121122246	121122247	+	Intron	INS	-	A	A	rs144131281	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121122246_121122247insA	uc001eis.2	+							NM_001042758	NP_001036223			SLIT-ROBO Rho GTPase activating protein 2																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	142567908	142567908	+	IGR	DEL	C	-	-	rs66470127		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142567908delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142574428	142574429	+	IGR	DEL	AT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142574428_142574429delAT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142576687	142576687	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142576687delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142583243	142583243	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142583243delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142660732	142660732	+	Intron	DEL	A	-	-	rs112376355		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142660732delA	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	142672993	142672993	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142672993delC	uc001eiw.1	+						uc001eix.1_Intron|uc001eiz.1_5'Flank					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	142782842	142782842	+	Intron	DEL	A	-	-	rs74330411		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142782842delA	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143125255	143125255	+	Intron	DEL	A	-	-	rs149679425		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143125255delA	uc001eiw.1	+						uc001ejf.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143181181	143181181	+	Intron	DEL	C	-	-	rs71237956		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143181181delC	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143188606	143188606	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143188606delA	uc001eiw.1	+						uc001eji.1_5'Flank					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143244093	143244093	+	Intron	DEL	T	-	-	rs113732395		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143244093delT	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143261111	143261112	+	IGR	INS	-	A	A	rs148713012		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143261111_143261112insA								None (None upstream) : LOC100286793 (386527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143262824	143262824	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143262824delT								None (None upstream) : LOC100286793 (384815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143538859	143538860	+	IGR	INS	-	C	C	rs143502487	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143538859_143538860insC								None (None upstream) : LOC100286793 (108779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	144030047	144030047	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144030047delA	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																														---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144536014	144536015	+	Intron	INS	-	A	A	rs143907098		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144536014_144536015insA	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144597216	144597217	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144597216_144597217delTT	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|uc001elc.2_RNA|NBPF9_uc009wif.1_Intron|uc001ele.2_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144614303	144614303	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144614303delA	uc009wig.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_5'Flank|NBPF9_uc010oyf.1_5'Flank|NBPF9_uc010oyg.1_5'Flank|NBPF9_uc009wii.1_5'Flank|NBPF9_uc009wif.1_Intron|C1orf152_uc001elf.3_5'Flank	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144681814	144681814	+	Intron	DEL	G	-	-	rs67467472		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144681814delG	uc009wig.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF9_uc009wii.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144840731	144840733	+	Intron	DEL	AAA	-	-	rs142028178		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144840731_144840733delAAA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144877597	144877597	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144877597delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144884983	144884984	+	Intron	INS	-	C	C	rs148304767		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144884983_144884984insC	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144904900	144904900	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144904900delT	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emb.1_Intron|PDE4DIP_uc001eme.1_Intron|PDE4DIP_uc001emf.1_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144914750	144914752	+	Intron	DEL	AAA	-	-	rs148144302		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144914750_144914752delAAA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emb.1_Intron|PDE4DIP_uc001eme.1_Intron|PDE4DIP_uc001emf.1_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144928113	144928113	+	Intron	DEL	A	-	-	rs67719372		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144928113delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emb.1_Intron|PDE4DIP_uc001emf.1_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144930235	144930235	+	Intron	DEL	A	-	-	rs67251782		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144930235delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emb.1_Intron|PDE4DIP_uc001emf.1_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	145024577	145024590	+	Intron	DEL	ACACACACACACAT	-	-	rs72183284		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145024577_145024590delACACACACACACAT	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								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	145036849	145036849	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145036849delA	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	145107771	145107774	+	Intron	DEL	AAAT	-	-	rs67910942		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145107771_145107774delAAAT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145176987	145176988	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145176987_145176988delGT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145207564	145207564	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145207564delT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_5'Flank|NOTCH2NL_uc001emn.3_5'Flank|NOTCH2NL_uc001emm.3_5'Flank|NOTCH2NL_uc001emo.2_5'Flank|NOTCH2NL_uc010oyh.1_5'Flank					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145276233	145276233	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145276233delT	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	145286464	145286467	+	Intron	DEL	ATAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145286464_145286467delATAA	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_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	145433223	145433223	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145433223delA	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	145434174	145434174	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145434174delT	uc001emp.3	+							NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
ITGA10	8515	broad.mit.edu	37	1	145528970	145528970	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145528970delA	uc001eoa.2	+						NBPF10_uc001emp.3_Intron|ITGA10_uc001enz.1_3'UTR|ITGA10_uc010oyv.1_Intron|ITGA10_uc009wiw.2_Intron|ITGA10_uc010oyw.1_Intron	NM_003637	NP_003628			integrin, alpha 10 precursor						cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)																	---	---	---	---
ITGA10	8515	broad.mit.edu	37	1	145533958	145533958	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145533958delC	uc001eoa.2	+						NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Intron|ITGA10_uc009wiw.2_Intron|ITGA10_uc010oyw.1_Intron	NM_003637	NP_003628			integrin, alpha 10 precursor						cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)																	---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145565576	145565577	+	Intron	INS	-	A	A	rs144166289	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145565576_145565577insA	uc001emp.3	+						ANKRD35_uc001eob.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	145645968	145645968	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145645968delA	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	145823365	145823365	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145823365delA	uc001emp.3	+						GPR89A_uc010ozb.1_Intron|GPR89A_uc001eos.2_Intron|GPR89A_uc001eot.2_Intron|GPR89A_uc010ozc.1_Intron|GPR89A_uc010ozd.1_Intron|GPR89A_uc010oze.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	146397477	146397477	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146397477delG	uc001emp.3	+						uc010ozk.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
PRKAB2	5565	broad.mit.edu	37	1	146639877	146639877	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146639877delA	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)													---	---	---	---
FMO5	2330	broad.mit.edu	37	1	146684173	146684173	+	Intron	DEL	T	-	-	rs17360066	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146684173delT	uc001epi.2	-						FMO5_uc001eph.3_Intron|FMO5_uc001epj.2_Intron|FMO5_uc001epk.3_Intron	NM_001461	NP_001452			flavin containing monooxygenase 5 isoform 1							integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			ovary(3)	3	all_hematologic(923;0.0487)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	146804220	146804220	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146804220delA	uc001epp.2	-											Homo sapiens cDNA clone IMAGE:5266739.																														---	---	---	---
ACP6	51205	broad.mit.edu	37	1	147125251	147125251	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147125251delT	uc001epr.2	-						ACP6_uc009wjj.1_Intron	NM_016361	NP_057445			acid phosphatase 6, lysophosphatidic precursor						lipid metabolic process	extracellular region|mitochondrion	acid phosphatase activity|protein binding			ovary(4)	4	all_hematologic(923;0.0276)																	---	---	---	---
ACP6	51205	broad.mit.edu	37	1	147139221	147139221	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147139221delA	uc001epr.2	-						ACP6_uc009wjj.1_Intron	NM_016361	NP_057445			acid phosphatase 6, lysophosphatidic precursor						lipid metabolic process	extracellular region|mitochondrion	acid phosphatase activity|protein binding			ovary(4)	4	all_hematologic(923;0.0276)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	147250909	147250909	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147250909delG								GJA5 (5425 upstream) : GJA8 (124027 downstream)																																			---	---	---	---
GJA8	2703	broad.mit.edu	37	1	147376981	147376982	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147376981_147376982insA	uc001epu.1	+							NM_005267	NP_005258			connexin 50						cell communication|visual perception	connexon complex|integral to plasma membrane	channel activity			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.0276)																	---	---	---	---
NBPF15	284565	broad.mit.edu	37	1	148560488	148560488	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																	---	---	---	---
NBPF15	284565	broad.mit.edu	37	1	148594260	148594260	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148594260delT	uc001esc.2	+							NM_173638	NP_775909			hypothetical protein LOC284565							cytoplasm					0	all_hematologic(923;0.032)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	148849748	148849752	+	IGR	DEL	TCATT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148849748_148849752delTCATT								NBPF16 (91437 upstream) : LOC645166 (78534 downstream)																																			---	---	---	---
LOC645166	645166	broad.mit.edu	37	1	148926670	148926672	+	5'Flank	DEL	AAA	-	-	rs145653374		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148926670_148926672delAAA	uc010pbc.1	+						LOC645166_uc010pbd.1_5'Flank	NR_027355				Homo sapiens cDNA, FLJ18771.												0																		---	---	---	---
LOC645166	645166	broad.mit.edu	37	1	148937182	148937182	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148937182delA	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	149143067	149143067	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149143067delA								LOC645166 (190013 upstream) : LOC388692 (136409 downstream)																																			---	---	---	---
LOC388692	388692	broad.mit.edu	37	1	149279615	149279615	+	RNA	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149279615delG	uc010pbf.1	+	1		c.140delG				NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	149300735	149300736	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149300735_149300736insA								LOC388692 (8993 upstream) : FCGR1C (68558 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149302931	149302931	+	IGR	DEL	A	-	-	rs148824221		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149302931delA								LOC388692 (11189 upstream) : FCGR1C (66363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149334245	149334246	+	IGR	DEL	AA	-	-	rs112206285		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149334245_149334246delAA								LOC388692 (42503 upstream) : FCGR1C (35048 downstream)																																			---	---	---	---
VPS45	11311	broad.mit.edu	37	1	150067713	150067715	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150067713_150067715delAAA	uc001etp.2	+						VPS45_uc010pbp.1_Intron|VPS45_uc010pbq.1_Intron|VPS45_uc010pbs.1_Intron|VPS45_uc001etq.2_Intron	NM_007259	NP_009190			vacuolar protein sorting 45A						blood coagulation|intracellular protein transport|vesicle docking involved in exocytosis	endosome membrane|Golgi membrane|integral to membrane of membrane fraction				central_nervous_system(1)|skin(1)	2	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	150147981	150147983	+	IGR	DEL	TTT	-	-	rs148965647		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150147981_150147983delTTT								PLEKHO1 (16165 upstream) : ANP32E (42735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	150188024	150188024	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150188024delA								PLEKHO1 (56208 upstream) : ANP32E (2694 downstream)																																			---	---	---	---
ANP32E	81611	broad.mit.edu	37	1	150195337	150195337	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150195337delA	uc001etw.2	-						ANP32E_uc010pbt.1_Intron|ANP32E_uc010pbu.1_Intron|ANP32E_uc010pbv.1_Intron|ANP32E_uc001etv.3_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)															---	---	---	---
RPRD2	23248	broad.mit.edu	37	1	150346314	150346317	+	Intron	DEL	AGAG	-	-	rs61008863	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150346314_150346317delAGAG	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																		---	---	---	---
RPRD2	23248	broad.mit.edu	37	1	150445908	150445908	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150445908delT	uc009wlr.2	+	11					RPRD2_uc010pcc.1_3'UTR|RPRD2_uc001eup.3_3'UTR	NM_015203	NP_056018			Regulation of nuclear pre-mRNA domain containing								protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	150590253	150590254	+	IGR	INS	-	T	T	rs145659791		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150590253_150590254insT								MCL1 (38117 upstream) : ENSA (4350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	150592893	150592893	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150592893delA								MCL1 (40757 upstream) : ENSA (1711 downstream)																																			---	---	---	---
ENSA	2029	broad.mit.edu	37	1	150595355	150595357	+	Intron	DEL	AAA	-	-	rs76951202		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150595355_150595357delAAA	uc001eve.2	-						ENSA_uc001evd.2_Intron|ENSA_uc001evb.2_Intron|ENSA_uc001evc.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)															---	---	---	---
GOLPH3L	55204	broad.mit.edu	37	1	150622777	150622777	+	Intron	DEL	G	-	-	rs11318883		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150622777delG	uc001evj.2	-						GOLPH3L_uc010pci.1_Intron	NM_018178	NP_060648			Golgi phosphoprotein 3-like							Golgi cisterna membrane				ovary(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;1.2e-23)|all cancers(9;4.81e-23)|OV - Ovarian serous cystadenocarcinoma(6;1.93e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
HORMAD1	84072	broad.mit.edu	37	1	150686600	150686600	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	150816407	150816408	+	Intron	INS	-	CTA	CTA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150816407_150816408insCTA	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								---	---	---	---
BNIPL	149428	broad.mit.edu	37	1	151016245	151016245	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151016245delT	uc001ewl.2	+						BNIPL_uc009wmi.2_Intron|BNIPL_uc009wmj.2_Intron	NM_138278	NP_612122			BCL2/adenovirus E1B 19kD interacting protein						apoptosis|induction of apoptosis|negative regulation of cell proliferation|regulation of growth rate	cytosol|nucleus	identical protein binding				0	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
CDC42SE1	56882	broad.mit.edu	37	1	151025964	151025965	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151025964_151025965insT	uc001ewo.2	-						CDC42SE1_uc001ewp.2_Intron	NM_001038707	NP_001033796			CDC42 small effector 1						phagocytosis|regulation of cell shape|signal transduction	cytoplasm|cytoskeleton|plasma membrane	GTPase inhibitor activity				0	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
PIP5K1A	8394	broad.mit.edu	37	1	151187678	151187678	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151187678delT	uc001exj.2	+						PIP5K1A_uc001exi.2_Intron|PIP5K1A_uc010pcu.1_Intron|PIP5K1A_uc001exk.2_Intron	NM_001135638	NP_001129110			phosphatidylinositol-4-phosphate 5-kinase, type						phospholipid biosynthetic process|signal transduction	endomembrane system|Golgi stack|lamellipodium|nuclear speck	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|kinase binding			ovary(1)|central_nervous_system(1)|skin(1)	3	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
PIP5K1A	8394	broad.mit.edu	37	1	151210138	151210139	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151210138_151210139delAA	uc001exj.2	+						PIP5K1A_uc001exi.2_Intron|PIP5K1A_uc010pcu.1_Intron|PIP5K1A_uc001exk.2_Intron|PIP5K1A_uc010pcv.1_Intron	NM_001135638	NP_001129110			phosphatidylinositol-4-phosphate 5-kinase, type						phospholipid biosynthetic process|signal transduction	endomembrane system|Golgi stack|lamellipodium|nuclear speck	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|kinase binding			ovary(1)|central_nervous_system(1)|skin(1)	3	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
POGZ	23126	broad.mit.edu	37	1	151434003	151434005	+	5'Flank	DEL	AAA	-	-	rs113344146		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151434003_151434005delAAA	uc001eyd.1	-						POGZ_uc001eye.1_5'Flank|POGZ_uc010pdb.1_5'Flank|POGZ_uc001eyf.1_5'Flank|POGZ_uc010pdc.1_5'Flank|POGZ_uc009wmv.1_5'Flank|POGZ_uc010pdd.1_5'Flank|POGZ_uc001eyg.1_5'Flank	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)															---	---	---	---
SNX27	81609	broad.mit.edu	37	1	151634967	151634967	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
RORC	6097	broad.mit.edu	37	1	151802847	151802847	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151802847delG	uc001ezh.2	-						RORC_uc010pdo.1_Intron|RORC_uc010pdp.1_Intron	NM_005060	NP_005051			RAR-related orphan receptor C isoform a						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)|skin(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
LOC100132111	100132111	broad.mit.edu	37	1	151808315	151808315	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151808315delA	uc010pdr.1	+							NR_024237				Homo sapiens hypothetical LOC100132111 (LOC100132111), non-coding RNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	151834858	151834858	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151834858delT								THEM5 (8685 upstream) : THEM4 (11202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	151842298	151842299	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151842298_151842299insT								THEM5 (16125 upstream) : THEM4 (3761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	152021846	152021847	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152021846_152021847delTG								S100A11 (12335 upstream) : TCHHL1 (34773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	152246959	152246959	+	IGR	DEL	T	-	-	rs111810662		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152246959delT								HRNR (50290 upstream) : FLG (27692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	153205958	153205958	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153205958delA								LELP1 (28364 upstream) : LOR (26221 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	153454758	153454758	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153454758delA								S100A7 (21621 upstream) : S100A6 (52318 downstream)																																			---	---	---	---
S100A4	6275	broad.mit.edu	37	1	153518773	153518774	+	5'Flank	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153518773_153518774delTT	uc001fby.2	-						S100A4_uc001fbz.2_5'Flank|uc009wog.1_Intron	NM_019554	NP_062427			S100 calcium-binding protein A4						epithelial to mesenchymal transition|positive regulation of I-kappaB kinase/NF-kappaB cascade	nucleus|perinuclear region of cytoplasm	calcium ion binding|RAGE receptor binding				0	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
S100A3	6274	broad.mit.edu	37	1	153520781	153520781	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153520781delC	uc001fca.1	-						S100A4_uc001fby.2_5'Flank|S100A4_uc001fbz.2_5'Flank|uc009wog.1_Intron	NM_002960	NP_002951			S100 calcium binding protein A3								calcium ion binding|protein binding				0	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
S100A16	140576	broad.mit.edu	37	1	153580804	153580804	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153580804delG	uc001fcc.2	-						S100A16_uc001fcd.1_Intron	NM_080388	NP_525127			S100 calcium binding protein A16							cytosol|nucleolus	calcium ion binding|protein homodimerization activity				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
S100A13	6284	broad.mit.edu	37	1	153595671	153595671	+	Intron	DEL	T	-	-	rs76795261		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153595671delT	uc001fcf.3	-						S100A13_uc001fcg.2_Intron|S100A13_uc009woh.2_Intron|S100A13_uc001fch.2_Intron|S100A13_uc001fci.2_Intron|S100A13_uc001fcj.2_Intron	NM_001024213	NP_001019384			S100 calcium binding protein A13						interleukin-1 alpha secretion|mast cell degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|extracellular space|nucleus|perinuclear region of cytoplasm	calcium ion binding|copper ion binding|fibroblast growth factor 1 binding|lipid binding|protein homodimerization activity|RAGE receptor binding|zinc ion binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)		Amlexanox(DB01025)													---	---	---	---
SLC27A3	11000	broad.mit.edu	37	1	153749150	153749150	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153749150delC	uc001fcz.2	+	2	1030	c.965delC	c.(964-966)TCCfs	p.S322fs	SLC27A3_uc009won.2_RNA	NM_024330	NP_077306	Q5K4L6	S27A3_HUMAN	solute carrier family 27 member 3	322					fatty acid metabolic process	integral to membrane|mitochondrial membrane	ligase activity|nucleotide binding			ovary(1)	1	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
GATAD2B	57459	broad.mit.edu	37	1	153807440	153807441	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153807440_153807441delAA	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	153815915	153815916	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153815915_153815916delAA	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)															---	---	---	---
CRTC2	200186	broad.mit.edu	37	1	153929691	153929691	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153929691delA	uc010ped.1	-						CRTC2_uc001fde.3_5'Flank|CRTC2_uc001fdf.3_5'Flank	NM_181715	NP_859066			CREB regulated transcription coactivator 2						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)	2	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)															---	---	---	---
CREB3L4	148327	broad.mit.edu	37	1	153943844	153943844	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153943844delA	uc001fdn.3	+						CREB3L4_uc010pef.1_Intron|CREB3L4_uc001fdo.3_Intron|CREB3L4_uc001fdm.1_Intron|CREB3L4_uc001fdp.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)															---	---	---	---
RAB13	5872	broad.mit.edu	37	1	153959184	153959184	+	5'Flank	DEL	A	-	-	rs111554216		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153959184delA	uc001fdt.1	-						RAB13_uc001fdu.1_5'Flank	NM_002870	NP_002861			RAB13, member RAS oncogene family						cell adhesion|protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	cytoplasmic vesicle membrane|tight junction	GTP binding|GTPase activity				0	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)													OREG0013830	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	153986095	153986095	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153986095delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	154014121	154014121	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154014121delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
C1orf189	388701	broad.mit.edu	37	1	154175281	154175281	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154175281delA	uc001fee.1	-							NM_001010979	NP_001010979			hypothetical protein LOC388701												0	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)																	---	---	---	---
C1orf43	25912	broad.mit.edu	37	1	154186760	154186760	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154186760delA	uc001fei.2	-						C1orf43_uc001fef.1_5'Flank|C1orf43_uc001feg.2_Intron|C1orf43_uc001feh.2_Intron|C1orf43_uc001fej.2_Intron|C1orf43_uc009wos.1_Intron|C1orf43_uc001fek.2_Intron|C1orf43_uc001fel.2_Intron	NM_001098616	NP_001092086			hypothetical protein LOC25912 isoform 3							integral to membrane	coenzyme binding|oxidoreductase activity				0	all_lung(78;1.98e-30)|Lung NSC(65;2.87e-28)|Hepatocellular(266;0.0877)																	---	---	---	---
UBAP2L	9898	broad.mit.edu	37	1	154200031	154200032	+	Intron	INS	-	T	T	rs66801580		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154200031_154200032insT	uc001fep.3	+						UBAP2L_uc009wot.2_Intron|UBAP2L_uc010pek.1_Intron|UBAP2L_uc010pel.1_Intron|UBAP2L_uc001fen.1_Intron|UBAP2L_uc010pem.1_Intron|UBAP2L_uc010pen.1_5'Flank	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	154266494	154266494	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154266494delA								HAX1 (18145 upstream) : AQP10 (27098 downstream)																																			---	---	---	---
IL6R	3570	broad.mit.edu	37	1	154412383	154412384	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154412383_154412384insT	uc001fez.1	+						IL6R_uc001ffa.1_Intron	NM_000565	NP_000556			interleukin 6 receptor isoform 1 precursor						acute-phase response|ciliary neurotrophic factor-mediated signaling pathway|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|endocrine pancreas development|hepatic immune response|negative regulation of collagen biosynthetic process|negative regulation of interleukin-8 production|positive regulation of activation of Janus kinase activity|positive regulation of anti-apoptosis|positive regulation of chemokine production|positive regulation of chemokine production|positive regulation of interleukin-6 production|positive regulation of leukocyte chemotaxis|positive regulation of MAPKKK cascade|positive regulation of osteoblast differentiation|positive regulation of smooth muscle cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of apoptosis	apical plasma membrane|basolateral plasma membrane|extracellular space|interleukin-6 receptor complex	ciliary neurotrophic factor binding|enzyme binding|protein homodimerization activity			ovary(3)|breast(1)	4	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
IL6R	3570	broad.mit.edu	37	1	154426947	154426947	+	Intron	DEL	T	-	-	rs4845374	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154426947delT	uc001fez.1	+						IL6R_uc001ffa.1_Intron	NM_000565	NP_000556			interleukin 6 receptor isoform 1 precursor						acute-phase response|ciliary neurotrophic factor-mediated signaling pathway|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|endocrine pancreas development|hepatic immune response|negative regulation of collagen biosynthetic process|negative regulation of interleukin-8 production|positive regulation of activation of Janus kinase activity|positive regulation of anti-apoptosis|positive regulation of chemokine production|positive regulation of chemokine production|positive regulation of interleukin-6 production|positive regulation of leukocyte chemotaxis|positive regulation of MAPKKK cascade|positive regulation of osteoblast differentiation|positive regulation of smooth muscle cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of apoptosis	apical plasma membrane|basolateral plasma membrane|extracellular space|interleukin-6 receptor complex	ciliary neurotrophic factor binding|enzyme binding|protein homodimerization activity			ovary(3)|breast(1)	4	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
KCNN3	3782	broad.mit.edu	37	1	154723762	154723762	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154723762delT	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)															---	---	---	---
KCNN3	3782	broad.mit.edu	37	1	154738272	154738273	+	Intron	INS	-	T	T	rs71576045		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154738272_154738273insT	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)															---	---	---	---
KCNN3	3782	broad.mit.edu	37	1	154762366	154762369	+	Intron	DEL	TTTG	-	-	rs151144384		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154762366_154762369delTTTG	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron|KCNN3_uc009wox.1_Intron	NM_002249	NP_002240			small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)															---	---	---	---
FLAD1	80308	broad.mit.edu	37	1	154964919	154964919	+	Intron	DEL	A	-	-	rs79704914		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154964919delA	uc001fgf.1	+						FLAD1_uc001fge.1_Intron|FLAD1_uc001fgg.1_Intron|FLAD1_uc001fgh.1_Intron|LENEP_uc001fgi.2_5'Flank	NM_025207	NP_079483			flavin adenine dinucleotide synthetase isoform						FAD biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|FMN adenylyltransferase activity			ovary(2)|skin(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)															---	---	---	---
ADAM15	8751	broad.mit.edu	37	1	155029614	155029614	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155029614delG	uc001fgr.1	+						ADAM15_uc001fgq.1_Intron|ADAM15_uc010pet.1_Intron|ADAM15_uc010peu.1_Intron|ADAM15_uc001fgt.1_Intron|ADAM15_uc010pev.1_Intron|ADAM15_uc001fgs.1_Intron|ADAM15_uc001fgu.1_Intron|ADAM15_uc001fgw.1_Intron|ADAM15_uc001fgv.1_Intron|ADAM15_uc001fgx.1_Intron|ADAM15_uc001fgz.1_Intron|ADAM15_uc001fgy.1_Intron|ADAM15_uc001fha.1_Intron|ADAM15_uc001fhb.1_5'Flank	NM_207197	NP_997080			a disintegrin and metalloproteinase domain 15						angiogenesis|cell-matrix adhesion|collagen catabolic process|proteolysis	acrosomal vesicle|adherens junction|endomembrane system|flagellum|integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			central_nervous_system(3)|skin(2)|ovary(1)	6	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	155073178	155073178	+	IGR	DEL	A	-	-	rs75372912		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155073178delA								EFNA3 (13172 upstream) : EFNA1 (27171 downstream)																																			---	---	---	---
FDPS	2224	broad.mit.edu	37	1	155283618	155283618	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155283618delT	uc001fkc.2	+						RAG1AP1_uc010pey.1_Intron|FDPS_uc001fkd.2_Intron|FDPS_uc001fke.2_Intron|FDPS_uc001fkf.2_Intron	NM_002004	NP_001995			farnesyl diphosphate synthase isoform a						cholesterol biosynthetic process|interspecies interaction between organisms|isoprenoid biosynthetic process	cytosol|nucleus	dimethylallyltranstransferase activity|geranyltranstransferase activity|metal ion binding				0	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)													---	---	---	---
RAG1AP1	55974	broad.mit.edu	37	1	155304572	155304573	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155304572_155304573insA	uc010pey.1	+							NM_018845				recombination activating gene 1 activating						positive regulation of gene expression, epigenetic	Golgi membrane|integral to membrane|plasma membrane	glucoside transmembrane transporter activity				0	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155365459	155365459	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155365459delA	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
YY1AP1	55249	broad.mit.edu	37	1	155644954	155644954	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																	---	---	---	---
YY1AP1	55249	broad.mit.edu	37	1	155651381	155651381	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155651381delA	uc001fln.2	-						YY1AP1_uc010pgh.1_5'Flank|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)																	---	---	---	---
KIAA0907	22889	broad.mit.edu	37	1	155898905	155898905	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155898905delA	uc001fmi.1	-						KIAA0907_uc001fmj.1_Intron|KIAA0907_uc009wrk.1_Intron|KIAA0907_uc009wrl.1_Intron|KIAA0907_uc001fml.1_Intron|KIAA0907_uc001fmm.2_Intron|KIAA0907_uc001fmo.2_Intron	NM_014949	NP_055764			hypothetical protein LOC22889												0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)															---	---	---	---
RXFP4	339403	broad.mit.edu	37	1	155910366	155910367	+	5'Flank	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155910366_155910367delTT	uc010pgs.1	+							NM_181885	NP_871001			relaxin 3 receptor 2							integral to membrane|plasma membrane	angiotensin type II receptor activity				0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
RAB25	57111	broad.mit.edu	37	1	156031316	156031316	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156031316delT	uc001fnc.2	+							NM_020387	NP_065120			RAB25						positive regulation of cell proliferation|protein transport|pseudopodium organization|small GTPase mediated signal transduction	cytoplasmic membrane-bounded vesicle|pseudopodium membrane	GTP binding|identical protein binding				0	Hepatocellular(266;0.158)|all_neural(408;0.195)																	---	---	---	---
CCT3	7203	broad.mit.edu	37	1	156287668	156287668	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156287668delT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	156371540	156371540	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156371540delT								RHBG (16531 upstream) : C1orf61 (2509 downstream)																																			---	---	---	---
IQGAP3	128239	broad.mit.edu	37	1	156512761	156512761	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156512761delA	uc001fpf.2	-							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)																	---	---	---	---
NES	10763	broad.mit.edu	37	1	156642804	156642804	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156642804delG	uc001fpq.2	-	4	1309	c.1176delC	c.(1174-1176)CCCfs	p.P392fs		NM_006617	NP_006608	P48681	NEST_HUMAN	nestin	392	Tail.				brain development|embryonic camera-type eye development|G2/M transition of mitotic cell cycle|negative regulation of apoptosis|positive regulation of intermediate filament depolymerization|positive regulation of neural precursor cell proliferation|stem cell proliferation	cytoplasm|intermediate filament	intermediate filament binding|structural molecule activity			ovary(6)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	156655253	156655254	+	IGR	DEL	AA	-	-	rs12030027	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156655253_156655254delAA								NES (8064 upstream) : CRABP2 (14156 downstream)																																			---	---	---	---
C1orf66	51093	broad.mit.edu	37	1	156702951	156702951	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156702951delT	uc001fpu.2	+						C1orf66_uc001fpv.2_Intron	NM_015997	NP_057081			hypothetical protein LOC51093 isoform 1							integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
PRCC	5546	broad.mit.edu	37	1	156761255	156761255	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156761255delA	uc001fqa.2	+						PRCC_uc001fqb.2_Intron	NM_005973	NP_005964			papillary renal cell carcinoma						cell cycle|mitotic cell cycle checkpoint	nucleus	protein binding		PRCC/TFE3(25)	kidney(25)|central_nervous_system(2)	27	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)							T	TFE3	papillary renal 								---	---	---	---
PRCC	5546	broad.mit.edu	37	1	156770553	156770553	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156770553delT	uc001fqa.2	+	7					PRCC_uc001fqb.2_3'UTR	NM_005973	NP_005964			papillary renal cell carcinoma						cell cycle|mitotic cell cycle checkpoint	nucleus	protein binding		PRCC/TFE3(25)	kidney(25)|central_nervous_system(2)	27	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)							T	TFE3	papillary renal 								---	---	---	---
ARHGEF11	9826	broad.mit.edu	37	1	157014344	157014344	+	5'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157014344delA	uc001fqo.2	-	1					ARHGEF11_uc001fqn.2_5'UTR	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	157061814	157061814	+	IGR	DEL	G	-	-	rs141946749		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157061814delG								ARHGEF11 (46652 upstream) : ETV3L (22 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157261331	157261331	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157261331delA								ETV3 (152948 upstream) : FCRL5 (221837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157468483	157468483	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157468483delA								ETV3 (360100 upstream) : FCRL5 (14685 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157642620	157642620	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157642620delT								FCRL4 (74750 upstream) : FCRL3 (3658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157951846	157951847	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157951846_157951847delAG								CD5L (140212 upstream) : KIRREL (11216 downstream)																																			---	---	---	---
KIRREL	55243	broad.mit.edu	37	1	157973592	157973593	+	Intron	DEL	AA	-	-	rs11327807		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157973592_157973593delAA	uc001frn.3	+						KIRREL_uc010pib.1_Intron	NM_018240	NP_060710			kin of IRRE like precursor							integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	158109074	158109075	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158109074_158109075insT	uc001frq.2	-											Homo sapiens cDNA clone IMAGE:5295410.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	158124069	158124069	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158124069delT								KIRREL (58227 upstream) : CD1D (25668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158181164	158181164	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158181164delT								CD1D (24950 upstream) : CD1A (42763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158348746	158348746	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158348746delA								CD1E (21405 upstream) : OR10T2 (19568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158401853	158401853	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158401853delT								OR10K2 (11197 upstream) : OR10K1 (33499 downstream)																																			---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158635224	158635225	+	Intron	INS	-	A	A	rs146874681	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158635224_158635225insA	uc001fst.1	-							NM_003126	NP_003117			spectrin, alpha, erythrocytic 1						actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	158769772	158769772	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158769772delA								OR6N2 (22347 upstream) : MNDA (31396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158846693	158846694	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158846693_158846694insC								MNDA (27423 upstream) : PYHIN1 (54648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158954737	158954737	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158954737delT								PYHIN1 (7896 upstream) : IFI16 (15021 downstream)																																			---	---	---	---
OR10J3	441911	broad.mit.edu	37	1	159286273	159286274	+	5'Flank	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159286273_159286274delTT	uc010piu.1	-							NM_001004467	NP_001004467			olfactory receptor, family 10, subfamily J,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_hematologic(112;0.0429)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	159300128	159300129	+	IGR	INS	-	C	C	rs111545936		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159300128_159300129insC								OR10J3 (15679 upstream) : OR10J1 (109420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159492655	159492655	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159492655delT								OR10J1 (82145 upstream) : OR10J5 (12215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159515153	159515154	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159515153_159515154insA								OR10J5 (9356 upstream) : APCS (42462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159534935	159534935	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159534935delA								OR10J5 (29138 upstream) : APCS (22681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159567682	159567683	+	IGR	DEL	TC	-	-	rs148551133		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159567682_159567683delTC								APCS (9022 upstream) : CRP (114397 downstream)																																			---	---	---	---
CASQ1	844	broad.mit.edu	37	1	160163733	160163734	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160163733_160163734delCA	uc010pja.1	+							NM_001231	NP_001222			calsequestrin 1							mitochondrial matrix|sarcoplasmic reticulum lumen|smooth endoplasmic reticulum	calcium ion binding			central_nervous_system(1)	1	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
VANGL2	57216	broad.mit.edu	37	1	160381654	160381655	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160381654_160381655delGT	uc001fwb.1	+						VANGL2_uc001fwc.1_Intron	NM_020335	NP_065068			vang-like 2						apical protein localization|heart looping|nonmotile primary cilium assembly	apical plasma membrane|integral to membrane				ovary(1)	1	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
SLAMF1	6504	broad.mit.edu	37	1	160609019	160609019	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160609019delT	uc001fwl.3	-						SLAMF1_uc010pjk.1_Intron|SLAMF1_uc010pjl.1_Intron|SLAMF1_uc010pjm.1_Intron|SLAMF1_uc001fwm.2_Intron	NM_003037	NP_003028			signaling lymphocytic activation molecule family						interspecies interaction between organisms|lymphocyte activation|positive regulation of cell proliferation	integral to membrane	antigen binding|transmembrane receptor activity			ovary(1)|breast(1)	2	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160696288	160696288	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160696288delT								CD48 (14703 upstream) : SLAMF7 (12789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	160762599	160762599	+	IGR	DEL	T	-	-	rs112774311		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160762599delT								SLAMF7 (37999 upstream) : LY9 (3329 downstream)																																			---	---	---	---
LY9	4063	broad.mit.edu	37	1	160775580	160775583	+	Intron	DEL	CTCA	-	-	rs147879300	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160775580_160775583delCTCA	uc001fwu.2	+						LY9_uc010pjs.1_Intron|LY9_uc001fwv.2_Intron|LY9_uc001fww.2_Intron|LY9_uc001fwx.2_Intron|LY9_uc001fwy.1_Intron	NM_002348	NP_002339			lymphocyte antigen 9 isoform a						cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160798237	160798237	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160798237delA								LY9 (194 upstream) : CD244 (1714 downstream)																																			---	---	---	---
CD244	51744	broad.mit.edu	37	1	160822647	160822647	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160822647delA	uc009wtq.2	-						CD244_uc001fxa.2_Intron|CD244_uc009wtp.2_Intron|CD244_uc009wtr.2_Intron|CD244_uc010pjt.1_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	160948045	160948045	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160948045delT								ITLN2 (23456 upstream) : F11R (16957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	160952585	160952585	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160952585delT								ITLN2 (27996 upstream) : F11R (12417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	160958695	160958696	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160958695_160958696insT								ITLN2 (34106 upstream) : F11R (6306 downstream)																																			---	---	---	---
F11R	50848	broad.mit.edu	37	1	160969818	160969818	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160969818delT	uc009wtt.2	-						F11R_uc010pjv.1_Intron|F11R_uc001fxe.3_Intron|F11R_uc009wtu.2_Intron|F11R_uc010pjw.1_Intron|F11R_uc001fxf.3_Intron	NM_016946	NP_058642			F11 receptor precursor						blood coagulation|inflammatory response|interspecies interaction between organisms|leukocyte migration|tight junction assembly	integral to membrane|tight junction				ovary(2)	2	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)															---	---	---	---
F11R	50848	broad.mit.edu	37	1	160991569	160991569	+	5'Flank	DEL	A	-	-	rs12567886	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160991569delA	uc009wtt.2	-						F11R_uc010pjv.1_5'Flank|F11R_uc001fxe.3_5'Flank|F11R_uc009wtu.2_5'Flank|F11R_uc010pjw.1_Intron|F11R_uc001fxf.3_Intron	NM_016946	NP_058642			F11 receptor precursor						blood coagulation|inflammatory response|interspecies interaction between organisms|leukocyte migration|tight junction assembly	integral to membrane|tight junction				ovary(2)	2	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)															---	---	---	---
USF1	7391	broad.mit.edu	37	1	161011737	161011738	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161011737_161011738delGA	uc001fxi.2	-						F11R_uc010pjw.1_5'Flank|F11R_uc001fxf.3_5'Flank|TSTD1_uc010pjx.1_5'Flank|TSTD1_uc009wtw.2_5'Flank|TSTD1_uc001fxh.3_5'Flank|USF1_uc001fxj.2_Intron	NM_007122	NP_009053			upstream stimulatory factor 1 isoform 1						cellular response to insulin stimulus|glucose homeostasis|late viral mRNA transcription|lipid homeostasis|positive regulation of transcription from RNA polymerase II promoter by glucose|response to hypoxia|response to UV	transcription factor complex	bHLH transcription factor binding|histone deacetylase binding|protein heterodimerization activity|protein homodimerization activity|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(52;6.73e-18)|Breast(13;0.012)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)															---	---	---	---
ADAMTS4	9507	broad.mit.edu	37	1	161164811	161164812	+	Intron	INS	-	AAAAC	AAAAC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161164811_161164812insAAAAC	uc001fyt.3	-							NM_005099	NP_005090			ADAM metallopeptidase with thrombospondin type 1						proteolysis|skeletal system development	extracellular space|proteinaceous extracellular matrix	metalloendopeptidase activity|protease binding|zinc ion binding			ovary(4)|central_nervous_system(1)	5	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)															---	---	---	---
NDUFS2	4720	broad.mit.edu	37	1	161182365	161182365	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161182365delT	uc001fyv.2	+						NDUFS2_uc001fyw.2_Intron|NDUFS2_uc010pkj.1_Intron|NDUFS2_uc001fyx.2_Intron|FCER1G_uc001fyz.1_5'Flank|FCER1G_uc001fza.1_5'Flank	NM_004550	NP_004541			NADH dehydrogenase (ubiquinone) Fe-S protein 2						mitochondrial electron transport, NADH to ubiquinone|response to oxidative stress|transport	mitochondrial respiratory chain complex I	4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NAD binding|NADH dehydrogenase (ubiquinone) activity|protein binding|quinone binding			skin(1)	1	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	161261703	161261704	+	IGR	INS	-	TT	TT	rs139909547	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161261703_161261704insTT								PCP4L1 (6464 upstream) : MPZ (12823 downstream)																																			---	---	---	---
SDHC	6391	broad.mit.edu	37	1	161309336	161309336	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161309336delT	uc001gag.2	+						SDHC_uc001gai.2_Intron|SDHC_uc001gaj.2_Intron|SDHC_uc001gak.2_Intron|SDHC_uc001gah.2_Intron	NM_003001	NP_002992			succinate dehydrogenase complex, subunit C						respiratory electron transport chain|transport|tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain complex II|plasma membrane succinate dehydrogenase complex	electron carrier activity|heme binding|succinate dehydrogenase activity				0	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Succinic acid(DB00139)			Mis|N|F			paraganglioma|pheochromocytoma			Familial_Paragangliomas|Carney-Stratakis_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	1	161413601	161413601	+	IGR	DEL	A	-	-	rs144019666	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161413601delA								C1orf192 (75937 upstream) : FCGR2A (61604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	161731092	161731092	+	IGR	DEL	G	-	-	rs34288540		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161731092delG								DUSP12 (4141 upstream) : ATF6 (4992 downstream)																																			---	---	---	---
ATF6	22926	broad.mit.edu	37	1	161817901	161817901	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161817901delA	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)															---	---	---	---
OLFML2B	25903	broad.mit.edu	37	1	161968431	161968432	+	Intron	INS	-	A	A	rs149405717	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161968431_161968432insA	uc001gbu.2	-						OLFML2B_uc010pkq.1_Intron	NM_015441	NP_056256			olfactomedin-like 2B precursor											skin(1)	1	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)															---	---	---	---
OLFML2B	25903	broad.mit.edu	37	1	161969163	161969164	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161969163_161969164insA	uc001gbu.2	-						OLFML2B_uc010pkq.1_Intron	NM_015441	NP_056256			olfactomedin-like 2B precursor											skin(1)	1	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)															---	---	---	---
UAP1	6675	broad.mit.edu	37	1	162540257	162540257	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162540257delT	uc001gce.3	+							NM_003115	NP_003106			UDP-N-acetylglucosamine pyrophosphorylase 1						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol|nucleus|plasma membrane	UDP-N-acetylglucosamine diphosphorylase activity			ovary(2)|skin(2)|kidney(1)	5	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)															---	---	---	---
UAP1	6675	broad.mit.edu	37	1	162550624	162550624	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162550624delT	uc001gce.3	+							NM_003115	NP_003106			UDP-N-acetylglucosamine pyrophosphorylase 1						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol|nucleus|plasma membrane	UDP-N-acetylglucosamine diphosphorylase activity			ovary(2)|skin(2)|kidney(1)	5	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	162874117	162874117	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162874117delG								C1orf110 (35512 upstream) : RGS4 (164279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	162920536	162920536	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162920536delA								C1orf110 (81931 upstream) : RGS4 (117860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	163074127	163074127	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163074127delT								RGS4 (27536 upstream) : RGS5 (37971 downstream)																																			---	---	---	---
RGS5	8490	broad.mit.edu	37	1	163137887	163137888	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163137887_163137888delAA	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	163607670	163607670	+	IGR	DEL	T	-	-	rs35254215		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163607670delT								NUF2 (282117 upstream) : PBX1 (921132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	163678154	163678155	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163678154_163678155delCT								NUF2 (352601 upstream) : PBX1 (850647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164342548	164342549	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164342548_164342549delGA								None (None upstream) : PBX1 (186253 downstream)																																			---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164540548	164540548	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164540548delA	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164632547	164632548	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164632547_164632548delCT	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Intron|uc001gcu.1_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164671427	164671427	+	Intron	DEL	T	-	-	rs66527828		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164671427delT	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	164726331	164726331	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164726331delT	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	164846493	164846493	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164846493delA	uc010pkw.1	+							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								---	---	---	---
LMX1A	4009	broad.mit.edu	37	1	165189514	165189514	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165189514delA	uc001gcy.1	-						LMX1A_uc001gcz.1_Intron	NM_177398	NP_796372			LIM homeobox transcription factor 1, alpha							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(3)|upper_aerodigestive_tract(1)|pancreas(1)	5	all_hematologic(923;0.248)																	---	---	---	---
TMCO1	54499	broad.mit.edu	37	1	165771705	165771705	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165771705delA	uc001gdn.3	-											Homo sapiens mRNA for putative membrane protein, complete cds.							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				central_nervous_system(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	166606069	166606069	+	IGR	DEL	A	-	-	rs67728729		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166606069delA								FMO9P (11598 upstream) : POGK (202655 downstream)																																			---	---	---	---
TADA1	117143	broad.mit.edu	37	1	166840759	166840761	+	Intron	DEL	TTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166840759_166840761delTTG	uc001gdw.2	-						TADA1_uc009wve.2_Intron	NM_053053	NP_444281			transcriptional adaptor 1-like						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(1)	1																		---	---	---	---
ILDR2	387597	broad.mit.edu	37	1	166890564	166890564	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166890564delC	uc001gdx.1	-	9	1320	c.1264delG	c.(1264-1266)GTGfs	p.V422fs		NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor	422	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1																		---	---	---	---
ILDR2	387597	broad.mit.edu	37	1	166944270	166944275	+	Intron	DEL	CTCTCA	-	-	rs59211434	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166944270_166944275delCTCTCA	uc001gdx.1	-							NM_199351	NP_955383			immunoglobulin-like domain containing receptor							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	166954562	166954563	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166954562_166954563insA								ILDR2 (10001 upstream) : MAEL (3956 downstream)																																			---	---	---	---
MAEL	84944	broad.mit.edu	37	1	166980240	166980240	+	Intron	DEL	T	-	-	rs74968502		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166980240delT	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																		---	---	---	---
POU2F1	5451	broad.mit.edu	37	1	167249598	167249601	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167249598_167249601delTTTT	uc001gec.2	+						POU2F1_uc010plg.1_Intron|POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron	NM_002697	NP_002688			POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5																		---	---	---	---
POU2F1	5451	broad.mit.edu	37	1	167354799	167354799	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167354799delA	uc001gec.2	+						POU2F1_uc010plg.1_Intron|POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron|POU2F1_uc001gef.2_Intron|POU2F1_uc001geg.2_Intron	NM_002697	NP_002688			POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5																		---	---	---	---
POU2F1	5451	broad.mit.edu	37	1	167371365	167371365	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167371365delT	uc001gec.2	+						POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron|POU2F1_uc001gef.2_Intron|POU2F1_uc001geg.2_Intron|POU2F1_uc009wvg.1_Intron	NM_002697	NP_002688			POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5																		---	---	---	---
CD247	919	broad.mit.edu	37	1	167456311	167456312	+	Intron	DEL	AA	-	-	rs72102505		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167456311_167456312delAA	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)															---	---	---	---
CREG1	8804	broad.mit.edu	37	1	167515879	167515880	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167515879_167515880delAA	uc001gel.2	-							NM_003851	NP_003842			cellular repressor of E1A-stimulated genes						cell proliferation|multicellular organismal development|regulation of growth|regulation of transcription from RNA polymerase II promoter	extracellular region	FMN binding|transcription corepressor activity				0																		---	---	---	---
MPZL1	9019	broad.mit.edu	37	1	167695608	167695608	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167695608delT	uc001geo.2	+						MPZL1_uc001gen.3_Intron|MPZL1_uc001gep.2_Intron|MPZL1_uc001geq.2_Intron|MPZL1_uc009wvh.2_Intron	NM_003953	NP_003944			myelin protein zero-like 1 isoform a						cell-cell signaling|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	protein binding|structural molecule activity			ovary(2)	2	all_hematologic(923;0.215)																	---	---	---	---
MPZL1	9019	broad.mit.edu	37	1	167707156	167707157	+	Intron	INS	-	TGTG	TGTG	rs147352181	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167707156_167707157insTGTG	uc001geo.2	+						MPZL1_uc001gen.3_Intron|MPZL1_uc001gep.2_Intron|MPZL1_uc001geq.2_Intron|MPZL1_uc009wvh.2_Intron	NM_003953	NP_003944			myelin protein zero-like 1 isoform a						cell-cell signaling|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	protein binding|structural molecule activity			ovary(2)	2	all_hematologic(923;0.215)																	---	---	---	---
TBX19	9095	broad.mit.edu	37	1	168224472	168224472	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168224472delT	uc001gfj.3	+							NM_005149	NP_005140			T-box 19						anatomical structure morphogenesis	nucleus	DNA binding				0	all_hematologic(923;0.215)																	---	---	---	---
XCL2	6846	broad.mit.edu	37	1	168512322	168512322	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168512322delC	uc001gfn.3	-							NM_003175	NP_003166			chemokine (C motif) ligand 2 precursor						blood circulation|chemotaxis|immune response|signal transduction	extracellular space	chemokine activity			ovary(1)	1	all_hematologic(923;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	168644824	168644825	+	IGR	INS	-	T	T	rs115824480	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168644824_168644825insT								XCL1 (93509 upstream) : DPT (19882 downstream)																																			---	---	---	---
MGC4473	79100	broad.mit.edu	37	1	168756802	168756803	+	Intron	DEL	GT	-	-	rs72185179	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168756802_168756803delGT	uc001gfq.2	+							NR_024160				Homo sapiens hypothetical protein MGC4473, mRNA (cDNA clone IMAGE:2961346), partial cds.												0																		---	---	---	---
NME7	29922	broad.mit.edu	37	1	169256191	169256192	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169256191_169256192insA	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron|NME7_uc001gfv.1_3'UTR	NM_013330	NP_037462			nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)																	---	---	---	---
NME7	29922	broad.mit.edu	37	1	169277910	169277910	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169277910delA	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron|NME7_uc001gfv.1_Intron	NM_013330	NP_037462			nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)																	---	---	---	---
NME7	29922	broad.mit.edu	37	1	169334798	169334798	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169334798delT	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron|BLZF1_uc001gfw.2_5'Flank|BLZF1_uc001gfx.1_5'Flank|BLZF1_uc001gfy.2_5'Flank|NME7_uc001gfv.1_Intron	NM_013330	NP_037462			nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)																	---	---	---	---
C1orf114	57821	broad.mit.edu	37	1	169366387	169366387	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169366387delT	uc001gga.1	-						C1orf114_uc001gfz.1_Intron|C1orf114_uc009wvq.1_Intron	NM_021179	NP_067002			hypothetical protein LOC57821												0	all_hematologic(923;0.208)																	---	---	---	---
C1orf114	57821	broad.mit.edu	37	1	169406229	169406229	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169406229delT	uc009wvq.1	-							NM_021179	NP_067002			hypothetical protein LOC57821												0	all_hematologic(923;0.208)																	---	---	---	---
C1orf114	57821	broad.mit.edu	37	1	169431438	169431438	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169431438delT	uc009wvq.1	-						uc001ggd.2_5'Flank	NM_021179	NP_067002			hypothetical protein LOC57821												0	all_hematologic(923;0.208)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	169607072	169607072	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169607072delA								SELP (7695 upstream) : C1orf112 (24173 downstream)																																			---	---	---	---
C1orf112	55732	broad.mit.edu	37	1	169640037	169640037	+	Intron	DEL	T	-	-	rs34668742		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169640037delT	uc001ggj.2	+											Homo sapiens cDNA FLJ10706 fis, clone NT2RP3000852.												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
SELE	6401	broad.mit.edu	37	1	169699840	169699841	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169699840_169699841delTT	uc001ggm.3	-						C1orf112_uc001ggj.2_Intron	NM_000450	NP_000441			selectin E precursor						actin filament-based process|activation of phospholipase C activity|calcium-mediated signaling|heterophilic cell-cell adhesion|leukocyte migration involved in inflammatory response|leukocyte tethering or rolling|positive regulation of receptor internalization|regulation of inflammatory response|response to interleukin-1|response to lipopolysaccharide|response to tumor necrosis factor	caveola|coated pit|cortical cytoskeleton|extracellular space|integral to membrane|perinuclear region of cytoplasm	oligosaccharide binding|phospholipase binding|sialic acid binding|transmembrane receptor activity			ovary(3)|skin(2)	5	all_hematologic(923;0.208)																	---	---	---	---
C1orf112	55732	broad.mit.edu	37	1	169753574	169753574	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169753574delT	uc001ggj.2	+											Homo sapiens cDNA FLJ10706 fis, clone NT2RP3000852.												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	170170670	170170670	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170170670delT								METTL11B (33747 upstream) : LOC284688 (69877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	170534164	170534165	+	IGR	INS	-	GAAA	GAAA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170534164_170534165insGAAA								GORAB (11190 upstream) : PRRX1 (99148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	170623564	170623564	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170623564delT								GORAB (100590 upstream) : PRRX1 (9749 downstream)																																			---	---	---	---
PRRX1	5396	broad.mit.edu	37	1	170705899	170705900	+	3'UTR	INS	-	T	T	rs143876556	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170705899_170705900insT	uc001ghf.2	+	4					PRRX1_uc001ghe.2_3'UTR	NM_022716	NP_073207			paired mesoderm homeobox 1 isoform pmx-1b							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	170783586	170783587	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170783586_170783587insA								PRRX1 (75046 upstream) : C1orf129 (121025 downstream)																																			---	---	---	---
C1orf129	80133	broad.mit.edu	37	1	170953886	170953887	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170953886_170953887insT	uc001ghg.2	+						C1orf129_uc009wvy.2_Intron|C1orf129_uc010plz.1_Intron	NM_025063	NP_079339			hypothetical protein LOC80133 isoform 2								binding			pancreas(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
FMO3	2328	broad.mit.edu	37	1	171060585	171060585	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171060585delA	uc001ghi.2	+						FMO3_uc010pma.1_Intron|FMO3_uc001ghh.2_Intron|FMO3_uc010pmb.1_Intron|FMO3_uc010pmc.1_Intron	NM_001002294	NP_001002294			flavin containing monooxygenase 3						xenobiotic metabolic process	integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
FMO4	2329	broad.mit.edu	37	1	171282100	171282100	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171282100delA	uc001gho.2	+							NM_002022	NP_002013			flavin containing monooxygenase 4						xenobiotic metabolic process	integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			kidney(2)|skin(1)	3	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171503605	171503605	+	Intron	DEL	T	-	-	rs11332424		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171503605delT	uc010pmg.1	+							NM_015172	NP_055987			HBxAg transactivated protein 2								protein C-terminus binding				0																		---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171537316	171537316	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171537316delA	uc010pmg.1	+						BAT2L2_uc010pmh.1_Intron|BAT2L2_uc010pmi.1_Intron	NM_015172	NP_055987			HBxAg transactivated protein 2								protein C-terminus binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	171627728	171627728	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171627728delT								MYOC (5905 upstream) : VAMP4 (41570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	171649845	171649846	+	IGR	DEL	TT	-	-	rs35910622		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171649845_171649846delTT								MYOC (28022 upstream) : VAMP4 (19452 downstream)																																			---	---	---	---
VAMP4	8674	broad.mit.edu	37	1	171686759	171686760	+	Intron	DEL	TT	-	-	rs112797491		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171686759_171686760delTT	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)																	---	---	---	---
VAMP4	8674	broad.mit.edu	37	1	171688417	171688417	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171688417delA	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)																	---	---	---	---
VAMP4	8674	broad.mit.edu	37	1	171697650	171697650	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	172114204	172114205	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172114204_172114205delAA	uc001gie.2	+						DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron|MIR199A2_hsa-mir-199a-2|MI0000281_5'Flank	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	172260119	172260120	+	Intron	INS	-	T	T	rs76154551	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172260119_172260120insT	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	172569177	172569177	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172569177delA	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	172583114	172583114	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172583114delA								C1orf9 (2143 upstream) : FASLG (45071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	173050339	173050340	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173050339_173050340insA								TNFSF18 (30236 upstream) : TNFSF4 (102531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	173108840	173108843	+	IGR	DEL	TTTT	-	-	rs143726330		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173108840_173108843delTTTT								TNFSF18 (88737 upstream) : TNFSF4 (44028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	173223537	173223537	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173223537delT	uc001gix.1	-											Homo sapiens cDNA FLJ45305 fis, clone BRHIP3004193.																														---	---	---	---
SLC9A11	284525	broad.mit.edu	37	1	173545908	173545908	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173545908delA	uc001giz.2	-						SLC9A11_uc009wwe.2_5'Flank|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																		---	---	---	---
KLHL20	27252	broad.mit.edu	37	1	173694219	173694221	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173694219_173694221delAAA	uc001gjc.2	+						KLHL20_uc010pmr.1_Intron|KLHL20_uc009wwf.2_Intron|KLHL20_uc001gjd.2_Intron	NM_014458	NP_055273			kelch-like 20						cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
ZBTB37	84614	broad.mit.edu	37	1	173851192	173851192	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173851192delA	uc009wwp.1	+						ZBTB37_uc001gjp.1_Intron|ZBTB37_uc001gjr.2_Intron	NM_001122770	NP_001116242			zinc finger and BTB domain containing 37 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173930736	173930736	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173930736delA	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	174012119	174012122	+	IGR	DEL	TTTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174012119_174012122delTTTG								RC3H1 (49909 upstream) : RABGAP1L (116512 downstream)																																			---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174166938	174166939	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174166938_174166939delAA	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.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	174245147	174245148	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174245147_174245148insA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	175008126	175008126	+	IGR	DEL	T	-	-	rs10713426		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175008126delT								MRPS14 (15565 upstream) : TNN (28868 downstream)																																			---	---	---	---
TNR	7143	broad.mit.edu	37	1	175510767	175510767	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175510767delA	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	175705350	175705350	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175705350delA	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	176145160	176145160	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	176220874	176220876	+	IGR	DEL	TTT	-	-	rs112029199		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176220874_176220876delTTT								RFWD2 (44504 upstream) : PAPPA2 (211431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	176248067	176248067	+	IGR	DEL	T	-	-	rs77593084		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176248067delT								RFWD2 (71697 upstream) : PAPPA2 (184240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	176813093	176813095	+	RNA	DEL	TTG	-	-	rs34164016		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176813093_176813095delTTG	uc001gla.1	+	1		c.714_716delTTG								Homo sapiens cDNA FLJ39399 fis, clone PLACE6011041.																														---	---	---	---
ASTN1	460	broad.mit.edu	37	1	176892824	176892824	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176892824delA	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron	NM_004319	NP_004310			astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15																		---	---	---	---
ASTN1	460	broad.mit.edu	37	1	176989996	176989997	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176989996_176989997delTG	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron|ASTN1_uc009wwx.1_Intron|ASTN1_uc001gle.3_Intron	NM_004319	NP_004310			astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15																		---	---	---	---
FAM5B	57795	broad.mit.edu	37	1	177157989	177157990	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177157989_177157990insT	uc001glf.2	+							NM_021165	NP_066988			family with sequence similarity 5, member B							extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
FAM5B	57795	broad.mit.edu	37	1	177193326	177193326	+	Intron	DEL	T	-	-	rs113986402		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177193326delT	uc001glf.2	+							NM_021165	NP_066988			family with sequence similarity 5, member B							extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
FAM5B	57795	broad.mit.edu	37	1	177206777	177206778	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177206777_177206778insG	uc001glf.2	+							NM_021165	NP_066988			family with sequence similarity 5, member B							extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	177783637	177783637	+	IGR	DEL	T	-	-	rs72457741		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177783637delT								FAM5B (532080 upstream) : SEC16B (113852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	178053453	178053453	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178053453delC								SEC16B (46311 upstream) : LOC100302401 (7190 downstream)																																			---	---	---	---
RASAL2	9462	broad.mit.edu	37	1	178237159	178237159	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178237159delT	uc001glq.2	+						RASAL2_uc009wxb.2_Intron	NM_170692	NP_733793			RAS protein activator like 2 isoform 2						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5																		---	---	---	---
RASAL2	9462	broad.mit.edu	37	1	178433786	178433786	+	Intron	DEL	T	-	-	rs68085428		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178433786delT	uc001glr.2	+						RASAL2_uc001glq.2_Intron|RASAL2_uc009wxc.2_Intron	NM_004841	NP_004832			RAS protein activator like 2 isoform 1						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5																		---	---	---	---
RALGPS2	55103	broad.mit.edu	37	1	178790728	178790728	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178790728delT	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	178929856	178929857	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178929856_178929857delCA								RALGPS2 (40621 upstream) : FAM20B (65217 downstream)																																			---	---	---	---
TDRD5	163589	broad.mit.edu	37	1	179580200	179580200	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179580200delT	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	179611242	179611243	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179611242_179611243delTT	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																		---	---	---	---
FAM163A	148753	broad.mit.edu	37	1	179780179	179780179	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179780179delA	uc009wxj.2	+						FAM163A_uc001gnj.2_Intron|FAM163A_uc009wxk.2_Intron	NM_173509	NP_775780			hypothetical protein LOC148753							integral to membrane				ovary(1)	1																		---	---	---	---
CEP350	9857	broad.mit.edu	37	1	179989021	179989021	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179989021delA	uc001gnt.2	+						CEP350_uc009wxl.2_Intron|CEP350_uc001gnu.2_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
CEP350	9857	broad.mit.edu	37	1	180044793	180044793	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180044793delA	uc001gnt.2	+						CEP350_uc009wxl.2_Intron|CEP350_uc001gnv.2_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
CEP350	9857	broad.mit.edu	37	1	180047269	180047269	+	Intron	DEL	A	-	-	rs111944313		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180047269delA	uc001gnt.2	+						CEP350_uc009wxl.2_Intron|CEP350_uc001gnv.2_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180710310	180710310	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180710310delT	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727			xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180728004	180728004	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180728004delA	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																		---	---	---	---
IER5	51278	broad.mit.edu	37	1	181057031	181057031	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181057031delA	uc001got.3	+							NM_016545	NP_057629			immediate early response 5											pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	181781243	181781243	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181781243delT								CACNA1E (10530 upstream) : ZNF648 (242464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182277116	182277116	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182277116delA								ZNF648 (246269 upstream) : GLUL (74553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182335188	182335188	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182335188delA								ZNF648 (304341 upstream) : GLUL (16481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182532594	182532594	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182532594delT								RGSL1 (2864 upstream) : RNASEL (10178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182755594	182755594	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182755594delA								RGS8 (113527 upstream) : NPL (3278 downstream)																																			---	---	---	---
NPL	80896	broad.mit.edu	37	1	182757063	182757064	+	5'Flank	DEL	CA	-	-	rs71759319		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182757063_182757064delCA	uc009wyb.2	+						NPL_uc010pnx.1_5'Flank|NPL_uc010pny.1_5'Flank|NPL_uc001gpo.1_5'Flank|NPL_uc009wyc.2_5'Flank|NPL_uc001gpp.3_5'Flank	NM_030769	NP_110396			N-acetylneuraminate pyruvate lyase						carbohydrate metabolic process	cytoplasm	N-acetylneuraminate lyase activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
DHX9	1660	broad.mit.edu	37	1	182819437	182819438	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182819437_182819438insA	uc001gpr.2	+						DHX9_uc001gps.2_Intron	NM_001357	NP_001348			DEAH (Asp-Glu-Ala-His) box polypeptide 9						CRD-mediated mRNA stabilization|nuclear mRNA splicing, via spliceosome	centrosome|CRD-mediated mRNA stability complex|nucleolus|nucleoplasm|ribonucleoprotein complex	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|double-stranded RNA binding|protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	182927276	182927276	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182927276delT								C1orf14 (4723 upstream) : LAMC1 (65319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182956451	182956451	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182956451delT								C1orf14 (33898 upstream) : LAMC1 (36144 downstream)																																			---	---	---	---
SMG7	9887	broad.mit.edu	37	1	183513992	183513992	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183513992delA	uc001gqg.2	+						SMG7_uc010pob.1_Intron|SMG7_uc001gqf.2_Intron|SMG7_uc001gqh.2_Intron|SMG7_uc001gqi.2_Intron|SMG7_uc010poc.1_Intron	NM_173156	NP_775179			SMG-7 homolog isoform 1						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
RGL1	23179	broad.mit.edu	37	1	183873948	183873948	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183873948delT	uc001gqo.2	+						RGL1_uc010pof.1_Intron|RGL1_uc001gqm.2_Intron|RGL1_uc010pog.1_Intron|RGL1_uc010poh.1_Intron|RGL1_uc010poi.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																		---	---	---	---
GLT25D2	23127	broad.mit.edu	37	1	183942612	183942612	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183942612delA	uc001gqr.2	-						GLT25D2_uc010poj.1_Intron|GLT25D2_uc001gqs.2_Intron	NM_015101	NP_055916			glycosyltransferase 25 domain containing 2						lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity			ovary(1)|breast(1)	2																		---	---	---	---
GLT25D2	23127	broad.mit.edu	37	1	184001143	184001144	+	Intron	INS	-	CCT	CCT	rs148450733	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184001143_184001144insCCT	uc001gqr.2	-						GLT25D2_uc010poj.1_Intron|GLT25D2_uc001gqs.2_Intron	NM_015101	NP_055916			glycosyltransferase 25 domain containing 2						lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity			ovary(1)|breast(1)	2																		---	---	---	---
C1orf21	81563	broad.mit.edu	37	1	184446574	184446574	+	5'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184446574delA	uc001gqv.1	+	2						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	185080675	185080675	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185080675delT								RNF2 (8935 upstream) : C1orf25 (6544 downstream)																																			---	---	---	---
C1orf26	54823	broad.mit.edu	37	1	185200690	185200690	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185200690delT	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988			hypothetical protein LOC54823												0																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185958905	185958905	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185958905delT	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	185992421	185992428	+	Intron	DEL	TTTTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185992421_185992428delTTTTTTTT	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	186026291	186026293	+	Intron	DEL	ACA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186026291_186026293delACA	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	186120313	186120313	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186120313delT	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																		---	---	---	---
PRG4	10216	broad.mit.edu	37	1	186274155	186274155	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186274155delG	uc001gru.3	+						PRG4_uc001grt.3_Intron|PRG4_uc009wyl.2_Intron|PRG4_uc009wym.2_Intron|PRG4_uc010poo.1_Intron	NM_005807	NP_005798			proteoglycan 4 isoform A						cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
PDC	5132	broad.mit.edu	37	1	186415429	186415429	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186415429delT	uc001gsa.2	-						PDC_uc001grz.2_Intron	NM_002597	NP_002588			phosducin isoform a						G-protein coupled receptor protein signaling pathway|phototransduction|visual perception	actin cytoskeleton|cytosol|nucleus|photoreceptor inner segment|photoreceptor outer segment	phospholipase inhibitor activity			skin(1)	1		Breast(1374;1.53e-05)		KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.0129)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	186993992	186993997	+	IGR	DEL	AAAAAA	-	-	rs78157091		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186993992_186993997delAAAAAA								PLA2G4A (35887 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187115981	187115982	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187115981_187115982insT								PLA2G4A (157876 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187331019	187331020	+	IGR	DEL	TT	-	-	rs35177663		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187331019_187331020delTT								PLA2G4A (372914 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188642571	188642573	+	IGR	DEL	AAA	-	-	rs35121478		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188642571_188642573delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188993723	188993734	+	IGR	DEL	TATCTATCTATC	-	-	rs71665621		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188993723_188993734delTATCTATCTATC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189223023	189223026	+	IGR	DEL	TTTT	-	-	rs113290842		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189223023_189223026delTTTT								None (None upstream) : FAM5C (843771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189388265	189388265	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189388265delA								None (None upstream) : FAM5C (678532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189674158	189674159	+	IGR	INS	-	AG	AG	rs147964735	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189674158_189674159insAG								None (None upstream) : FAM5C (392638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189738659	189738659	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189738659delG								None (None upstream) : FAM5C (328138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189961457	189961457	+	IGR	DEL	T	-	-	rs74494395		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189961457delT								None (None upstream) : FAM5C (105340 downstream)																																			---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190067106	190067106	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190067106delA	uc001gse.1	-	8					FAM5C_uc010pot.1_3'UTR	NM_199051	NP_950252			family with sequence similarity 5, member C							extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)																	---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190067583	190067583	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190067583delA	uc001gse.1	-	8	2098	c.1866delT	c.(1864-1866)TTTfs	p.F622fs	FAM5C_uc010pot.1_Frame_Shift_Del_p.F520fs	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	622						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)																	---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190325467	190325467	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190325467delT	uc001gse.1	-						FAM5C_uc010pot.1_Intron	NM_199051	NP_950252			family with sequence similarity 5, member C							extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	190891531	190891532	+	IGR	DEL	CA	-	-	rs34839379		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190891531_190891532delCA								FAM5C (444772 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191792494	191792495	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191792494_191792495delGT								None (None upstream) : RGS18 (335097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192117934	192117935	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192117934_192117935delAA								None (None upstream) : RGS18 (9657 downstream)																																			---	---	---	---
RGS13	6003	broad.mit.edu	37	1	192613357	192613357	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192613357delT	uc001gsj.2	+						RGS13_uc001gsk.2_Intron	NM_002927	NP_002918			regulator of G-protein signalling 13							plasma membrane	GTPase activator activity|signal transducer activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	193297121	193297121	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193297121delA								CDC73 (73181 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193392269	193392269	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193392269delT								CDC73 (168329 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193570077	193570077	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193570077delA								CDC73 (346137 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193929155	193929155	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193929155delA								CDC73 (705215 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194073624	194073632	+	IGR	DEL	GCAGCAGCA	-	-	rs113697132		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194073624_194073632delGCAGCAGCA								CDC73 (849684 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195213055	195213056	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195213055_195213056delTT								None (None upstream) : KCNT2 (981857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195330748	195330749	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195330748_195330749insA								None (None upstream) : KCNT2 (864164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195660911	195660911	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195660911delA								None (None upstream) : KCNT2 (534002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195861850	195861850	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195861850delC								None (None upstream) : KCNT2 (333063 downstream)																																			---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196416010	196416011	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196416010_196416011delAG	uc001gtd.1	-						KCNT2_uc009wyt.1_Intron|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.1_Intron	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196456539	196456540	+	Intron	INS	-	GT	GT	rs149378823	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196456539_196456540insGT	uc001gtd.1	-						KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.1_Intron	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	196739608	196739609	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196739608_196739609insA								CFH (22977 upstream) : CFHR3 (4321 downstream)																																			---	---	---	---
CFHR3	10878	broad.mit.edu	37	1	196759035	196759037	+	Intron	DEL	AAG	-	-	rs374905	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196759035_196759037delAAG	uc001gtl.2	+						CFHR3_uc001gtk.2_3'UTR|CFHR3_uc010poy.1_Intron|CFHR1_uc001gtm.2_Intron	NM_021023	NP_066303			complement factor H-related 3 precursor							extracellular space					0																		---	---	---	---
ASPM	259266	broad.mit.edu	37	1	197061246	197061246	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197061246delT	uc001gtu.2	-						ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606			asp (abnormal spindle)-like, microcephaly						mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197233925	197233925	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197233925delT	uc010poz.1	+							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	197297540	197297540	+	Intron	DEL	A	-	-	rs12042179	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197297540delA	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc001gty.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.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																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197389479	197389479	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197389479delA	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron|CRB1_uc010ppc.1_Intron|CRB1_uc010ppd.1_Intron|CRB1_uc001gub.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																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197411572	197411573	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197411572_197411573insA	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																		---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197741949	197741949	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197741949delC	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	198086985	198086985	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198086985delT								LHX9 (185270 upstream) : NEK7 (39123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198097080	198097080	+	IGR	DEL	T	-	-	rs59967617	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198097080delT								LHX9 (195365 upstream) : NEK7 (29028 downstream)																																			---	---	---	---
NEK7	140609	broad.mit.edu	37	1	198143501	198143501	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198143501delA	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	198351478	198351478	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198351478delT								NEK7 (59932 upstream) : ATP6V1G3 (140878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198452735	198452735	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198452735delA								NEK7 (161189 upstream) : ATP6V1G3 (39621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198804351	198804354	+	IGR	DEL	AAGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198804351_198804354delAAGG								PTPRC (77806 upstream) : MIR181B1 (23648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198870334	198870334	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198870334delA	uc001guz.2	-											Homo sapiens familial acute myelogenous leukemia related factor mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	199975364	199975365	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199975364_199975365delTC								None (None upstream) : NR5A2 (21405 downstream)																																			---	---	---	---
NR5A2	2494	broad.mit.edu	37	1	200042828	200042829	+	Intron	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200042828_200042829insCA	uc001gvb.2	+						NR5A2_uc001gvc.2_Intron|NR5A2_uc009wzh.2_Intron|NR5A2_uc010pph.1_Intron	NM_205860	NP_995582			nuclear receptor subfamily 5, group A, member 2						embryo development|positive regulation of viral genome replication|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	lipid binding|protein binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Prostate(682;0.19)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	200484079	200484079	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200484079delT								ZNF281 (104913 upstream) : KIF14 (36546 downstream)																																			---	---	---	---
CAMSAP1L1	23271	broad.mit.edu	37	1	200719701	200719702	+	Intron	INS	-	TGTG	TGTG	rs145051907	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200719701_200719702insTGTG	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																		---	---	---	---
CAMSAP1L1	23271	broad.mit.edu	37	1	200729254	200729256	+	Intron	DEL	ACT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200729254_200729256delACT	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	201039540	201039541	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201039540_201039541delGA	uc001gvv.2	-							NM_000069	NP_000060			calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	201090956	201090957	+	IGR	INS	-	A	A	rs112364594		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201090956_201090957insA								CACNA1S (9262 upstream) : TMEM9 (12944 downstream)																																			---	---	---	---
IGFN1	91156	broad.mit.edu	37	1	201195812	201195812	+	Intron	DEL	A	-	-	rs34207437		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201195812delA	uc001gwc.2	+						IGFN1_uc001gwb.2_Intron	NM_178275	NP_840059			RecName: Full=Immunoglobulin-like and fibronectin type III domain-containing protein 1; AltName: Full=EEF1A2-binding protein 1; AltName: Full=KY-interacting protein 1;											ovary(2)|pancreas(1)	3																		---	---	---	---
PKP1	5317	broad.mit.edu	37	1	201292551	201292552	+	Intron	DEL	CA	-	-	rs148317060		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201292551_201292552delCA	uc001gwd.2	+						PKP1_uc001gwe.2_Intron|PKP1_uc009wzm.2_Intron	NM_000299	NP_000290			plakophilin 1 isoform 1b						cell adhesion|cellular component disassembly involved in apoptosis|multicellular organismal development	desmosome|intermediate filament|nucleus	intermediate filament binding|signal transducer activity|structural constituent of epidermis			ovary(2)	2																		---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201634991	201634991	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201634991delA	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	201680630	201680630	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201680630delA	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																		---	---	---	---
LGR6	59352	broad.mit.edu	37	1	202209504	202209506	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202209504_202209506delAAA	uc001gxu.2	+						LGR6_uc001gxv.2_Intron|LGR6_uc009xab.2_Intron|LGR6_uc001gxw.2_Intron|LGR6_uc009xac.1_Intron	NM_001017403	NP_001017403			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	202297175	202297175	+	IGR	DEL	T	-	-	rs149963854		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202297175delT								LGR6 (8287 upstream) : UBE2T (3611 downstream)																																			---	---	---	---
SYT2	127833	broad.mit.edu	37	1	202594472	202594473	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202594472_202594473delGT	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)													---	---	---	---
KDM5B	10765	broad.mit.edu	37	1	202710853	202710853	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202710853delA	uc001gyf.2	-						KDM5B_uc009xag.2_Intron|KDM5B_uc001gyg.1_Intron	NM_006618	NP_006609			jumonji, AT rich interactive domain 1B						negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5																		---	---	---	---
KDM5B	10765	broad.mit.edu	37	1	202717840	202717841	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202717840_202717841delTT	uc001gyf.2	-						KDM5B_uc009xag.2_Intron|KDM5B_uc001gyg.1_Intron	NM_006618	NP_006609			jumonji, AT rich interactive domain 1B						negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	202788400	202788400	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202788400delT	uc001gyh.2	+											Homo sapiens hypothetical protein LOC641515, mRNA (cDNA clone MGC:33633 IMAGE:4827085), complete cds.																														---	---	---	---
KLHL12	59349	broad.mit.edu	37	1	202888634	202888634	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202888634delT	uc001gyo.1	-						KLHL12_uc001gyn.1_5'Flank|KLHL12_uc010pqc.1_Intron|KLHL12_uc009xah.1_Intron	NM_021633	NP_067646			kelch-like 12						Wnt receptor signaling pathway		protein binding				0			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	202941433	202941433	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202941433delT								CYB5R1 (5029 upstream) : TMEM183A (35101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203366192	203366194	+	IGR	DEL	CAA	-	-	rs146145836		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203366192_203366194delCAA								FMOD (45903 upstream) : PRELP (78689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203373835	203373835	+	IGR	DEL	A	-	-	rs78883793		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203373835delA								FMOD (53546 upstream) : PRELP (71048 downstream)																																			---	---	---	---
GOLT1A	127845	broad.mit.edu	37	1	204170836	204170836	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204170836delC	uc001has.1	-	3	407	c.221delG	c.(220-222)GGTfs	p.G74fs	GOLT1A_uc001hat.1_Frame_Shift_Del_p.G74fs	NM_198447	NP_940849	Q6ZVE7	GOT1A_HUMAN	golgi transport 1 homolog A	74	Helical; Name=3; (Potential).				protein transport|vesicle-mediated transport	Golgi membrane|integral to membrane					0	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.244)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	204470084	204470085	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204470084_204470085delAA								PIK3C2B (6232 upstream) : MDM4 (15426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	204757585	204757585	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204757585delA								MDM4 (79924 upstream) : NFASC (40197 downstream)																																			---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204844794	204844794	+	Intron	DEL	T	-	-	rs80034218		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204844794delT	uc001hbj.2	+						NFASC_uc001hbh.2_Intron|NFASC_uc010pqz.1_Intron|NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc009xbg.1_Intron	NM_001005388	NP_001005388			neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
RBBP5	5929	broad.mit.edu	37	1	205060063	205060064	+	Intron	DEL	AA	-	-	rs72199877		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205060063_205060064delAA	uc001hbu.1	-						RBBP5_uc010prd.1_Intron|RBBP5_uc001hbv.1_Intron|RBBP5_uc010pre.1_Intron	NM_005057	NP_005048			retinoblastoma binding protein 5						histone H3-K4 methylation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription, DNA-dependent	MLL1 complex|Set1C/COMPASS complex	methylated histone residue binding|transcription regulatory region DNA binding			lung(1)	1	Breast(84;0.0505)		BRCA - Breast invasive adenocarcinoma(75;0.0923)															---	---	---	---
RBBP5	5929	broad.mit.edu	37	1	205070859	205070859	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205070859delA	uc001hbu.1	-						RBBP5_uc010prd.1_Intron|RBBP5_uc001hbv.1_Intron|RBBP5_uc010pre.1_Intron	NM_005057	NP_005048			retinoblastoma binding protein 5						histone H3-K4 methylation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription, DNA-dependent	MLL1 complex|Set1C/COMPASS complex	methylated histone residue binding|transcription regulatory region DNA binding			lung(1)	1	Breast(84;0.0505)		BRCA - Breast invasive adenocarcinoma(75;0.0923)															---	---	---	---
TMCC2	9911	broad.mit.edu	37	1	205207367	205207367	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205207367delT	uc001hbz.1	+						TMCC2_uc010prf.1_Intron	NM_014858	NP_055673			transmembrane and coiled-coil domain family 2							integral to membrane	protein binding			pancreas(1)	1	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	205416889	205416890	+	IGR	INS	-	C	C	rs142309800	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205416889_205416890insC								LEMD1 (25708 upstream) : MIR135B (540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	205420876	205420877	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205420876_205420877delTT								MIR135B (3350 upstream) : CDK18 (52850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	205458864	205458864	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205458864delC								MIR135B (41338 upstream) : CDK18 (14863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	205463682	205463682	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205463682delT								MIR135B (46156 upstream) : CDK18 (10045 downstream)																																			---	---	---	---
ELK4	2005	broad.mit.edu	37	1	205595700	205595700	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205595700delA	uc001hcy.1	-						ELK4_uc001hcz.2_Intron|SLC45A3_uc010prn.1_Intron|SLC45A3_uc010pro.1_Intron|SLC45A3_uc010prp.1_Intron|ELK4_uc010prq.1_Intron	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								---	---	---	---
SLC45A3	85414	broad.mit.edu	37	1	205610757	205610758	+	Intron	DEL	CC	-	-	rs78014635		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205610757_205610758delCC	uc010pro.1	-						SLC45A3_uc010prn.1_Intron|SLC45A3_uc010prp.1_Intron|ELK4_uc010prq.1_Intron	NM_033102	NP_149093			prostein						transmembrane transport	integral to membrane			SLC45A3/BRAF(2)	ovary(2)|prostate(2)	4	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)					T	ETV1|ETV5|ELK4|ERG	prostate 								---	---	---	---
Unknown	0	broad.mit.edu	37	1	205822858	205822858	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205822858delA								PM20D1 (3613 upstream) : SLC26A9 (59321 downstream)																																			---	---	---	---
SLC26A9	115019	broad.mit.edu	37	1	205907372	205907375	+	Intron	DEL	TTCC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205907372_205907375delTTCC	uc001hdq.2	-						SLC26A9_uc001hdp.2_Intron	NM_052934	NP_443166			solute carrier family 26, member 9 isoform a							integral to membrane	chloride channel activity|secondary active sulfate transmembrane transporter activity			ovary(1)|skin(1)	2	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	206236158	206236159	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206236158_206236159insG								AVPR1B (4676 upstream) : C1orf186 (2713 downstream)																																			---	---	---	---
SRGAP2	23380	broad.mit.edu	37	1	206513622	206513623	+	5'Flank	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206513622_206513623delCT	uc001hdy.2	+						SRGAP2_uc009xbt.2_5'Flank|SRGAP2_uc010prt.1_5'Flank|SRGAP2_uc001hdx.2_5'Flank|SRGAP2_uc010pru.1_5'Flank	NM_015326	NP_056141			SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)																	---	---	---	---
SRGAP2	23380	broad.mit.edu	37	1	206530245	206530245	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206530245delT	uc001hdy.2	+						SRGAP2_uc009xbt.2_Intron|SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron	NM_015326	NP_056141			SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	206953201	206953202	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206953201_206953202insT								IL10 (7167 upstream) : IL19 (19013 downstream)																																			---	---	---	---
CR1	1378	broad.mit.edu	37	1	207684173	207684175	+	Intron	DEL	TTT	-	-	rs12080969		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207684173_207684175delTTT	uc001hfy.2	+						CR1_uc009xcl.1_Intron|CR1_uc001hfx.2_Intron|CR1_uc009xcj.1_Intron|CR1_uc009xck.1_Intron	NM_000573	NP_000564			complement receptor 1 isoform F precursor						complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	209263713	209263713	+	IGR	DEL	G	-	-	rs12756213	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209263713delG								PLXNA2 (846048 upstream) : LOC642587 (338455 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	209486779	209486780	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209486779_209486780insA								None (None upstream) : LOC642587 (115388 downstream)																																			---	---	---	---
IRF6	3664	broad.mit.edu	37	1	209966922	209966926	+	Intron	DEL	TTTTA	-	-	rs67606266		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209966922_209966926delTTTTA	uc001hhq.1	-						IRF6_uc010psm.1_Intron|IRF6_uc009xct.1_Intron	NM_006147	NP_006138			interferon regulatory factor 6						cell cycle arrest|interferon-gamma-mediated signaling pathway|mammary gland epithelial cell differentiation|negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0351)											HNSCC(57;0.16)			---	---	---	---
IRF6	3664	broad.mit.edu	37	1	209978473	209978483	+	Intron	DEL	TCAACACCAGC	-	-	rs66995425		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209978473_209978483delTCAACACCAGC	uc001hhq.1	-						IRF6_uc010psm.1_Intron|IRF6_uc009xct.1_Intron	NM_006147	NP_006138			interferon regulatory factor 6						cell cycle arrest|interferon-gamma-mediated signaling pathway|mammary gland epithelial cell differentiation|negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0351)											HNSCC(57;0.16)			---	---	---	---
C1orf107	27042	broad.mit.edu	37	1	210030204	210030205	+	3'UTR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210030204_210030205delAC	uc001hhr.1	+	12					C1orf107_uc009xcu.1_3'UTR	NM_014388	NP_055203			digestive-organ expansion factor homolog						multicellular organismal development	nucleus					0				OV - Ovarian serous cystadenocarcinoma(81;0.0367)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	210052958	210052958	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210052958delT								C1orf107 (22050 upstream) : SYT14 (58580 downstream)																																			---	---	---	---
SYT14	255928	broad.mit.edu	37	1	210109845	210109861	+	5'Flank	DEL	AGTCTCCTGGACAAATA	-	-	rs68158224		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210109845_210109861delAGTCTCCTGGACAAATA	uc009xcv.2	+						SYT14_uc001hhs.3_5'Flank|SYT14_uc001hht.3_5'Flank|SYT14_uc001hhu.3_5'Flank|SYT14_uc010psn.1_5'Flank|SYT14_uc010pso.1_5'Flank	NM_153262	NP_694994			synaptotagmin XIV isoform 4							integral to membrane				ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.085)														---	---	---	---
SYT14	255928	broad.mit.edu	37	1	210262228	210262228	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210262228delT	uc009xcv.2	+						SYT14_uc001hhs.3_Intron|SYT14_uc001hht.3_Intron|SYT14_uc001hhu.3_Intron|SYT14_uc010psn.1_Intron|SYT14_uc010pso.1_Intron	NM_153262	NP_694994			synaptotagmin XIV isoform 4							integral to membrane				ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.085)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	210339944	210339946	+	IGR	DEL	GGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210339944_210339946delGGA								SYT14 (2313 upstream) : C1orf133 (64858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	210492743	210492743	+	IGR	DEL	C	-	-	rs7548236	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210492743delC								SERTAD4 (76305 upstream) : HHAT (8863 downstream)																																			---	---	---	---
HHAT	55733	broad.mit.edu	37	1	210619222	210619223	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210619222_210619223delTT	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	211194287	211194288	+	Intron	INS	-	A	A	rs139300863	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211194287_211194288insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	211675155	211675156	+	IGR	INS	-	TG	TG	rs139060878	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211675155_211675156insTG								RD3 (8896 upstream) : SLC30A1 (73225 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	211885750	211885750	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211885750delG								NEK2 (36783 upstream) : LPGAT1 (31050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	212046793	212046794	+	IGR	INS	-	C	C	rs140007529	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212046793_212046794insC								LPGAT1 (42679 upstream) : INTS7 (67904 downstream)																																			---	---	---	---
DTL	51514	broad.mit.edu	37	1	212271245	212271245	+	Intron	DEL	C	-	-	rs74958833		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212271245delC	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	212417235	212417235	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212417235delT								DTL (139049 upstream) : PPP2R5A (41644 downstream)																																			---	---	---	---
PPP2R5A	5525	broad.mit.edu	37	1	212525797	212525798	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212525797_212525798delTT	uc001hjb.2	+						PPP2R5A_uc010ptd.1_Intron|SNORA16B_uc009xdf.1_5'Flank	NM_006243	NP_006234			protein phosphatase 2, regulatory subunit B						negative regulation of establishment of protein localization in plasma membrane|negative regulation of lipid kinase activity|positive regulation of protein dephosphorylation|signal transduction	chromosome, centromeric region|cytoplasm|nucleus|protein phosphatase type 2A complex	kinase binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	212630599	212630599	+	IGR	DEL	A	-	-	rs145323231		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212630599delA								NENF (10880 upstream) : ATF3 (108098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	212726397	212726400	+	IGR	DEL	AAAG	-	-	rs72241615		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212726397_212726400delAAAG								NENF (106678 upstream) : ATF3 (12297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	212804238	212804238	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212804238delG								FAM71A (4124 upstream) : BATF3 (55522 downstream)																																			---	---	---	---
BATF3	55509	broad.mit.edu	37	1	212861335	212861362	+	Intron	DEL	AAGAAAGGAAGGAAGGAAGGAAGGAAGG	-	-	rs72333347	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212861335_212861362delAAGAAAGGAAGGAAGGAAGGAAGGAAGG	uc001hjl.1	-							NM_018664	NP_061134			basic leucine zipper transcription factor,						transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0046)|all cancers(67;0.00785)|GBM - Glioblastoma multiforme(131;0.0731)|Epithelial(68;0.0781)														---	---	---	---
RPS6KC1	26750	broad.mit.edu	37	1	213398740	213398740	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213398740delT	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	214393285	214393285	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214393285delA								PROX1 (183525 upstream) : SMYD2 (61280 downstream)																																			---	---	---	---
SMYD2	56950	broad.mit.edu	37	1	214501805	214501806	+	Intron	INS	-	C	C	rs147436613	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214501805_214501806insC	uc010ptx.1	+						SMYD2_uc009xdj.2_Intron|SMYD2_uc010ptw.1_Intron|SMYD2_uc009xdl.1_Intron	NM_020197	NP_064582			SET and MYND domain containing 2						negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|regulation of DNA damage response, signal transduction by p53 class mediator|transcription, DNA-dependent	cytosol|nucleus	histone methyltransferase activity (H3-K36 specific)|p53 binding|RNA polymerase II core binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)												OREG0014249	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	214524658	214524658	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214524658delA								SMYD2 (14181 upstream) : PTPN14 (6353 downstream)																																			---	---	---	---
PTPN14	5784	broad.mit.edu	37	1	214591236	214591236	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214591236delA	uc001hkk.1	-						PTPN14_uc010pty.1_Intron	NM_005401	NP_005392			protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	214998517	214998517	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214998517delT								CENPF (160605 upstream) : KCNK2 (180368 downstream)																																			---	---	---	---
KCNK2	3776	broad.mit.edu	37	1	215195804	215195805	+	Intron	INS	-	GT	GT	rs145436124	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215195804_215195805insGT	uc001hko.2	+						KCNK2_uc009xdm.2_Intron|KCNK2_uc001hkp.2_Intron	NM_001017424	NP_001017424			potassium channel, subfamily K, member 2 isoform								outward rectifier potassium channel activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)													---	---	---	---
KCNK2	3776	broad.mit.edu	37	1	215256673	215256673	+	5'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215256673delA	uc001hkq.2	+	1					KCNK2_uc001hko.2_Intron|KCNK2_uc009xdm.2_Intron|KCNK2_uc001hkp.2_Intron|KCNK2_uc010pua.1_RNA|KCNK2_uc001hkr.3_Intron	NM_001017425	NP_001017425			potassium channel, subfamily K, member 2 isoform								outward rectifier potassium channel activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	215675273	215675273	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215675273delA								KCNK2 (264838 upstream) : KCTD3 (65462 downstream)																																			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215814143	215814143	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215814143delA	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	215914592	215914592	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215914592delA	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	215972505	215972505	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215972505delA	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)			---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	216765846	216765846	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216765846delT	uc001hkw.1	-						ESRRG_uc001hky.1_Intron|ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron|ESRRG_uc001hkx.1_Intron|ESRRG_uc009xdo.1_Intron|ESRRG_uc001hle.1_Intron	NM_001438	NP_001429			estrogen-related receptor gamma isoform 1						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	217082174	217082175	+	Intron	DEL	AA	-	-	rs5780943		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217082174_217082175delAA	uc001hky.1	-						ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318			estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	217294462	217294463	+	Intron	DEL	AC	-	-	rs72215303		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217294462_217294463delAC	uc001hlc.1	-						ESRRG_uc001hld.1_Intron	NM_206595	NP_996318			estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
GPATCH2	55105	broad.mit.edu	37	1	217645054	217645054	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217645054delT	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)														---	---	---	---
SPATA17	128153	broad.mit.edu	37	1	217952978	217952978	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217952978delT	uc001hlh.1	+						SPATA17_uc009xdr.1_Intron|SPATA17_uc001hli.2_Intron	NM_138796	NP_620151			spermatogenesis associated 17							cytoplasm	calmodulin binding			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	219219831	219219832	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219219831_219219832delTT								TGFB2 (601872 upstream) : LYPLAL1 (127360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219545107	219545110	+	IGR	DEL	TGTC	-	-	rs146867197		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219545107_219545110delTGTC								LYPLAL1 (158901 upstream) : SLC30A10 (313659 downstream)																																			---	---	---	---
SLC30A10	55532	broad.mit.edu	37	1	219860756	219860756	+	Intron	DEL	G	-	-	rs72736728	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219860756delG	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	219918729	219918730	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219918729_219918730insT	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)														---	---	---	---
EPRS	2058	broad.mit.edu	37	1	220215524	220215527	+	Intron	DEL	AAAA	-	-	rs12238988		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220215524_220215527delAAAA	uc001hly.1	-						EPRS_uc010puf.1_Intron|EPRS_uc001hlz.1_Intron|EPRS_uc009xdt.1_Intron	NM_004446	NP_004437			glutamyl-prolyl tRNA synthetase						glutamyl-tRNA aminoacylation|prolyl-tRNA aminoacylation|protein complex assembly	cytosol|soluble fraction	ATP binding|glutamate-tRNA ligase activity|proline-tRNA ligase activity|protein binding|RNA binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0735)	L-Glutamic Acid(DB00142)|L-Proline(DB00172)													---	---	---	---
BPNT1	10380	broad.mit.edu	37	1	220257674	220257675	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220257674_220257675insA	uc001hma.2	-						BPNT1_uc010pug.1_Intron|BPNT1_uc010puh.1_Intron|BPNT1_uc001hmb.3_Intron	NM_006085	NP_006076			3'(2'), 5'-bisphosphate nucleotidase 1						3'-phosphoadenosine 5'-phosphosulfate metabolic process|nervous system development|xenobiotic metabolic process	cytosol	3'(2'),5'-bisphosphate nucleotidase activity			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0558)														---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220324483	220324483	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	220372511	220372511	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220372511delA	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	220883309	220883310	+	IGR	INS	-	C	C	rs139900060	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220883309_220883310insC								C1orf115 (10810 upstream) : MOSC2 (38366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221576373	221576373	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221576373delC								LOC400804 (66735 upstream) : DUSP10 (298393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221710519	221710520	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221710519_221710520delTG								LOC400804 (200881 upstream) : DUSP10 (164246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222435596	222435596	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222435596delT								DUSP10 (520135 upstream) : HHIPL2 (260006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222639785	222639785	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222639785delT								DUSP10 (724324 upstream) : HHIPL2 (55817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222641415	222641415	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222641415delA								DUSP10 (725954 upstream) : HHIPL2 (54187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	223220745	223220746	+	IGR	INS	-	AGTC	AGTC	rs138535020	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223220745_223220746insAGTC								DISP1 (41410 upstream) : TLR5 (62838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	223561300	223561300	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223561300delA								SUSD4 (23756 upstream) : C1orf65 (5415 downstream)																																			---	---	---	---
CAPN2	824	broad.mit.edu	37	1	223954336	223954336	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223954336delC	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)														---	---	---	---
TP53BP2	7159	broad.mit.edu	37	1	223980974	223980974	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223980974delA	uc010pvb.1	-						TP53BP2_uc001hod.2_Intron|TP53BP2_uc010puz.1_Intron|TP53BP2_uc010pva.1_Intron	NM_001031685	NP_001026855			tumor protein p53 binding protein, 2 isoform 1						apoptosis|cell cycle|induction of apoptosis|negative regulation of cell cycle|signal transduction	nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protein binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(2)|lung(1)	3				GBM - Glioblastoma multiforme(131;0.0958)														---	---	---	---
TP53BP2	7159	broad.mit.edu	37	1	224027487	224027487	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224027487delT	uc010pvb.1	-						TP53BP2_uc001hod.2_Intron	NM_001031685	NP_001026855			tumor protein p53 binding protein, 2 isoform 1						apoptosis|cell cycle|induction of apoptosis|negative regulation of cell cycle|signal transduction	nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protein binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(2)|lung(1)	3				GBM - Glioblastoma multiforme(131;0.0958)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	224276716	224276717	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224276716_224276717insA								TP53BP2 (243042 upstream) : FBXO28 (25074 downstream)																																			---	---	---	---
FBXO28	23219	broad.mit.edu	37	1	224318044	224318044	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224318044delA	uc001hoh.2	+						FBXO28_uc009xef.2_Intron|FBXO28_uc010pvc.1_Intron	NM_015176	NP_055991			F-box protein 28 isoform a											ovary(2)|kidney(2)|lung(1)	5	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)														---	---	---	---
NVL	4931	broad.mit.edu	37	1	224432070	224432070	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224432070delA	uc001hok.2	-						NVL_uc001hol.2_Intron|NVL_uc010pvd.1_Intron|NVL_uc010pve.1_Intron|NVL_uc010pvf.1_Intron	NM_002533	NP_002524			nuclear VCP-like isoform 1							aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)														---	---	---	---
NVL	4931	broad.mit.edu	37	1	224432396	224432397	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224432396_224432397delTT	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)														---	---	---	---
CNIH4	29097	broad.mit.edu	37	1	224553459	224553459	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224553459delA	uc001hom.1	+						CNIH4_uc001hon.1_Intron	NM_014184	NP_054903			cornichon homolog 4						intracellular signal transduction	endoplasmic reticulum|integral to membrane	protein binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.00341)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	224693989	224693990	+	Intron	INS	-	CACA	CACA	rs56687766		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224693989_224693990insCACA	uc001hor.1	+											full-length cDNA clone CS0DC026YN07 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
DNAH14	127602	broad.mit.edu	37	1	225200085	225200085	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225200085delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	225885912	225885912	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225885912delA	uc001hpe.1	+											Homo sapiens cDNA FLJ42062 fis, clone SYNOV2005673.																														---	---	---	---
SRP9	6726	broad.mit.edu	37	1	225970839	225970839	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225970839delT	uc001hpg.2	+						SRP9_uc001hpf.3_Intron|SRP9_uc001hph.2_Intron|SRP9_uc001hpi.3_Intron|SRP9_uc001hpj.1_Intron	NM_003133	NP_003124			signal recognition particle 9kDa isoform 2						negative regulation of translational elongation|SRP-dependent cotranslational protein targeting to membrane	cytosol|signal recognition particle receptor complex|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding				0																		---	---	---	---
TMEM63A	9725	broad.mit.edu	37	1	226059795	226059795	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226059795delA	uc001hpm.1	-						TMEM63A_uc010pvi.1_Intron	NM_014698	NP_055513			transmembrane protein 63A							integral to membrane|lysosomal membrane	nucleotide binding			ovary(1)|breast(1)	2	Breast(184;0.197)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	226279858	226279858	+	IGR	DEL	A	-	-	rs78242302		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226279858delA								H3F3A (20156 upstream) : ACBD3 (52524 downstream)																																			---	---	---	---
LIN9	286826	broad.mit.edu	37	1	226438518	226438518	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
C1orf95	375057	broad.mit.edu	37	1	226764721	226764722	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226764721_226764722insC	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)														---	---	---	---
ITPKB	3707	broad.mit.edu	37	1	226879951	226879951	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226879951delT	uc010pvo.1	-							NM_002221	NP_002212			1D-myo-inositol-trisphosphate 3-kinase B								ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)																---	---	---	---
PSEN2	5664	broad.mit.edu	37	1	227057355	227057356	+	5'Flank	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227057355_227057356delAC	uc009xeo.1	+						PSEN2_uc009xep.1_5'Flank	NM_000447	NP_000438			presenilin 2 isoform 1						amyloid precursor protein catabolic process|anti-apoptosis|apoptosis|beta-amyloid metabolic process|calcium ion transport|induction of apoptosis by extracellular signals|intracellular signal transduction|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity	apical plasma membrane|axon|cell cortex|cell surface|centrosome|ciliary rootlet|dendritic shaft|endoplasmic reticulum membrane|Golgi membrane|growth cone|integral to plasma membrane|kinetochore|lysosomal membrane|membrane raft|mitochondrial inner membrane|neuromuscular junction|neuronal cell body|nuclear inner membrane|perinuclear region of cytoplasm|Z disc	aspartic-type endopeptidase activity|protein binding			lung(2)	2		Prostate(94;0.0771)																---	---	---	---
CABC1	56997	broad.mit.edu	37	1	227147122	227147122	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227147122delA	uc001hqm.1	+						CABC1_uc010pvp.1_Intron|CABC1_uc001hqn.1_Intron|CABC1_uc009xeq.1_Intron|CABC1_uc010pvq.1_Intron	NM_020247	NP_064632			chaperone, ABC1 activity of bc1 complex like						cell death	mitochondrion	ATP binding|protein serine/threonine kinase activity				0		Prostate(94;0.0771)																---	---	---	---
CABC1	56997	broad.mit.edu	37	1	227171736	227171736	+	Intron	DEL	G	-	-	rs149374145	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227171736delG	uc001hqm.1	+						CABC1_uc001hqn.1_Intron|CABC1_uc009xeq.1_Intron|CABC1_uc010pvq.1_Intron|CABC1_uc010pvr.1_Intron|CABC1_uc001hqo.1_Intron|CABC1_uc009xer.1_5'UTR	NM_020247	NP_064632			chaperone, ABC1 activity of bc1 complex like						cell death	mitochondrion	ATP binding|protein serine/threonine kinase activity				0		Prostate(94;0.0771)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	227556748	227556748	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227556748delA								CDC42BPA (50922 upstream) : ZNF678 (194496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	227561931	227561932	+	IGR	INS	-	TAGTT	TAGTT	rs147743138	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227561931_227561932insTAGTT								CDC42BPA (56105 upstream) : ZNF678 (189312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	228325478	228325479	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228325478_228325479delAA								MRPL55 (28465 upstream) : GUK1 (2450 downstream)																																			---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228451277	228451278	+	Intron	DEL	AG	-	-	rs59491779		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228451277_228451278delAG	uc009xez.1	+						OBSCN_uc001hsn.2_Intron	NM_001098623	NP_001092093			obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	228791910	228791910	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228791910delT								DUSP5P (3751 upstream) : RHOU (78959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229811338	229811345	+	IGR	DEL	CCATCCAT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229811338_229811345delCCATCCAT								URB2 (15392 upstream) : GALNT2 (382191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230180188	230180188	+	IGR	DEL	G	-	-	rs34750823		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230180188delG								URB2 (384242 upstream) : GALNT2 (13348 downstream)																																			---	---	---	---
COG2	22796	broad.mit.edu	37	1	230796633	230796633	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230796633delA	uc001htw.2	+						COG2_uc001htx.2_Intron|COG2_uc010pwc.1_Intron	NM_007357	NP_031383			component of oligomeric golgi complex 2 isoform						Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)																---	---	---	---
COG2	22796	broad.mit.edu	37	1	230810620	230810621	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230810620_230810621insT	uc001htw.2	+						COG2_uc001htx.2_Intron|COG2_uc010pwc.1_Intron	NM_007357	NP_031383			component of oligomeric golgi complex 2 isoform						Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)																---	---	---	---
FAM89A	375061	broad.mit.edu	37	1	231178431	231178431	+	5'Flank	DEL	T	-	-	rs11368232		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231178431delT	uc001hui.2	-						FAM89A_uc009xfm.2_5'Flank	NM_198552	NP_940954			family with sequence similarity 89, member A												0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	231495910	231495910	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231495910delA								C1orf124 (5922 upstream) : EGLN1 (3587 downstream)																																			---	---	---	---
DISC1	27185	broad.mit.edu	37	1	231827176	231827176	+	Intron	DEL	A	-	-	rs79065174		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231827176delA	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	231912496	231912496	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	232025489	232025489	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232025489delT	uc001huz.2	+						TSNAX-DISC1_uc010pwl.1_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)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	232252176	232252177	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232252176_232252177delAG								DISC1 (75160 upstream) : SIPA1L2 (281537 downstream)																																			---	---	---	---
SIPA1L2	57568	broad.mit.edu	37	1	232625601	232625602	+	Intron	DEL	TA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232625601_232625602delTA	uc001hvg.2	-							NM_020808	NP_065859			signal-induced proliferation-associated 1 like						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)																---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233135199	233135203	+	Intron	DEL	TTTTT	-	-	rs137857886		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233135199_233135203delTTTTT	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	233673779	233673781	+	IGR	DEL	TCC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233673779_233673781delTCC								KIAA1804 (152886 upstream) : KCNK1 (75969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	233814664	233814664	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233814664delA								KCNK1 (6406 upstream) : SLC35F3 (226015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	234007020	234007026	+	IGR	DEL	AAAAAAA	-	-	rs66527757		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234007020_234007026delAAAAAAA								KCNK1 (198762 upstream) : SLC35F3 (33653 downstream)																																			---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234455479	234455479	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234455479delA	uc001hwa.1	+						SLC35F3_uc001hvy.1_Intron	NM_173508	NP_775779			solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
TARBP1	6894	broad.mit.edu	37	1	234586105	234586105	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234586105delA	uc001hwd.2	-							NM_005646	NP_005637			TAR RNA binding protein 1						regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)|skin(1)	3	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)															---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235345419	235345419	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235345419delT	uc001hwq.2	-	20	3313	c.2815delA	c.(2815-2817)ACGfs	p.T939fs	ARID4B_uc001hwr.2_Frame_Shift_Del_p.T853fs|ARID4B_uc001hws.3_Frame_Shift_Del_p.T853fs|ARID4B_uc001hwp.2_RNA|ARID4B_uc001hwt.3_Frame_Shift_Del_p.T620fs	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1	939					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)															---	---	---	---
TBCE	6905	broad.mit.edu	37	1	235609499	235609499	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235609499delT	uc001hwz.1	+						TBCE_uc001hxa.1_Intron|TBCE_uc010pxr.1_Intron|TBCE_uc001hxb.1_Intron	NM_003193	NP_003184			beta-tubulin cofactor E						'de novo' posttranslational protein folding|post-chaperonin tubulin folding pathway	cytoplasm|microtubule|nucleus|plasma membrane	chaperone binding				0	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;2.56e-05)															---	---	---	---
GNG4	2786	broad.mit.edu	37	1	235712930	235712932	+	3'UTR	DEL	CTG	-	-	rs71799487		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235712930_235712932delCTG	uc001hxe.3	-	4					GNG4_uc009xfz.2_3'UTR|GNG4_uc001hxh.3_3'UTR	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	235932851	235932851	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235932851delA	uc001hxj.2	-						LYST_uc009xgb.1_Intron|LYST_uc010pxs.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				---	---	---	---
NID1	4811	broad.mit.edu	37	1	236220192	236220192	+	Intron	DEL	A	-	-	rs35411911		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236220192delA	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	236271217	236271218	+	IGR	INS	-	G	G	rs150801565	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236271217_236271218insG								NID1 (42736 upstream) : GPR137B (34614 downstream)																																			---	---	---	---
GPR137B	7107	broad.mit.edu	37	1	236317719	236317720	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236317719_236317720insT	uc001hxq.2	+							NM_003272	NP_003263			G protein-coupled receptor 137B							integral to plasma membrane|membrane fraction					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	237164003	237164003	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237164003delA								MTR (96723 upstream) : RYR2 (41699 downstream)																																			---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237401258	237401260	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237401258_237401260delTTT	uc001hyl.1	+							NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237806607	237806607	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237806607delT	uc001hyl.1	+							NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237819091	237819091	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237819091delT	uc001hyl.1	+							NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237875200	237875200	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237875200delT	uc001hyl.1	+						RYR2_uc010pxz.1_Intron	NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	238273030	238273031	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238273030_238273031delAC								LOC100130331 (181413 upstream) : LOC339535 (370655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	238949947	238949948	+	IGR	INS	-	C	C	rs138490743	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238949947_238949948insC								LOC339535 (300630 upstream) : CHRM3 (599917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239311478	239311478	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239311478delA								LOC339535 (662161 upstream) : CHRM3 (238387 downstream)																																			---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	239643563	239643563	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239643563delA	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)													---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	239933181	239933182	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239933181_239933182delAA	uc001hyp.2	+						CHRM3_uc001hyo.1_Intron	NM_000740	NP_000731			cholinergic receptor, muscarinic 3						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)													---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240406431	240406431	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240406431delA	uc010pyd.1	+						FMN2_uc010pye.1_Intron|FMN2_uc010pyf.1_5'Flank|FMN2_uc010pyg.1_5'Flank	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)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241228228	241228228	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241228228delA	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915			regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241319815	241319815	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241319815delA	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	241359686	241359686	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241359686delA	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	241476144	241476147	+	Intron	DEL	CAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241476144_241476147delCAAA	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-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
KMO	8564	broad.mit.edu	37	1	241747946	241747947	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241747946_241747947delTG	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)															---	---	---	---
WDR64	128025	broad.mit.edu	37	1	241876446	241876447	+	Intron	DEL	AA	-	-	rs71809025		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241876446_241876447delAA	uc001hze.1	+						WDR64_uc001hzf.1_Intron					RecName: Full=WD repeat-containing protein 64;											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	242788982	242788982	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242788982delA								PLD5 (100984 upstream) : CEP170 (498749 downstream)																																			---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243599041	243599042	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243599041_243599042delTG	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron|SDCCAG8_uc001hzx.2_Intron	NM_006642	NP_006633			serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	244162301	244162302	+	Intron	DEL	CA	-	-	rs10531261		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244162301_244162302delCA	uc001iac.2	+											Homo sapiens cDNA clone IMAGE:5244187.																														---	---	---	---
PPPDE1	51029	broad.mit.edu	37	1	244849569	244849570	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244849569_244849570delTG	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	244919394	244919396	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244919394_244919396delTTT								PPPDE1 (47062 upstream) : FAM36A (79243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	245065342	245065343	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245065342_245065343delTT								HNRNPU (37515 upstream) : EFCAB2 (67828 downstream)																																			---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245319204	245319205	+	Intron	INS	-	C	C	rs111553943		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245319204_245319205insC	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245332630	245332631	+	Intron	INS	-	GT	GT	rs113622566		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245332630_245332631insGT	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245403465	245403465	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245403465delA	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245704320	245704321	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245704320_245704321insA	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	245935178	245935178	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245935178delA	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	246537457	246537457	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246537457delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
SCCPDH	51097	broad.mit.edu	37	1	246923456	246923456	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246923456delT	uc001ibr.2	+							NM_016002	NP_057086			saccharopine dehydrogenase (putative)							midbody	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity			ovary(1)	1	all_cancers(71;6.8e-05)|all_epithelial(71;7.93e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0545)|Lung NSC(105;0.0618)	all_cancers(173;0.0343)	OV - Ovarian serous cystadenocarcinoma(106;0.00323)	GBM - Glioblastoma multiforme(49;0.0896)														---	---	---	---
AHCTF1	25909	broad.mit.edu	37	1	247016383	247016383	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247016383delT	uc001ibu.1	-						AHCTF1_uc001ibv.1_Intron|AHCTF1_uc009xgs.1_Intron|AHCTF1_uc001ibw.1_Intron	NM_015446	NP_056261			transcription factor ELYS						cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)															---	---	---	---
ZNF695	57116	broad.mit.edu	37	1	247110970	247110971	+	Intron	INS	-	CA	CA	rs145847336	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247110970_247110971insCA	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)															---	---	---	---
ZNF670	93474	broad.mit.edu	37	1	247235461	247235461	+	Intron	DEL	T	-	-	rs12131419	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247235461delT	uc001icd.1	-						ZNF695_uc001ica.2_Intron|ZNF695_uc001icb.1_Intron	NM_033213	NP_149990			zinc finger protein 670						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	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;0.00427)															---	---	---	---
NLRP3	114548	broad.mit.edu	37	1	247606878	247606878	+	Intron	DEL	G	-	-	rs141229378		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247606878delG	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	247801427	247801434	+	IGR	DEL	ACACACAT	-	-	rs113860473		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247801427_247801434delACACACAT								OR2G3 (31611 upstream) : OR13G1 (33986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	248062023	248062023	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248062023delT								OR2W3 (1881 upstream) : OR2T8 (22297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	248609625	248609625	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248609625delG								OR2T1 (39221 upstream) : OR2T2 (6474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	248872090	248872090	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248872090delG								OR14I1 (26485 upstream) : LOC646627 (30628 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84037	84037	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84037delT								FAM110C (37652 upstream) : SH3YL1 (134101 downstream)																																			---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	1312651	1312651	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1312651delA	uc002qwq.2	+						SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841			syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)														---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	1329612	1329612	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1329612delT	uc002qwq.2	+						SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841			syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)														---	---	---	---
TPO	7173	broad.mit.edu	37	2	1532115	1532115	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1532115delC	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)													---	---	---	---
TSSC1	7260	broad.mit.edu	37	2	3203578	3203579	+	Intron	INS	-	GA	GA	rs142971768	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3203578_3203579insGA	uc002qxj.2	-						TSSC1_uc002qxi.2_Intron	NM_003310	NP_003301			tumor suppressing subtransferable candidate 1								protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)														---	---	---	---
TSSC1	7260	broad.mit.edu	37	2	3229406	3229407	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3229406_3229407insT	uc002qxj.2	-						TSSC1_uc002qxi.2_Intron	NM_003310	NP_003301			tumor suppressing subtransferable candidate 1								protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	3967378	3967396	+	IGR	DEL	TGGTTCTGCGGGTGAGATC	-	-	rs13023381		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3967378_3967396delTGGTTCTGCGGGTGAGATC								ALLC (217120 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4123464	4123465	+	IGR	INS	-	CCCTC	CCCTC	rs77317567	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4123464_4123465insCCCTC								ALLC (373206 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4221580	4221581	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4221580_4221581insA								ALLC (471322 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4945876	4945877	+	IGR	INS	-	TG	TG	rs145874192	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4945876_4945877insTG								None (None upstream) : SOX11 (886922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5604126	5604126	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5604126delA								None (None upstream) : SOX11 (228673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6343758	6343758	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6343758delT								LOC400940 (215394 upstream) : CMPK2 (636745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6447116	6447116	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6447116delT								LOC400940 (318752 upstream) : CMPK2 (533387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6750247	6750248	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6750247_6750248insA								LOC400940 (621883 upstream) : CMPK2 (230255 downstream)																																			---	---	---	---
CMPK2	129607	broad.mit.edu	37	2	7001234	7001235	+	Intron	DEL	CG	-	-	rs3085147		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7001234_7001235delCG	uc002qyo.2	-						CMPK2_uc010yis.1_Intron|CMPK2_uc010ewv.2_Intron	NM_207315	NP_997198			UMP-CMP kinase 2 precursor						dTDP biosynthetic process	mitochondrion	ATP binding|cytidylate kinase activity|thymidylate kinase activity|UMP kinase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
CMPK2	129607	broad.mit.edu	37	2	7001250	7001259	+	Intron	DEL	CACACACACC	-	-	rs57039812		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7001250_7001259delCACACACACC	uc002qyo.2	-						CMPK2_uc010yis.1_Intron|CMPK2_uc010ewv.2_Intron	NM_207315	NP_997198			UMP-CMP kinase 2 precursor						dTDP biosynthetic process	mitochondrion	ATP binding|cytidylate kinase activity|thymidylate kinase activity|UMP kinase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	7335129	7335130	+	IGR	INS	-	GAGGAAGGAAGG	GAGGAAGGAAGG	rs149250835	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7335129_7335130insGAGGAAGGAAGG								RNF144A (150822 upstream) : LOC339788 (727428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	7751523	7751524	+	IGR	INS	-	CA	CA	rs145454416	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7751523_7751524insCA								RNF144A (567216 upstream) : LOC339788 (311034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8209958	8209958	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8209958delT	uc010eww.1	-											Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	8808450	8808451	+	IGR	INS	-	TGGATGGA	TGGATGGA	rs148366581	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8808450_8808451insTGGATGGA								LOC339788 (691473 upstream) : ID2 (10889 downstream)																																			---	---	---	---
KIDINS220	57498	broad.mit.edu	37	2	8877236	8877236	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8877236delA	uc002qzc.2	-						KIDINS220_uc010yiv.1_Intron|KIDINS220_uc002qzd.2_Intron|KIDINS220_uc010yiw.1_Intron|KIDINS220_uc002qzb.2_Intron	NM_020738	NP_065789			kinase D-interacting substrate of 220 kDa						activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	9269098	9269099	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9269098_9269099delTT								MBOAT2 (125222 upstream) : ASAP2 (77795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	9275189	9275190	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9275189_9275190insA								MBOAT2 (131313 upstream) : ASAP2 (71704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	9288769	9288769	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9288769delA								MBOAT2 (144893 upstream) : ASAP2 (58125 downstream)																																			---	---	---	---
ASAP2	8853	broad.mit.edu	37	2	9344465	9344466	+	5'Flank	INS	-	A	A	rs35245451	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9344465_9344466insA	uc002qzh.2	+						ASAP2_uc002qzi.2_5'Flank	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																		---	---	---	---
ASAP2	8853	broad.mit.edu	37	2	9405841	9405842	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9405841_9405842delTG	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																		---	---	---	---
ITGB1BP1	9270	broad.mit.edu	37	2	9548026	9548027	+	Intron	INS	-	G	G	rs149330858	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9548026_9548027insG	uc002qzj.2	-						ITGB1BP1_uc002qzk.2_Intron|ITGB1BP1_uc002qzl.2_Intron|ITGB1BP1_uc002qzm.2_Intron|ITGB1BP1_uc010yiy.1_Intron|ITGB1BP1_uc002qzn.1_Intron	NM_004763	NP_004754			integrin cytoplasmic domain-associated protein 1						cell migration|cell-matrix adhesion|intracellular protein kinase cascade	cytosol|lamellipodium|membrane|ruffle	protein binding|protein binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.23)														---	---	---	---
CYS1	192668	broad.mit.edu	37	2	10222247	10222248	+	5'Flank	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10222247_10222248delAA	uc002rag.2	-							NM_001037160	NP_001032237			cystin 1							cilium axoneme					0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.166)|OV - Ovarian serous cystadenocarcinoma(76;0.227)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	10231141	10231141	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10231141delA								CYS1 (10603 upstream) : RRM2 (31594 downstream)																																			---	---	---	---
HPCAL1	3241	broad.mit.edu	37	2	10472905	10472905	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10472905delG	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)														---	---	---	---
NOL10	79954	broad.mit.edu	37	2	10721537	10721538	+	Intron	INS	-	G	G	rs146224537	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10721537_10721538insG	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-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
PDIA6	10130	broad.mit.edu	37	2	10930021	10930021	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10930021delA	uc002rau.2	-						PDIA6_uc010yjg.1_Intron|PDIA6_uc002rav.2_Intron|PDIA6_uc010yjh.1_Intron|PDIA6_uc002raw.2_Intron	NM_005742	NP_005733			protein disulfide isomerase A6 precursor						cell redox homeostasis|glycerol ether metabolic process|protein folding	endoplasmic reticulum lumen|ER-Golgi intermediate compartment|melanosome|plasma membrane	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	11098682	11098683	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11098682_11098683insT								KCNF1 (44332 upstream) : C2orf50 (174496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	11624970	11624973	+	IGR	DEL	TTTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11624970_11624973delTTTG								E2F6 (18673 upstream) : GREB1 (49269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	12439356	12439356	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12439356delT	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12439954	12439954	+	Intron	DEL	C	-	-	rs12997999	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12439954delC	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12466585	12466586	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12466585_12466586delAC	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	13404779	13404779	+	IGR	DEL	T	-	-	rs143612412		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13404779delT								TRIB2 (521923 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	13523983	13523983	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13523983delA								TRIB2 (641127 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	13978964	13978964	+	IGR	DEL	A	-	-	rs5829414		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13978964delA								None (None upstream) : FAM84A (793892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	15035464	15035464	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15035464delA								FAM84A (244531 upstream) : NBAS (271568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	15043188	15043188	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15043188delA								FAM84A (252255 upstream) : NBAS (263844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	15067606	15067607	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15067606_15067607insA								FAM84A (276673 upstream) : NBAS (239425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	15173906	15173906	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15173906delA								FAM84A (382973 upstream) : NBAS (133126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	15299910	15299911	+	IGR	INS	-	AC	AC	rs140797890	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15299910_15299911insAC								FAM84A (508977 upstream) : NBAS (7121 downstream)																																			---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15476856	15476857	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15476856_15476857delAA	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	15567274	15567274	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15567274delA	uc002rcc.1	-						NBAS_uc010exl.1_5'Flank|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	16165723	16165723	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16165723delA								MYCN (78595 upstream) : FAM49A (568178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16575448	16575448	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16575448delC								MYCN (488320 upstream) : FAM49A (158453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16874797	16874797	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16874797delT								FAM49A (27701 upstream) : RAD51AP2 (817189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16949126	16949126	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16949126delC								FAM49A (102030 upstream) : RAD51AP2 (742860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17328263	17328264	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17328263_17328264insT								FAM49A (481167 upstream) : RAD51AP2 (363722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17395730	17395731	+	IGR	INS	-	TG	TG	rs150137468	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17395730_17395731insTG								FAM49A (548634 upstream) : RAD51AP2 (296255 downstream)																																			---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17852304	17852307	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17852304_17852307delTTTT	uc002rco.2	-						SMC6_uc010exo.2_Intron|SMC6_uc002rcn.2_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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	18443158	18443159	+	IGR	INS	-	T	T	rs147928013	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18443158_18443159insT								KCNS3 (328934 upstream) : NT5C1B (292832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	18493372	18493373	+	IGR	INS	-	C	C	rs145208820	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18493372_18493373insC								KCNS3 (379148 upstream) : NT5C1B (242618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	18592094	18592094	+	IGR	DEL	T	-	-	rs112304956		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18592094delT								KCNS3 (477870 upstream) : NT5C1B (143897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	18707593	18707593	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18707593delA								KCNS3 (593369 upstream) : NT5C1B (28398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	18973781	18973781	+	IGR	DEL	T	-	-	rs144235529		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18973781delT								NT5C1B (202943 upstream) : OSR1 (577466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19109638	19109639	+	IGR	INS	-	GA	GA	rs139400618	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19109638_19109639insGA								NT5C1B (338800 upstream) : OSR1 (441608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19638396	19638397	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19638396_19638397insTG								OSR1 (80024 upstream) : TTC32 (458121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	20358213	20358213	+	IGR	DEL	T	-	-	rs114822482	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20358213delT								LAPTM4A (106424 upstream) : SDC1 (42345 downstream)																																			---	---	---	---
PUM2	23369	broad.mit.edu	37	2	20454512	20454512	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20454512delA	uc002rds.1	-						PUM2_uc002rdq.1_Intron|PUM2_uc002rdt.1_Intron|PUM2_uc002rdr.2_Intron|PUM2_uc010yjy.1_Intron|PUM2_uc002rdu.1_Intron|PUM2_uc010yjz.1_Intron	NM_015317	NP_056132			pumilio homolog 2						regulation of translation	perinuclear region of cytoplasm|stress granule	protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
PUM2	23369	broad.mit.edu	37	2	20482560	20482560	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20482560delT	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	20521398	20521398	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20521398delA	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	20675476	20675476	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20675476delA								RHOB (26276 upstream) : HS1BP3 (142088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	20679576	20679577	+	IGR	INS	-	CCTGAGCAT	CCTGAGCAT	rs142548497	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20679576_20679577insCCTGAGCAT								RHOB (30376 upstream) : HS1BP3 (137987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	21329199	21329199	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21329199delA								APOB (62254 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	21967184	21967185	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21967184_21967185delTT								APOB (700239 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	22708239	22708240	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22708239_22708240delCA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	22735002	22735002	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22735002delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23028248	23028248	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23028248delC								None (None upstream) : KLHL29 (727207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23426434	23426435	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23426434_23426435delAC								None (None upstream) : KLHL29 (329020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23623543	23623545	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23623543_23623545delAAA								None (None upstream) : KLHL29 (131910 downstream)																																			---	---	---	---
KLHL29	114818	broad.mit.edu	37	2	23802570	23802570	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23802570delT	uc002reg.2	+						KLHL29_uc002ref.2_Intron					RecName: Full=Kelch-like protein 29; AltName: Full=Kelch repeat and BTB domain-containing protein 9;											ovary(1)|lung(1)	2																		---	---	---	---
ATAD2B	54454	broad.mit.edu	37	2	23977774	23977774	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23977774delT	uc002rek.3	-						ATAD2B_uc010yki.1_Intron|ATAD2B_uc002rei.3_Intron|ATAD2B_uc002rej.3_Intron	NM_017552	NP_060022			ATPase family, AAA domain containing 2B								ATP binding|nucleoside-triphosphatase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
ATAD2B	54454	broad.mit.edu	37	2	24124060	24124060	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24124060delA	uc002rek.3	-						ATAD2B_uc010yki.1_Intron|ATAD2B_uc010exx.1_Intron	NM_017552	NP_060022			ATPase family, AAA domain containing 2B								ATP binding|nucleoside-triphosphatase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
UBXN2A	165324	broad.mit.edu	37	2	24218086	24218086	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24218086delT	uc010exy.2	+						UBXN2A_uc002rem.2_Intron|UBXN2A_uc002ren.2_Intron|UBXN2A_uc010ykj.1_Intron	NM_181713	NP_859064			UBX domain containing 4												0																		---	---	---	---
LOC375190	375190	broad.mit.edu	37	2	24332042	24332047	+	Intron	DEL	AAAAAA	-	-	rs71395199		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24332042_24332047delAAAAAA	uc002rew.2	+											SubName: Full=Putative uncharacterized protein C2orf84;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	24720127	24720129	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24720127_24720129delTTT								ITSN2 (136730 upstream) : NCOA1 (67050 downstream)																																			---	---	---	---
EFR3B	22979	broad.mit.edu	37	2	25314946	25314946	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25314946delT	uc010eyh.2	+						EFR3B_uc002rfw.2_Intron	NM_014971	NP_055786			EFR3 homolog B								binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	25411588	25411588	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25411588delT								POMC (20029 upstream) : DNMT3A (44258 downstream)																																			---	---	---	---
DTNB	1838	broad.mit.edu	37	2	25705871	25705872	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25705871_25705872insG	uc002rgh.2	-						DTNB_uc002rgg.2_5'Flank|DTNB_uc010yko.1_Intron|DTNB_uc010ykp.1_Intron|DTNB_uc002rgo.2_Intron|DTNB_uc002rgi.2_Intron|DTNB_uc002rgj.2_Intron|DTNB_uc002rgk.2_Intron|DTNB_uc002rgl.2_Intron|DTNB_uc002rgq.2_Intron|DTNB_uc002rgm.2_Intron|DTNB_uc002rgn.2_Intron|DTNB_uc002rgr.1_Intron|DTNB_uc010ykq.1_Intron	NM_021907	NP_068707			dystrobrevin, beta isoform 1							cytoplasm	calcium ion binding|zinc ion binding			large_intestine(2)|ovary(2)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
DTNB	1838	broad.mit.edu	37	2	25750389	25750389	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25750389delA	uc002rgh.2	-						DTNB_uc010yko.1_Intron|DTNB_uc010ykp.1_Intron|DTNB_uc002rgo.2_Intron|DTNB_uc002rgi.2_Intron|DTNB_uc002rgj.2_Intron|DTNB_uc002rgk.2_Intron|DTNB_uc002rgl.2_Intron|DTNB_uc002rgq.2_Intron|DTNB_uc002rgm.2_Intron|DTNB_uc002rgn.2_Intron|DTNB_uc002rgr.1_Intron|DTNB_uc010ykq.1_Intron	NM_021907	NP_068707			dystrobrevin, beta isoform 1							cytoplasm	calcium ion binding|zinc ion binding			large_intestine(2)|ovary(2)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	25940534	25940534	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25940534delA								DTNB (44031 upstream) : ASXL2 (21719 downstream)																																			---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	26044264	26044265	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26044264_26044265delAA	uc002rgs.2	-							NM_018263	NP_060733			additional sex combs like 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	26363043	26363043	+	IGR	DEL	A	-	-	rs112696641		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26363043delA								RAB10 (2721 upstream) : HADHA (50462 downstream)																																			---	---	---	---
HADHA	3030	broad.mit.edu	37	2	26440052	26440052	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26440052delA	uc002rgy.2	-						HADHA_uc010yks.1_Intron|HADHA_uc010ykt.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)													---	---	---	---
C2orf39	92749	broad.mit.edu	37	2	26656797	26656797	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26656797delA	uc002rhg.2	+						C2orf39_uc010eym.1_Intron	NM_145038	NP_659475			hypothetical protein LOC92749												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
OTOF	9381	broad.mit.edu	37	2	26783110	26783110	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26783110delA	uc002rhk.2	-						C2orf70_uc010eyn.2_5'Flank	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)																	---	---	---	---
AGBL5	60509	broad.mit.edu	37	2	27292719	27292719	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27292719delT	uc002rie.2	+						AGBL5_uc002rif.2_Intron	NM_021831	NP_068603			ATP/GTP binding protein-like 5 isoform 1						protein branching point deglutamylation|proteolysis	cytosol|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	27413560	27413561	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27413560_27413561delTT								TCF23 (37827 upstream) : SLC5A6 (8898 downstream)																																			---	---	---	---
TRIM54	57159	broad.mit.edu	37	2	27519638	27519638	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27519638delT	uc002rjo.2	+						TRIM54_uc002rjn.2_Intron	NM_187841	NP_912730			ring finger protein 30 isoform 2						cell differentiation|microtubule-based process|multicellular organismal development|negative regulation of microtubule depolymerization	microtubule|sarcomere	signal transducer activity|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
GTF3C2	2976	broad.mit.edu	37	2	27556385	27556385	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27556385delT	uc002rjv.1	-						GTF3C2_uc010eyy.1_Intron|GTF3C2_uc002rju.1_Intron|GTF3C2_uc002rjw.1_Intron|uc002rjy.1_5'Flank	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)																	---	---	---	---
IFT172	26160	broad.mit.edu	37	2	27689722	27689723	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27689722_27689723delAA	uc002rku.2	-							NM_015662	NP_056477			selective LIM binding factor homolog						cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SLC4A1AP	22950	broad.mit.edu	37	2	27900010	27900010	+	Intron	DEL	A	-	-	rs79004601		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27900010delA	uc002rlk.3	+							NM_018158	NP_060628			solute carrier family 4 (anion exchanger),							cytoplasm|nucleus	double-stranded RNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BRE	9577	broad.mit.edu	37	2	28183321	28183321	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28183321delT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664			brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	28644720	28644720	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28644720delA								FOSL2 (7206 upstream) : PLB1 (74262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	28692208	28692208	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28692208delC								FOSL2 (54694 upstream) : PLB1 (26774 downstream)																																			---	---	---	---
PLB1	151056	broad.mit.edu	37	2	28848378	28848379	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28848378_28848379delTT	uc002rmb.1	+						PLB1_uc010ezj.1_Intron|PLB1_uc002rme.1_Intron|PLB1_uc002rmf.1_Intron	NM_153021	NP_694566			phospholipase B1 precursor						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)																	---	---	---	---
ALK	238	broad.mit.edu	37	2	29456860	29456860	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29456860delT	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				---	---	---	---
ALK	238	broad.mit.edu	37	2	29830737	29830738	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29830737_29830738insT	uc002rmy.2	-							NM_004304	NP_004295			anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	30264719	30264720	+	IGR	INS	-	C	C	rs147629982	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30264719_30264720insC								ALK (120287 upstream) : YPEL5 (105030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	30275578	30275578	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30275578delA								ALK (131146 upstream) : YPEL5 (94172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	30386128	30386129	+	IGR	DEL	AA	-	-	rs35070322		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30386128_30386129delAA								YPEL5 (2730 upstream) : LBH (68268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	30562754	30562754	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30562754delA								LBH (79855 upstream) : LCLAT1 (107369 downstream)																																			---	---	---	---
LCLAT1	253558	broad.mit.edu	37	2	30833056	30833056	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30833056delT	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																		---	---	---	---
CAPN13	92291	broad.mit.edu	37	2	30981889	30981892	+	Intron	DEL	CTTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30981889_30981892delCTTC	uc002rnn.2	-						CAPN13_uc002rnp.1_Intron	NM_144575	NP_653176			calpain 13						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
GALNT14	79623	broad.mit.edu	37	2	31268261	31268261	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31268261delT	uc002rnr.2	-						GALNT14_uc002rnq.2_Intron|GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron|GALNT14_uc010ezo.1_Intron|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848			N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	31501122	31501122	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31501122delT								EHD3 (9863 upstream) : XDH (56066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	31882799	31882799	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31882799delA								SRD5A2 (76759 upstream) : MEMO1 (210097 downstream)																																			---	---	---	---
MEMO1	51072	broad.mit.edu	37	2	32221613	32221613	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32221613delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	32272302	32272303	+	IGR	DEL	AA	-	-	rs33931903		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32272302_32272303delAA								MEMO1 (7440 upstream) : SPAST (16377 downstream)																																			---	---	---	---
NLRC4	58484	broad.mit.edu	37	2	32460361	32460361	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32460361delA	uc002roi.2	-						NLRC4_uc002roj.1_Intron|NLRC4_uc010ezt.1_Intron	NM_021209	NP_067032			caspase recruitment domain protein 12						activation of caspase activity|defense response to bacterium|detection of bacterium|interleukin-1 beta secretion|positive regulation of apoptosis	cytoplasm	ATP binding|magnesium ion binding|protein homodimerization activity			ovary(3)|large_intestine(1)|lung(1)|skin(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32617233	32617234	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32617233_32617234insA	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32646603	32646603	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32646603delT	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32836817	32836817	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32836817delT	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
LOC285045	285045	broad.mit.edu	37	2	33143613	33143613	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33143613delT	uc002roo.2	+						LOC285045_uc002rop.1_Intron|LOC285045_uc010ymy.1_Intron|LOC285045_uc002roq.1_Intron	NR_027098				Homo sapiens cDNA FLJ37863 fis, clone BRSSN2015907.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	33892829	33892830	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33892829_33892830delTT								FAM98A (68467 upstream) : MYADML (58302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	33898765	33898765	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33898765delT								FAM98A (74403 upstream) : MYADML (52367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34869533	34869533	+	IGR	DEL	T	-	-	rs111630578	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34869533delT								MYADML (916249 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35066148	35066148	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35066148delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35654008	35654008	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35654008delA								None (None upstream) : CRIM1 (929389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35743478	35743478	+	IGR	DEL	A	-	-	rs67567442		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35743478delA								None (None upstream) : CRIM1 (839919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36145053	36145053	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36145053delA								None (None upstream) : CRIM1 (438344 downstream)																																			---	---	---	---
VIT	5212	broad.mit.edu	37	2	36935254	36935254	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36935254delC	uc002rpl.2	+						VIT_uc002rpk.2_Intron|VIT_uc010ynf.1_Intron|VIT_uc002rpm.2_Intron|VIT_uc010ezv.2_Intron|VIT_uc010ezw.2_Intron	NM_053276	NP_444506			vitrin							proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)																---	---	---	---
VIT	5212	broad.mit.edu	37	2	37019080	37019080	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37019080delA	uc002rpl.2	+						VIT_uc002rpm.2_Intron|VIT_uc010ezv.2_Intron|VIT_uc010ezw.2_Intron	NM_053276	NP_444506			vitrin							proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)																---	---	---	---
VIT	5212	broad.mit.edu	37	2	37032452	37032456	+	Intron	DEL	AAAAA	-	-	rs146745193		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37032452_37032456delAAAAA	uc002rpl.2	+						VIT_uc002rpm.2_Intron|VIT_uc010ezv.2_Intron|VIT_uc010ezw.2_Intron	NM_053276	NP_444506			vitrin							proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)																---	---	---	---
STRN	6801	broad.mit.edu	37	2	37110607	37110607	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37110607delA	uc002rpn.2	-						STRN_uc010ezx.2_Intron	NM_003162	NP_003153			striatin, calmodulin binding protein						dendrite development|locomotory behavior|negative regulation of cell proliferation|tight junction assembly|Wnt receptor signaling pathway	cytoplasm|dendritic spine|neuronal cell body|postsynaptic density|postsynaptic membrane|tight junction	armadillo repeat domain binding|calmodulin binding|estrogen receptor binding|protein complex binding|protein phosphatase 2A binding			skin(1)	1		Ovarian(717;0.0129)|all_hematologic(82;0.21)																---	---	---	---
CCDC75	253635	broad.mit.edu	37	2	37315175	37315175	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37315175delA	uc010ezz.2	+						CCDC75_uc002rpr.3_Intron	NM_174931	NP_777591			coiled-coil domain containing 75							intracellular	nucleic acid binding				0		all_hematologic(82;0.21)																---	---	---	---
CDC42EP3	10602	broad.mit.edu	37	2	37887932	37887933	+	Intron	DEL	AA	-	-	rs112775378		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37887932_37887933delAA	uc002rqi.1	-							NM_006449	NP_006440			Cdc42 effector protein 3						regulation of cell shape|signal transduction	actin cytoskeleton|cytoplasm|endomembrane system|membrane	cytoskeletal regulatory protein binding				0		all_hematologic(82;0.172)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	38353341	38353341	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38353341delA								CYP1B1 (50018 upstream) : C2orf58 (4906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	38438480	38438480	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38438480delA								C2orf58 (29489 upstream) : ATL2 (83551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	38613528	38613531	+	IGR	DEL	AAGA	-	-	rs55746794		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38613528_38613531delAAGA								ATL2 (9096 upstream) : HNRPLL (176797 downstream)																																			---	---	---	---
DHX57	90957	broad.mit.edu	37	2	39027496	39027496	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39027496delA	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)																---	---	---	---
DHX57	90957	broad.mit.edu	37	2	39053547	39053548	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39053547_39053548insT	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	39294567	39294567	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39294567delA	uc002rrk.3	-						SOS1_uc010ynr.1_Intron	NM_005633	NP_005624			son of sevenless homolog 1						apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)												Noonan_syndrome				---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39340499	39340503	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39340499_39340503delTTTTT	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				---	---	---	---
MAP4K3	8491	broad.mit.edu	37	2	39494285	39494287	+	Intron	DEL	AGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39494285_39494287delAGG	uc002rro.2	-						MAP4K3_uc002rrp.2_Intron|MAP4K3_uc010yns.1_Intron	NM_003618	NP_003609			mitogen-activated protein kinase kinase kinase						JNK cascade		ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(3)|lung(3)|stomach(1)|pancreas(1)	8		all_hematologic(82;0.211)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	40125616	40125616	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40125616delT								THUMPD2 (119200 upstream) : SLC8A1 (213671 downstream)																																			---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40611239	40611239	+	Intron	DEL	G	-	-	rs68098250		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40611239delG	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	40928308	40928309	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40928308_40928309insG								SLC8A1 (188733 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41166854	41166854	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41166854delA								SLC8A1 (427279 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41766147	41766149	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41766147_41766149delTTT								None (None upstream) : PKDCC (509012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42303348	42303348	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42303348delA								PKDCC (17682 upstream) : EML4 (93142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42335068	42335069	+	IGR	INS	-	TC	TC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42335068_42335069insTC								PKDCC (49402 upstream) : EML4 (61421 downstream)																																			---	---	---	---
EML4	27436	broad.mit.edu	37	2	42488302	42488302	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42488302delA	uc002rsi.2	+	4	642	c.380delA	c.(379-381)GAAfs	p.E127fs	EML4_uc002rsh.3_Frame_Shift_Del_p.E127fs|EML4_uc010fap.2_Intron	NM_019063	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	127					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	42836769	42836769	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42836769delA	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	42872367	42872367	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42872367delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	43330878	43330878	+	IGR	DEL	T	-	-	rs77033258		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43330878delT								HAAO (311127 upstream) : ZFP36L2 (118664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	43387262	43387262	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43387262delT								HAAO (367511 upstream) : ZFP36L2 (62280 downstream)																																			---	---	---	---
PLEKHH2	130271	broad.mit.edu	37	2	43964136	43964137	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43964136_43964137delAG	uc010yny.1	+						PLEKHH2_uc002rtf.3_Intron	NM_172069	NP_742066			pleckstrin homology domain containing, family H							cytoplasm|cytoskeleton|integral to membrane	binding			skin(2)|central_nervous_system(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
ABCG8	64241	broad.mit.edu	37	2	44101418	44101418	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44101418delA	uc002rtq.2	+						ABCG8_uc010yoa.1_Intron	NM_022437	NP_071882			ATP-binding cassette sub-family G member 8						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	44293377	44293377	+	IGR	DEL	G	-	-	rs61062797		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44293377delG								LRPPRC (70233 upstream) : PPM1B (102623 downstream)																																			---	---	---	---
SLC3A1	6519	broad.mit.edu	37	2	44502504	44502504	+	5'Flank	DEL	T	-	-	rs75346091		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44502504delT	uc002ruc.3	+						SLC3A1_uc002rty.2_5'Flank|SLC3A1_uc002rtz.2_5'Flank|SLC3A1_uc002rua.2_5'Flank|SLC3A1_uc002rub.2_5'Flank	NM_000341	NP_000332			solute carrier family 3, member 1						carbohydrate metabolic process|cellular amino acid metabolic process|ion transport	integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity|catalytic activity|cation binding|L-cystine transmembrane transporter activity				0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)													---	---	---	---
C2orf34	79823	broad.mit.edu	37	2	44902025	44902025	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44902025delA	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	44919831	44919832	+	Intron	INS	-	T	T	rs148455759	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44919831_44919832insT	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	45098624	45098625	+	IGR	INS	-	TCTG	TCTG	rs144924645	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45098624_45098625insTCTG								C2orf34 (98895 upstream) : SIX3 (70412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45371536	45371539	+	IGR	DEL	GTGG	-	-	rs112416419	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45371536_45371539delGTGG								SIX2 (134993 upstream) : SRBD1 (244281 downstream)																																			---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45645816	45645817	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45645816_45645817delAA	uc002rus.2	-						SRBD1_uc010yoc.1_Intron	NM_018079	NP_060549			S1 RNA binding domain 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)															---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	45910769	45910769	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45910769delG	uc002rut.2	+						PRKCE_uc002ruu.2_Intron	NM_005400	NP_005391			protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)															---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	46014494	46014495	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46014494_46014495delAG	uc002rut.2	+						PRKCE_uc002ruu.2_Intron	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)															---	---	---	---
EPAS1	2034	broad.mit.edu	37	2	46538025	46538025	+	Intron	DEL	T	-	-	rs66974414		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46538025delT	uc002ruv.2	+							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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	46871034	46871034	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46871034delG								CRIPT (18154 upstream) : SOCS5 (55065 downstream)																																			---	---	---	---
C2orf61	285051	broad.mit.edu	37	2	47307648	47307648	+	Intron	DEL	T	-	-	rs11297773		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47307648delT	uc010fbd.2	-											Homo sapiens cDNA FLJ40172 fis, clone TESTI2016896.												0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
C2orf61	285051	broad.mit.edu	37	2	47386646	47386647	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47386646_47386647insT	uc010fbd.2	-											Homo sapiens cDNA FLJ40172 fis, clone TESTI2016896.									p.0?(2)			0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	47480523	47480523	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47480523delA	uc002rvu.1	-											Homo sapiens cDNA FLJ37024 fis, clone BRACE2010837.									p.?(1)																					---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47673611	47673612	+	Intron	INS	-	TTC	TTC	rs10673567		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47673611_47673612insTTC	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron|MSH2_uc010fbh.1_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.?(1)		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	47822619	47822619	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47822619delT	uc002rvz.2	+							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	47862269	47862269	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47862269delC	uc002rvz.2	+							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				---	---	---	---
FBXO11	80204	broad.mit.edu	37	2	48049460	48049460	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48049460delA	uc010fbl.2	-						FBXO11_uc002rwe.2_Intron|FBXO11_uc002rwf.2_Intron|FBXO11_uc002rwg.1_Intron|FBXO11_uc010fbk.2_Intron	NM_025133	NP_079409			F-box only protein 11 isoform 1						ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	48260004	48260004	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48260004delT								FBXO11 (127190 upstream) : FOXN2 (281791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48427832	48427832	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48427832delA								FBXO11 (295018 upstream) : FOXN2 (113963 downstream)																																			---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49334397	49334397	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49334397delT	uc002rww.2	-						FSHR_uc002rwx.2_Intron|FSHR_uc010fbn.2_Intron|FSHR_uc010fbo.1_Intron	NM_000145	NP_000136			follicle stimulating hormone receptor isoform 1						female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
Unknown	0	broad.mit.edu	37	2	49531876	49531876	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49531876delA								FSHR (150246 upstream) : NRXN1 (613768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	50009746	50009747	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50009746_50009747delTT								FSHR (628116 upstream) : NRXN1 (135897 downstream)																																			---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50693641	50693641	+	Intron	DEL	A	-	-	rs78516173	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	51067556	51067556	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51067556delC	uc010fbq.2	-						NRXN1_uc002rxe.3_Intron	NM_001135659	NP_001129131			neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	51747214	51747214	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51747214delA								NRXN1 (487540 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	51780159	51780159	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51780159delT								NRXN1 (520485 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53694533	53694533	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53694533delA								None (None upstream) : ASB3 (202585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53810060	53810060	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53810060delA								None (None upstream) : ASB3 (87058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53839298	53839298	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53839298delA								None (None upstream) : ASB3 (57820 downstream)																																			---	---	---	---
ASB3	51130	broad.mit.edu	37	2	53933585	53933585	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53933585delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	54268615	54268615	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54268615delA								PSME4 (70638 upstream) : ACYP2 (73795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	54325103	54325105	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54325103_54325105delTTT								PSME4 (127126 upstream) : ACYP2 (17305 downstream)																																			---	---	---	---
ACYP2	98	broad.mit.edu	37	2	54392226	54392226	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54392226delT	uc002rxq.3	+							NM_138448	NP_612457			acylphosphatase 2						phosphate metabolic process		acylphosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	54633780	54633783	+	IGR	DEL	GGAA	-	-	rs35673636		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54633780_54633783delGGAA								C2orf73 (45066 upstream) : SPTBN1 (49671 downstream)																																			---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54803602	54803602	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54803602delT	uc002rxu.2	+						SPTBN1_uc002rxv.1_Intron|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)															---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54860570	54860571	+	Intron	INS	-	TGTC	TGTC	rs141798903	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54860570_54860571insTGTC	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	54945524	54945525	+	IGR	INS	-	T	T	rs112262849	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54945524_54945525insT								SPTBN1 (46942 upstream) : EML6 (6624 downstream)																																			---	---	---	---
EML6	400954	broad.mit.edu	37	2	55018856	55018856	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55018856delA	uc002ryb.3	+							NM_001039753	NP_001034842			echinoderm microtubule associated protein like							cytoplasm|microtubule					0																		---	---	---	---
EML6	400954	broad.mit.edu	37	2	55094893	55094893	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55094893delA	uc002ryb.3	+							NM_001039753	NP_001034842			echinoderm microtubule associated protein like							cytoplasm|microtubule					0																		---	---	---	---
EML6	400954	broad.mit.edu	37	2	55176077	55176077	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55176077delA	uc002ryb.3	+	28	4113	c.4063delA	c.(4063-4065)AAAfs	p.K1355fs		NM_001039753	NP_001034842	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like	1355	Poly-Lys.					cytoplasm|microtubule					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	55356246	55356246	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55356246delA								RTN4 (78512 upstream) : C2orf63 (43441 downstream)																																			---	---	---	---
C2orf63	130162	broad.mit.edu	37	2	55401083	55401083	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55401083delT	uc002ryi.2	-	13					C2orf63_uc002ryh.2_3'UTR|C2orf63_uc002ryj.2_3'UTR	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)															---	---	---	---
PNPT1	87178	broad.mit.edu	37	2	55883510	55883512	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55883510_55883512delAAA	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)															---	---	---	---
PNPT1	87178	broad.mit.edu	37	2	55894901	55894902	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55894901_55894902insA	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	56313417	56313418	+	Intron	INS	-	GT	GT	rs147769149	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56313417_56313418insGT	uc002rzk.2	+						uc002rzl.1_Intron					Homo sapiens, clone IMAGE:3873411, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	56319312	56319314	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56319312_56319314delTTT	uc002rzk.2	+						uc002rzl.1_5'Flank					Homo sapiens, clone IMAGE:3873411, mRNA.																														---	---	---	---
CCDC85A	114800	broad.mit.edu	37	2	56426705	56426705	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56426705delT	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)															---	---	---	---
CCDC85A	114800	broad.mit.edu	37	2	56478863	56478863	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56478863delT	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	56634661	56634662	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56634661_56634662insG								CCDC85A (21353 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	57843410	57843410	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57843410delT								None (None upstream) : VRK2 (291376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	58107244	58107244	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58107244delT								None (None upstream) : VRK2 (27542 downstream)																																			---	---	---	---
VRK2	7444	broad.mit.edu	37	2	58312004	58312004	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58312004delT	uc002rzo.2	+						VRK2_uc010fcb.2_Intron|VRK2_uc002rzs.2_Intron|VRK2_uc002rzr.2_Intron|VRK2_uc010fcc.2_Intron|VRK2_uc002rzv.2_Intron|VRK2_uc010fcd.2_Intron|VRK2_uc002rzp.2_Intron|VRK2_uc010ypg.1_Intron|VRK2_uc002rzq.2_Intron|VRK2_uc002rzu.2_Intron|VRK2_uc002rzt.2_Intron|VRK2_uc010yph.1_5'Flank	NM_001130482	NP_001123954			vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
VRK2	7444	broad.mit.edu	37	2	58362151	58362151	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58362151delA	uc002rzo.2	+						VRK2_uc010fcb.2_Intron|VRK2_uc002rzs.2_Intron|VRK2_uc002rzr.2_Intron|VRK2_uc010fcc.2_Intron|VRK2_uc002rzv.2_Intron|VRK2_uc010fcd.2_Intron|VRK2_uc002rzp.2_Intron|VRK2_uc010ypg.1_Intron|VRK2_uc002rzq.2_Intron|VRK2_uc002rzu.2_Intron|VRK2_uc002rzt.2_Intron	NM_001130482	NP_001123954			vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	58687298	58687298	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58687298delT								FANCL (218783 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	58719194	58719196	+	IGR	DEL	AAC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58719194_58719196delAAC								FANCL (250679 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59192244	59192244	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59192244delT	uc002rzy.2	+						uc002rzz.2_Intron					Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	59522608	59522609	+	IGR	INS	-	A	A	rs35887524		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59522608_59522609insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60125156	60125163	+	IGR	DEL	AAAAAAAA	-	-	rs71952146		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60125156_60125163delAAAAAAAA								None (None upstream) : BCL11A (553140 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60317949	60317950	+	IGR	INS	-	A	A	rs143520346	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60317949_60317950insA								None (None upstream) : BCL11A (360353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60426149	60426149	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60426149delT								None (None upstream) : BCL11A (252154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60530407	60530409	+	IGR	DEL	CTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60530407_60530409delCTT								None (None upstream) : BCL11A (147894 downstream)																																			---	---	---	---
PAPOLG	64895	broad.mit.edu	37	2	61009788	61009788	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61009788delC	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)															---	---	---	---
PAPOLG	64895	broad.mit.edu	37	2	61023857	61023857	+	Intron	DEL	T	-	-	rs71400300		TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	61072514	61072515	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61072514_61072515insA								PAPOLG (46418 upstream) : REL (36237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	61083123	61083123	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61083123delA	uc002sal.1	-											Homo sapiens cDNA FLJ16341 fis, clone TESTI2013381.																														---	---	---	---
KIAA1841	84542	broad.mit.edu	37	2	61304724	61304724	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61304724delA	uc002saw.3	+						KIAA1841_uc002sax.3_Intron|KIAA1841_uc002say.2_Intron|KIAA1841_uc002sav.3_Intron	NM_001129993	NP_001123465			KIAA1841 protein isoform a												0			Epithelial(17;0.193)															---	---	---	---
KIAA1841	84542	broad.mit.edu	37	2	61344482	61344482	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	61483709	61483709	+	Intron	DEL	A	-	-	rs34025877		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61483709delA	uc002sbe.2	-						USP34_uc002sbf.2_Intron	NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61616874	61616874	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61616874delT	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	61848925	61848925	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61848925delT								XPO1 (83507 upstream) : FAM161A (203060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	62038251	62038252	+	IGR	INS	-	A	A	rs143636039	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62038251_62038252insA								XPO1 (272833 upstream) : FAM161A (13733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	62510616	62510617	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62510616_62510617insT								B3GNT2 (58752 upstream) : TMEM17 (216739 downstream)																																			---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	63013015	63013015	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63013015delT	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc010fcq.1_Intron|EHBP1_uc002sbx.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	63069230	63069230	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63069230delT	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbx.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	63204309	63204309	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63204309delA	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	63553698	63553701	+	Intron	DEL	AGAA	-	-	rs138486357		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63553698_63553701delAGAA	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	64041486	64041486	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64041486delA								LOC388955 (191327 upstream) : UGP2 (26612 downstream)																																			---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64124487	64124487	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64124487delA	uc002scq.2	-						VPS54_uc002scp.2_Intron|VPS54_uc002scn.2_Intron|VPS54_uc002sco.2_Intron|VPS54_uc010fct.2_Intron	NM_016516	NP_057600			vacuolar protein sorting 54 isoform 1						protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64165193	64165194	+	Intron	INS	-	TGGT	TGGT	rs150503045	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64165193_64165194insTGGT	uc002scq.2	-						VPS54_uc002scp.2_Intron|VPS54_uc002sco.2_5'Flank|VPS54_uc010fct.2_Intron	NM_016516	NP_057600			vacuolar protein sorting 54 isoform 1						protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64235148	64235149	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64235148_64235149delAA	uc002scq.2	-						VPS54_uc002scp.2_Intron	NM_016516	NP_057600			vacuolar protein sorting 54 isoform 1						protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64239826	64239827	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64239826_64239827delAA	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	64327701	64327701	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64327701delA	uc002scs.3	-						PELI1_uc002sct.3_Intron|PELI1_uc002scr.3_5'Flank	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	64566567	64566568	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64566567_64566568delTT								PELI1 (194962 upstream) : HSPC159 (114759 downstream)																																			---	---	---	---
ACTR2	10097	broad.mit.edu	37	2	65472687	65472687	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65472687delT	uc002sdq.2	+						ACTR2_uc010yqf.1_Intron|ACTR2_uc002sdp.2_Intron|ACTR2_uc010yqg.1_Intron	NM_005722	NP_005713			actin-related protein 2 isoform b						cellular component movement	Arp2/3 protein complex|cell projection|cytoplasm	actin binding|ATP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	65815032	65815033	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65815032_65815033delTG	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	65886780	65886780	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65886780delT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	66097847	66097856	+	Intron	DEL	GTGTGTGTGT	-	-	rs71741680		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66097847_66097856delGTGTGTGTGT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	66562123	66562124	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66562123_66562124insA								SPRED2 (902467 upstream) : MEIS1 (100408 downstream)																																			---	---	---	---
MEIS1	4211	broad.mit.edu	37	2	66663082	66663082	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66663082delT	uc002sdu.2	+						MEIS1_uc002sdt.2_Intron|MEIS1_uc002sdv.2_5'Flank|MEIS1_uc010yqh.1_5'Flank	NM_002398	NP_002389			Meis homeobox 1								sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	66866733	66866734	+	IGR	DEL	AC	-	-	rs112253489		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66866733_66866734delAC								MEIS1 (66843 upstream) : ETAA1 (757708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	66872235	66872235	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66872235delT								MEIS1 (72345 upstream) : ETAA1 (752207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	66973114	66973114	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66973114delT								MEIS1 (173224 upstream) : ETAA1 (651328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67155944	67155944	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67155944delG								MEIS1 (356054 upstream) : ETAA1 (468498 downstream)																																			---	---	---	---
ETAA1	54465	broad.mit.edu	37	2	67629928	67629928	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67629928delT	uc002sdz.1	+							NM_019002	NP_061875			ETAA16 protein							cytoplasm|nucleus				ovary(3)|large_intestine(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	67813580	67813580	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67813580delT								ETAA1 (176047 upstream) : C1D (455753 downstream)																																			---	---	---	---
PPP3R1	5534	broad.mit.edu	37	2	68417698	68417699	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68417698_68417699insA	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)													---	---	---	---
CNRIP1	25927	broad.mit.edu	37	2	68538334	68538335	+	Intron	INS	-	G	G	rs144206261	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68538334_68538335insG	uc002sek.3	-						CNRIP1_uc002sej.3_Intron|CNRIP1_uc002sel.3_Intron	NM_015463	NP_056278			cannabinoid receptor interacting protein 1								protein binding			liver(1)	1																		---	---	---	---
ARHGAP25	9938	broad.mit.edu	37	2	68950283	68950283	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68950283delG	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																		---	---	---	---
AAK1	22848	broad.mit.edu	37	2	69716145	69716145	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69716145delT	uc002sfp.2	-						AAK1_uc010fdk.2_Intron|AAK1_uc010yqm.1_Intron	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	69747000	69747001	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69747000_69747001insT	uc002sfp.2	-						AAK1_uc010fdk.2_Intron|AAK1_uc010yqm.1_Intron	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	69790574	69790574	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69790574delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	69928310	69928310	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69928310delT								AAK1 (57333 upstream) : ANXA4 (40817 downstream)																																			---	---	---	---
ANXA4	307	broad.mit.edu	37	2	70030916	70030916	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
ANXA4	307	broad.mit.edu	37	2	70048610	70048611	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70048610_70048611delTT	uc002sfr.3	+						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																		---	---	---	---
C2orf42	54980	broad.mit.edu	37	2	70406777	70406777	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70406777delA	uc002sgh.2	-							NM_017880	NP_060350			hypothetical protein LOC54980												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	70596648	70596648	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70596648delA								FAM136A (67428 upstream) : TGFA (77771 downstream)																																			---	---	---	---
TGFA	7039	broad.mit.edu	37	2	70759747	70759748	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70759747_70759748insT	uc002sgs.3	-						TGFA_uc010fdq.2_Intron|TGFA_uc010fdr.2_Intron|TGFA_uc002sgt.3_Intron|TGFA_uc002sgu.2_Intron|TGFA_uc002sgv.2_Intron|TGFA_uc002sgw.2_Intron	NM_003236	NP_003227			transforming growth factor, alpha isoform 1						activation of MAPK activity|cell proliferation|positive regulation of cell division|positive regulation of epidermal growth factor receptor activity|positive regulation of epithelial cell proliferation|positive regulation of mitosis	cell surface|extracellular space|integral to membrane|plasma membrane	epidermal growth factor receptor binding|growth factor activity|MAP kinase kinase activity|signal transducer activity			prostate(1)	1																		---	---	---	---
ADD2	119	broad.mit.edu	37	2	70850490	70850490	+	Intron	DEL	C	-	-	rs34511625		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70850490delC	uc010fds.1	-							NM_001617				adducin 2 isoform a						actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding			ovary(2)|pancreas(1)	3																		---	---	---	---
ADD2	119	broad.mit.edu	37	2	70994234	70994234	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70994234delC	uc002sgz.2	-						ADD2_uc010fds.1_Intron|ADD2_uc002sgy.2_Intron|ADD2_uc002sha.2_Intron|ADD2_uc002shc.1_Intron|ADD2_uc002shd.1_Intron|ADD2_uc010fdu.1_Intron	NM_001617	NP_001608			adducin 2 isoform a						actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding			ovary(2)|pancreas(1)	3																		---	---	---	---
VAX2	25806	broad.mit.edu	37	2	71139880	71139880	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71139880delG	uc002shh.2	+							NM_012476	NP_036608			ventral anterior homeobox 2						ectoderm development|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	71396899	71396899	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71396899delA								MPHOSPH10 (19669 upstream) : PAIP2B (12969 downstream)																																			---	---	---	---
ZNF638	27332	broad.mit.edu	37	2	71567235	71567235	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71567235delT	uc002shx.2	+						ZNF638_uc010fec.2_Intron|ZNF638_uc010yqw.1_Intron|ZNF638_uc002shw.2_Intron|ZNF638_uc002shy.2_Intron|ZNF638_uc002shz.2_Intron|ZNF638_uc002sia.2_Intron	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																		---	---	---	---
ZNF638	27332	broad.mit.edu	37	2	71626818	71626818	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71626818delT	uc002shx.2	+						ZNF638_uc010yqw.1_Intron|ZNF638_uc002shy.2_Intron|ZNF638_uc002shz.2_Intron|ZNF638_uc002sia.2_Intron|ZNF638_uc002sib.1_Intron|ZNF638_uc010fed.2_Intron|ZNF638_uc002sic.2_Intron	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																		---	---	---	---
CYP26B1	56603	broad.mit.edu	37	2	72370275	72370275	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72370275delA	uc002sih.1	-						CYP26B1_uc010yra.1_Intron|CYP26B1_uc010yrb.1_Intron	NM_019885	NP_063938			cytochrome P450, family 26, subfamily b,						cell fate determination|embryonic limb morphogenesis|male meiosis|negative regulation of retinoic acid receptor signaling pathway|proximal/distal pattern formation|retinoic acid catabolic process|spermatogenesis|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity|retinoic acid binding			skin(2)	2																		---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72593410	72593410	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72593410delA	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	72725736	72725738	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72725736_72725738delTTT	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72913242	72913242	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72913242delT	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	73023817	73023817	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73023817delA	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																		---	---	---	---
SFXN5	94097	broad.mit.edu	37	2	73201985	73201986	+	Intron	DEL	AA	-	-	rs68090627		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73201985_73201986delAA	uc002siq.2	-						SFXN5_uc002sio.2_Intron|SFXN5_uc010yrc.1_Intron|SFXN5_uc002sip.2_Intron|SFXN5_uc010fet.2_Intron|SFXN5_uc010fer.2_Intron|SFXN5_uc010feq.2_Intron|SFXN5_uc010fes.2_Intron	NM_144579	NP_653180			sideroflexin 5						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity			ovary(1)	1																		---	---	---	---
RAB11FIP5	26056	broad.mit.edu	37	2	73308448	73308448	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73308448delG	uc002siu.3	-						RAB11FIP5_uc002sis.3_5'Flank|RAB11FIP5_uc002sit.3_Intron|uc002siv.2_5'Flank	NM_015470	NP_056285			RAB11 family interacting protein 5 (class I)						protein transport	mitochondrial outer membrane|recycling endosome membrane	gamma-tubulin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	73376780	73376780	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73376780delT								RAB11FIP5 (36634 upstream) : NOTO (52606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	73419719	73419719	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73419719delA								RAB11FIP5 (79573 upstream) : NOTO (9667 downstream)																																			---	---	---	---
SMYD5	10322	broad.mit.edu	37	2	73444087	73444087	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73444087delT	uc002siw.2	+						SMYD5_uc010yre.1_Intron	NM_006062	NP_006053			SMYD family member 5								metal ion binding				0																		---	---	---	---
CCT7	10574	broad.mit.edu	37	2	73479170	73479171	+	Intron	INS	-	GTG	GTG	rs149581390	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73479170_73479171insGTG	uc002siz.2	+						CCT7_uc002sja.2_Intron|CCT7_uc010yrf.1_Intron|CCT7_uc010feu.2_Intron|CCT7_uc010yrg.1_Intron|CCT7_uc010yrh.1_Intron|CCT7_uc010yri.1_Intron	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	73974436	73974436	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73974436delA								TPRKB (9919 upstream) : DUSP11 (14890 downstream)																																			---	---	---	---
DGUOK	1716	broad.mit.edu	37	2	74160736	74160736	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74160736delT	uc002sjx.2	+						DGUOK_uc002sjy.2_Intron|DGUOK_uc002sjz.2_Intron	NM_080916	NP_550438			deoxyguanosine kinase isoform a precursor						guanosine metabolic process|purine base metabolic process|purine deoxyribonucleoside metabolic process|purine-containing compound salvage	mitochondrial matrix	ATP binding|deoxyguanosine kinase activity|phosphotransferase activity, alcohol group as acceptor				0																		---	---	---	---
DGUOK	1716	broad.mit.edu	37	2	74162605	74162606	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74162605_74162606insA	uc002sjx.2	+						DGUOK_uc002sjy.2_Intron|DGUOK_uc002sjz.2_Intron	NM_080916	NP_550438			deoxyguanosine kinase isoform a precursor						guanosine metabolic process|purine base metabolic process|purine deoxyribonucleoside metabolic process|purine-containing compound salvage	mitochondrial matrix	ATP binding|deoxyguanosine kinase activity|phosphotransferase activity, alcohol group as acceptor				0																		---	---	---	---
TET3	200424	broad.mit.edu	37	2	74324240	74324241	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74324240_74324241delAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	74622102	74622103	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74622102_74622103insT								LOC100189589 (1094 upstream) : C2orf81 (19200 downstream)																																			---	---	---	---
SEMA4F	10505	broad.mit.edu	37	2	74904563	74904563	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74904563delA	uc002sna.1	+						SEMA4F_uc010ffr.1_Intron|SEMA4F_uc002snb.1_Intron|SEMA4F_uc002snc.1_Intron	NM_004263	NP_004254			semaphorin W precursor						cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
SEMA4F	10505	broad.mit.edu	37	2	74904920	74904920	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74904920delA	uc002sna.1	+						SEMA4F_uc010ffr.1_Intron|SEMA4F_uc002snb.1_Intron|SEMA4F_uc002snc.1_Intron	NM_004263	NP_004254			semaphorin W precursor						cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	75149540	75149541	+	IGR	INS	-	ATCCC	ATCCC	rs145005002	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75149540_75149541insATCCC								HK2 (29066 upstream) : POLE4 (36234 downstream)																																			---	---	---	---
FAM176A	84141	broad.mit.edu	37	2	75778267	75778268	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75778267_75778268insA	uc002sni.2	-						FAM176A_uc002snj.1_Intron|FAM176A_uc002snk.1_Intron	NM_001135032	NP_001128504			family with sequence similarity 176, member A						apoptosis|autophagy	endoplasmic reticulum membrane|integral to membrane|lysosomal membrane|plasma membrane					0																		---	---	---	---
C2orf3	6936	broad.mit.edu	37	2	75923144	75923145	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75923144_75923145insG	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	75974304	75974304	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75974304delT								C2orf3 (36193 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76106341	76106341	+	IGR	DEL	A	-	-	rs112764869		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76106341delA								C2orf3 (168230 upstream) : LRRTM4 (868517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76187377	76187377	+	IGR	DEL	T	-	-	rs78067351		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76187377delT								C2orf3 (249266 upstream) : LRRTM4 (787481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76383294	76383294	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76383294delA								C2orf3 (445183 upstream) : LRRTM4 (591564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76593924	76593924	+	IGR	DEL	T	-	-	rs72047865		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76593924delT								C2orf3 (655813 upstream) : LRRTM4 (380934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76728661	76728663	+	IGR	DEL	GTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76728661_76728663delGTG								C2orf3 (790550 upstream) : LRRTM4 (246195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76813246	76813248	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76813246_76813248delTTT								C2orf3 (875135 upstream) : LRRTM4 (161610 downstream)																																			---	---	---	---
LRRTM4	80059	broad.mit.edu	37	2	77603678	77603678	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77603678delA	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217			leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	78258665	78258665	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78258665delA	uc002snu.3	-											Homo sapiens cDNA clone IMAGE:4816654.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	78476716	78476716	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78476716delA	uc002snu.3	-											Homo sapiens cDNA clone IMAGE:4816654.																														---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	79684171	79684171	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79684171delA	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	80576682	80576682	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80576682delT	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	82677124	82677124	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82677124delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82906653	82906653	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82906653delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83125055	83125056	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83125055_83125056insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83526026	83526026	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83526026delT								None (None upstream) : FUNDC2P2 (991780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84487259	84487259	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84487259delA								None (None upstream) : FUNDC2P2 (30547 downstream)																																			---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	84912421	84912421	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84912421delT	uc010fgb.2	+						DNAH6_uc002sor.2_Intron	NM_001370	NP_001361			dynein, axonemal, heavy polypeptide 6						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
C2orf89	129293	broad.mit.edu	37	2	85057001	85057002	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85057001_85057002delAC	uc010ysl.1	-						C2orf89_uc002sou.3_Intron	NM_001080824	NP_001074293			hypothetical protein LOC129293 precursor							integral to membrane				ovary(1)	1																		---	---	---	---
KCMF1	56888	broad.mit.edu	37	2	85259213	85259213	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85259213delT	uc002sox.3	+							NM_020122	NP_064507			potassium channel modulatory factor 1							intracellular	ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
TCF7L1	83439	broad.mit.edu	37	2	85400455	85400455	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85400455delG	uc002soy.2	+							NM_031283	NP_112573			HMG-box transcription factor TCF-3						chromatin organization|regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|breast(1)|central_nervous_system(1)	3																		---	---	---	---
TCF7L1	83439	broad.mit.edu	37	2	85535617	85535617	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85535617delC	uc002soy.2	+							NM_031283	NP_112573			HMG-box transcription factor TCF-3						chromatin organization|regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|breast(1)|central_nervous_system(1)	3																		---	---	---	---
ELMOD3	84173	broad.mit.edu	37	2	85612900	85612900	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85612900delT	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	85960285	85960285	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85960285delA								GNLY (34411 upstream) : ATOH8 (20624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	86046789	86046789	+	IGR	DEL	T	-	-	rs111713637		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86046789delT								ATOH8 (28284 upstream) : ST3GAL5 (19482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	86206994	86206995	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86206994_86206995delTT								ST3GAL5 (90837 upstream) : LOC90784 (40344 downstream)																																			---	---	---	---
IMMT	10989	broad.mit.edu	37	2	86400704	86400704	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86400704delA	uc002sqz.3	-						IMMT_uc002sqy.3_5'Flank|IMMT_uc002srb.3_Intron|IMMT_uc002sra.3_Intron|IMMT_uc010ytd.1_Intron|IMMT_uc010yte.1_Intron|IMMT_uc002src.1_5'Flank|IMMT_uc002srd.2_Intron|IMMT_uc002sre.3_Intron|IMMT_uc010ytf.1_Intron|IMMT_uc010fgs.1_Intron	NM_006839	NP_006830			inner membrane protein, mitochondrial isoform 1							integral to mitochondrial inner membrane	protein binding			skin(1)	1																		---	---	---	---
REEP1	65055	broad.mit.edu	37	2	86498159	86498161	+	Intron	DEL	ATA	-	-	rs144574034		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86498159_86498161delATA	uc002srh.3	-						REEP1_uc010ytg.1_Intron|REEP1_uc010yth.1_Intron|REEP1_uc010yti.1_Intron	NM_022912	NP_075063			receptor accessory protein 1 isoform 2						cell death|protein insertion into membrane	integral to membrane|mitochondrial membrane	olfactory receptor binding				0																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86855699	86855700	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86855699_86855700delTT	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	87100265	87100265	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87100265delA	uc002srs.3	+						uc010fgu.1_Intron					SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87116862	87116862	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87116862delA	uc002srs.3	+						uc010fgu.1_Intron					SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87586774	87586778	+	Intron	DEL	GAGAT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87586774_87586778delGAGAT	uc002srs.3	+											SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87588539	87588541	+	Intron	DEL	GAT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87588539_87588541delGAT	uc002srs.3	+											SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87626723	87626723	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87626723delA	uc002srs.3	+											SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87744249	87744250	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87744249_87744250delTC	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	88160247	88160248	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88160247_88160248insTG								RMND5A (121481 upstream) : KRCC1 (166476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88290267	88290267	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88290267delA								RMND5A (251501 upstream) : KRCC1 (36457 downstream)																																			---	---	---	---
THNSL2	55258	broad.mit.edu	37	2	88478290	88478290	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88478290delC	uc002ssz.3	+						THNSL2_uc002ssv.2_Intron|THNSL2_uc002ssw.3_Intron|THNSL2_uc002ssx.3_Intron|THNSL2_uc002sta.3_Intron|THNSL2_uc002ssy.3_Intron|THNSL2_uc010fhe.2_Intron	NM_018271	NP_060741			threonine synthase-like 2						threonine biosynthetic process		threonine synthase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	88619214	88619214	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88619214delT								THNSL2 (133069 upstream) : FOXI3 (128512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88839111	88839111	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88839111delT								C2orf51 (10009 upstream) : EIF2AK3 (17150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88852157	88852158	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88852157_88852158delAA								C2orf51 (23055 upstream) : EIF2AK3 (4103 downstream)																																			---	---	---	---
FLJ40330	645784	broad.mit.edu	37	2	89071361	89071361	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89071361delA	uc002stf.2	+						FLJ40330_uc010fhf.2_Intron|FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0																		---	---	---	---
FLJ40330	645784	broad.mit.edu	37	2	89083543	89083543	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89083543delG	uc010fhf.2	+						FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	89199594	89199595	+	Intron	DEL	TG	-	-	rs71947963		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89199594_89199595delTG	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	91685551	91685551	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91685551delA								None (None upstream) : LOC654342 (119641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91802160	91802161	+	IGR	INS	-	G	G	rs140424741		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91802160_91802161insG								None (None upstream) : LOC654342 (3031 downstream)																																			---	---	---	---
LOC654342	654342	broad.mit.edu	37	2	91839225	91839225	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91839225delT	uc002sts.3	-						LOC654342_uc002stt.2_Intron|LOC654342_uc010yub.1_Intron					Homo sapiens cDNA clone IMAGE:4801360.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	91875151	91875151	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91875151delA								LOC654342 (27176 upstream) : GGT8P (88217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91914574	91914575	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91914574_91914575insT								LOC654342 (66599 upstream) : GGT8P (48793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92057933	92057934	+	IGR	INS	-	G	G	rs149571408	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92057933_92057934insG								GGT8P (87780 upstream) : FKSG73 (71225 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92076694	92076695	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92076694_92076695delTT								GGT8P (106541 upstream) : FKSG73 (52464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92079273	92079274	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92079273_92079274delAA								GGT8P (109120 upstream) : FKSG73 (49885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92145698	92145698	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92145698delC								FKSG73 (15204 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92163260	92163260	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92163260delC								FKSG73 (32766 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92302448	92302448	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92302448delC								FKSG73 (171954 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92317890	92317890	+	IGR	DEL	T	-	-	rs7597972		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92317890delT								FKSG73 (187396 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	95361816	95361816	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95361816delA								None (None upstream) : ANKRD20B (64859 downstream)																																			---	---	---	---
ANKRD20B	729171	broad.mit.edu	37	2	95483039	95483039	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95483039delT	uc010fhq.1	-	1	508	c.116delA	c.(115-117)AATfs	p.N39fs	ANKRD20B_uc010fhp.2_RNA	NM_001012421	NP_001012421			ankyrin repeat domain 20 family, member A2												0																		---	---	---	---
ANKRD20B	729171	broad.mit.edu	37	2	95503614	95503614	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95503614delA	uc010fhp.2	-							NR_003366				Homo sapiens ankyrin repeat domain 20B (ANKRD20B), non-coding RNA.												0																		---	---	---	---
MAL	4118	broad.mit.edu	37	2	95719032	95719032	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95719032delC	uc002stx.1	+						MAL_uc002sty.1_Intron|MAL_uc002stz.1_Intron|MAL_uc002sua.1_Intron	NM_002371	NP_002362			T-lymphocyte maturation-associated protein						apical protein localization|cell differentiation|central nervous system development|induction of apoptosis|membrane raft polarization|myelination	apical plasma membrane|endoplasmic reticulum|endosome|integral to plasma membrane|membrane raft	apoptotic protease activator activity|channel activity|lipid binding|structural constituent of myelin sheath				0				STAD - Stomach adenocarcinoma(1183;0.18)														---	---	---	---
ZNF2	7549	broad.mit.edu	37	2	95830155	95830155	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95830155delT	uc002suf.2	+						ZNF2_uc002sug.2_5'Flank|ZNF2_uc010yue.1_5'Flank|ZNF2_uc010fhs.2_5'Flank	NM_021088	NP_066574			zinc finger protein 2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(717;0.00768)		READ - Rectum adenocarcinoma(193;0.0222)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	95893532	95893532	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95893532delT								ZNF2 (43470 upstream) : PROM2 (46669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	96484029	96484029	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96484029delT	uc002sux.1	-						uc002suy.1_Intron					Homo sapiens cDNA FLJ33030 fis, clone THYMU2000171.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	96485670	96485670	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96485670delT	uc002suy.1	-											Homo sapiens cDNA FLJ33030 fis, clone THYMU2000171.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	96557435	96557436	+	RNA	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96557435_96557436insT	uc002sva.1	-	27		c.1338_1339insA			uc002suz.1_5'UTR|uc002svb.1_5'UTR					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	96730750	96730751	+	IGR	INS	-	CATC	CATC	rs147426996	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96730750_96730751insCATC								GPAT2 (29028 upstream) : ADRA2B (47875 downstream)																																			---	---	---	---
DUSP2	1844	broad.mit.edu	37	2	96811763	96811763	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96811763delC	uc002svk.3	-							NM_004418	NP_004409			dual specificity phosphatase 2						endoderm formation|inactivation of MAPK activity|regulation of apoptosis	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/threonine phosphatase activity			breast(1)	1		Ovarian(717;0.0228)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	96849300	96849302	+	IGR	DEL	TTT	-	-	rs112277947		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96849300_96849302delTTT								DUSP2 (38121 upstream) : STARD7 (1303 downstream)																																			---	---	---	---
SNRNP200	23020	broad.mit.edu	37	2	96966575	96966575	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
KIAA1310	55683	broad.mit.edu	37	2	97298703	97298709	+	Intron	DEL	AAAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97298703_97298709delAAAAAAA	uc002swn.3	-						KIAA1310_uc002swh.3_5'Flank|KIAA1310_uc002swi.3_5'Flank|KIAA1310_uc002swj.3_Intron|KIAA1310_uc002swk.3_Intron|KIAA1310_uc010fhz.2_Intron|KIAA1310_uc002swl.3_Intron|KIAA1310_uc002swm.3_Intron|KIAA1310_uc010yur.1_Intron|KIAA1310_uc002swp.1_5'Flank|KIAA1310_uc002swq.1_Intron|KIAA1310_uc010fhy.1_Intron	NM_001115016	NP_001108488			hypothetical protein LOC55683 isoform a												0																		---	---	---	---
FER1L5	90342	broad.mit.edu	37	2	97325026	97325049	+	Intron	DEL	CTTTCCTTCCTTCCTTCCTTCCTT	-	-	rs72054521	by1000genomes;by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97325026_97325049delCTTTCCTTCCTTCCTTCCTTCCTT	uc010fia.2	+							NM_001113382	NP_001106853			fer-1-like 5 isoform 2							integral to membrane				ovary(1)	1																		---	---	---	---
FAM178B	51252	broad.mit.edu	37	2	97580850	97580851	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97580850_97580851delTT	uc002sxl.3	-						FAM178B_uc002sxk.3_Intron	NM_001122646	NP_001116118			hypothetical protein LOC51252 isoform A												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	98253608	98253608	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98253608delT								ANKRD36B (47180 upstream) : COX5B (8913 downstream)																																			---	---	---	---
VWA3B	200403	broad.mit.edu	37	2	98833446	98833447	+	Intron	INS	-	CA	CA	rs67163987		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98833446_98833447insCA	uc002syo.2	+						VWA3B_uc002syj.2_Intron|VWA3B_uc002syk.1_Intron|VWA3B_uc002syl.1_Intron|VWA3B_uc002sym.2_Intron|VWA3B_uc002syn.1_Intron|VWA3B_uc010yvi.1_Intron|VWA3B_uc002syp.1_Intron|VWA3B_uc002syq.1_Intron|VWA3B_uc002syr.1_Intron	NM_144992	NP_659429			von Willebrand factor A domain containing 3B											ovary(3)|large_intestine(2)|skin(1)	6																		---	---	---	---
MGAT4A	11320	broad.mit.edu	37	2	99263767	99263768	+	Intron	INS	-	TT	TT	rs149078896	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99263767_99263768insTT	uc002sze.2	-						C2orf64_uc002sza.2_5'Flank|MGAT4A_uc010yvm.1_Intron|MGAT4A_uc010fil.2_Intron	NM_012214	NP_036346			alpha-1,3-mannosyl-glycoprotein						N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1																		---	---	---	---
C2orf55	343990	broad.mit.edu	37	2	99443770	99443770	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99443770delT	uc002szf.1	-							NM_207362	NP_997245			hypothetical protein LOC343990												0																		---	---	---	---
LYG2	254773	broad.mit.edu	37	2	99870873	99870893	+	Intron	DEL	AGATAGTATTCTCACAGGCTC	-	-	rs80345491		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99870873_99870893delAGATAGTATTCTCACAGGCTC	uc002szw.1	-						MRPL30_uc002szl.1_Intron|LYG2_uc010fip.1_5'Flank|LYG2_uc002szx.1_Intron	NM_175735	NP_783862			lysozyme G-like 2 precursor						cell wall macromolecule catabolic process|peptidoglycan catabolic process	extracellular region	lysozyme activity			ovary(1)	1																		---	---	---	---
EIF5B	9669	broad.mit.edu	37	2	99968989	99968991	+	Intron	DEL	TTT	-	-	rs75968311		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99968989_99968991delTTT	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	100160395	100160396	+	IGR	DEL	TT	-	-	rs75022232		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100160395_100160396delTT								REV1 (53915 upstream) : AFF3 (3322 downstream)																																			---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100377386	100377386	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100377386delT	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100429006	100429006	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100429006delA	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100553563	100553564	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100553563_100553564insT	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100625789	100625789	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100625789delT	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron|AFF3_uc002tai.2_5'Flank	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100672500	100672500	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100672500delA	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	100817139	100817139	+	IGR	DEL	T	-	-	rs67392547		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100817139delT								AFF3 (58102 upstream) : LONRF2 (72615 downstream)																																			---	---	---	---
LONRF2	164832	broad.mit.edu	37	2	100916473	100916473	+	Intron	DEL	A	-	-	rs2871342	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100916473delA	uc002tal.3	-						LONRF2_uc010yvs.1_Intron	NM_198461	NP_940863			LON peptidase N-terminal domain and ring finger						proteolysis		ATP-dependent peptidase activity|zinc ion binding			large_intestine(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	101412810	101412811	+	IGR	DEL	AA	-	-	rs67966573		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101412810_101412811delAA								PDCL3 (219609 upstream) : NPAS2 (23802 downstream)																																			---	---	---	---
TBC1D8	11138	broad.mit.edu	37	2	101640087	101640087	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101640087delT	uc010fiv.2	-						TBC1D8_uc002tau.3_Intron	NM_001102426	NP_001095896			TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3																		---	---	---	---
TBC1D8	11138	broad.mit.edu	37	2	101660414	101660414	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101660414delA	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-4292-01	TCGA-BR-4292-01									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	102423504	102423505	+	Intron	DEL	TT	-	-	rs113890224		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102423504_102423505delTT	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Intron|MAP4K4_uc010fiw.1_Intron	NM_145687	NP_663720			mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	102537499	102537499	+	IGR	DEL	T	-	-	rs75557381		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102537499delT								MAP4K4 (26348 upstream) : IL1R2 (70807 downstream)																																			---	---	---	---
IL1R1	3554	broad.mit.edu	37	2	102686616	102686617	+	5'Flank	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102686616_102686617delGT	uc010fix.2	+							NM_000877	NP_000868			interleukin 1 receptor, type I precursor						innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity|platelet-derived growth factor receptor binding			skin(1)	1					Anakinra(DB00026)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	103659739	103659739	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103659739delC								TMEM182 (225603 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	103778982	103778982	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103778982delC								TMEM182 (344846 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	104017021	104017022	+	IGR	INS	-	GTGT	GTGT	rs141661793	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104017021_104017022insGTGT								TMEM182 (582885 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	104766732	104766733	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104766732_104766733insA								None (None upstream) : LOC150568 (284072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	104855069	104855069	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104855069delT								None (None upstream) : LOC150568 (195736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	105200199	105200199	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105200199delA								LOC150568 (70985 upstream) : POU3F3 (271770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	105364352	105364355	+	Intron	DEL	TTGT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105364352_105364355delTTGT	uc002tci.1	-						uc002tcj.1_Intron					Homo sapiens cDNA FLJ33475 fis, clone BRAMY2002479.																														---	---	---	---
TGFBRAP1	9392	broad.mit.edu	37	2	105925221	105925221	+	Intron	DEL	A	-	-	rs5833131		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105925221delA	uc002tcq.2	-						TGFBRAP1_uc002tcr.3_Intron	NM_004257	NP_004248			transforming growth factor, beta receptor						regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
FHL2	2274	broad.mit.edu	37	2	106049161	106049162	+	Intron	DEL	AT	-	-	rs150925416		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106049161_106049162delAT	uc002tdd.2	-						FHL2_uc002tdc.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	106254228	106254228	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106254228delT								FHL2 (198998 upstream) : NCK2 (107126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	106270136	106270136	+	IGR	DEL	T	-	-	rs67106943		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106270136delT								FHL2 (214906 upstream) : NCK2 (91218 downstream)																																			---	---	---	---
NCK2	8440	broad.mit.edu	37	2	106396150	106396150	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106396150delT	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	106847895	106847896	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106847895_106847896delTT								UXS1 (37100 upstream) : PLGLA (154873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	106987360	106987361	+	IGR	DEL	TT	-	-	rs78019139		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106987360_106987361delTT								UXS1 (176565 upstream) : PLGLA (15408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107315190	107315190	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107315190delA								RGPD3 (230389 upstream) : ST6GAL2 (102868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107791651	107791651	+	IGR	DEL	C	-	-	rs7573311	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107791651delC								ST6GAL2 (288088 upstream) : LOC729121 (647869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107874066	107874071	+	IGR	DEL	CAACAG	-	-	rs11276796		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107874066_107874071delCAACAG								ST6GAL2 (370503 upstream) : LOC729121 (565449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108938019	108938020	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108938019_108938020delAA								SULT1C2 (11649 upstream) : SULT1C4 (56401 downstream)																																			---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109065333	109065334	+	5'Flank	DEL	GA	-	-	rs3840470		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109065333_109065334delGA	uc002tec.2	+						GCC2_uc002ted.2_5'Flank	NM_181453	NP_852118			GRIP and coiled-coil domain-containing 2						Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	109316264	109316264	+	IGR	DEL	C	-	-	rs10204289	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109316264delC								LIMS1 (15377 upstream) : RANBP2 (19673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	109326764	109326764	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109326764delA								LIMS1 (25877 upstream) : RANBP2 (9173 downstream)																																			---	---	---	---
CCDC138	165055	broad.mit.edu	37	2	109405189	109405190	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109405189_109405190insA	uc002ten.1	+						CCDC138_uc002teo.1_Intron|CCDC138_uc002tep.1_Intron|CCDC138_uc010fjm.1_Intron	NM_144978	NP_659415			coiled-coil domain containing 138												0																		---	---	---	---
SEPT10	151011	broad.mit.edu	37	2	110325591	110325591	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110325591delT	uc002tew.2	-						SEPT10_uc010ywu.1_Intron|SEPT10_uc002tex.2_Intron|SEPT10_uc002tey.2_Intron|SEPT10_uc010ywv.1_Intron|SEPT10_uc002tev.1_Intron|SEPT10_uc010fjo.2_Intron|SEPT10_uc002tez.1_5'Flank	NM_144710	NP_653311			septin 10 isoform 1						cell cycle|cell division	septin complex	GTP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	110453412	110453412	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110453412delT								ANKRD57 (76849 upstream) : RGPD5 (96923 downstream)																																			---	---	---	---
NPHP1	4867	broad.mit.edu	37	2	110882862	110882862	+	Intron	DEL	T	-	-	rs112428035		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110882862delT	uc002tfn.3	-						NPHP1_uc002tfm.3_Intron|NPHP1_uc002tfl.3_Intron|NPHP1_uc002tfo.3_Intron|NPHP1_uc010ywx.1_Intron	NM_207181	NP_997064			nephrocystin 1 isoform 2						actin cytoskeleton organization|cell projection organization|cell-cell adhesion|excretion|retina development in camera-type eye|signal transduction|spermatid differentiation|visual behavior	adherens junction|cell-cell junction|cilium axoneme|cytoplasm|cytoskeleton|motile cilium|photoreceptor connecting cilium	protein binding|structural molecule activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	111476204	111476204	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111476204delA								BUB1 (40520 upstream) : ACOXL (13946 downstream)																																			---	---	---	---
ACOXL	55289	broad.mit.edu	37	2	111493782	111493782	+	Intron	DEL	T	-	-	rs112278989		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111493782delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	112424202	112424204	+	IGR	DEL	TGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112424202_112424204delTGG								LOC541471 (171510 upstream) : ANAPC1 (102437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	112459722	112459723	+	IGR	DEL	GA	-	-	rs35087094	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112459722_112459723delGA								LOC541471 (207030 upstream) : ANAPC1 (66918 downstream)																																	OREG0014894	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MERTK	10461	broad.mit.edu	37	2	112704982	112704982	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112704982delT	uc002thk.1	+	4	717	c.595delT	c.(595-597)TTTfs	p.F199fs	MERTK_uc002thl.1_Frame_Shift_Del_p.F23fs	NM_006343	NP_006334	Q12866	MERTK_HUMAN	MER receptor tyrosine kinase precursor	199	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	112800461	112800462	+	IGR	INS	-	C	C	rs138110413	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112800461_112800462insC								MERTK (13516 upstream) : TMEM87B (12338 downstream)																																			---	---	---	---
CKAP2L	150468	broad.mit.edu	37	2	113497539	113497539	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113497539delT	uc002tie.2	-						CKAP2L_uc002tif.2_Intron|CKAP2L_uc010yxp.1_Intron|uc002tid.2_Intron	NM_152515	NP_689728			cytoskeleton associated protein 2-like							centrosome					0																		---	---	---	---
IL1B	3553	broad.mit.edu	37	2	113596524	113596525	+	5'Flank	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113596524_113596525delTC	uc002tii.1	-							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	113756726	113756726	+	IGR	DEL	G	-	-	rs60145750		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113756726delG								IL1F9 (13499 upstream) : IL1F6 (6723 downstream)																																			---	---	---	---
PAX8	7849	broad.mit.edu	37	2	113976198	113976198	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113976198delA	uc010yxt.1	-						PAX8_uc010yxu.1_Intron|PAX8_uc010yxv.1_Intron|PAX8_uc002tjm.2_Intron|PAX8_uc002tjn.2_Intron	NM_003466	NP_003457			paired box 8 isoform PAX8A						branching involved in ureteric bud morphogenesis|cellular response to gonadotropin stimulus|central nervous system development|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric comma-shaped body morphogenesis|metanephric distal convoluted tubule development|metanephric nephron tubule formation|metanephric S-shaped body morphogenesis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|otic vesicle development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of thyroid-stimulating hormone secretion|thyroid gland development|transcription, DNA-dependent	nucleoplasm	protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity			ovary(1)|lung(1)	2								T	PPARG	follicular thyroid		Thyroid dysgenesis 						---	---	---	---
Unknown	0	broad.mit.edu	37	2	114177101	114177102	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114177101_114177102insA								PAX8 (140603 upstream) : CBWD2 (18166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	114300314	114300315	+	5'Flank	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114300314_114300315delAC	uc002tjx.3	-											Homo sapiens chromosome 2 mRNA sequence.																														---	---	---	---
RABL2A	11159	broad.mit.edu	37	2	114388924	114388924	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114388924delC	uc002tkn.3	+						RABL2A_uc010flb.2_Intron|RABL2A_uc002tkl.3_Intron|RABL2A_uc002tkm.3_Intron|RABL2A_uc002tks.3_Intron|RABL2A_uc002tkr.2_Intron|RABL2A_uc002tkp.3_Intron|RABL2A_uc002tkq.2_Intron	NM_007082	NP_009013			RAB, member of RAS oncogene family-like 2A						small GTPase mediated signal transduction		GTP binding|GTPase activity			skin(1)	1																		---	---	---	---
SLC35F5	80255	broad.mit.edu	37	2	114475434	114475434	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114475434delA	uc002tku.1	-						SLC35F5_uc002tkt.2_Intron	NM_025181	NP_079457			solute carrier family 35, member F5						transport	integral to membrane					0																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115257151	115257152	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115257151_115257152delTT	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115317469	115317469	+	Intron	DEL	A	-	-	rs78358942		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115317469delA	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115466212	115466212	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115466212delA	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115480504	115480505	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115480504_115480505insA	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115902723	115902723	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115902723delA	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|uc002tld.2_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	116487391	116487391	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116487391delA	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	117105613	117105614	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117105613_117105614delAA								DPP10 (503677 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117358968	117358968	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117358968delA								DPP10 (757032 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117519250	117519250	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117519250delA								DPP10 (917314 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117608352	117608354	+	IGR	DEL	ACA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117608352_117608354delACA								None (None upstream) : DDX18 (963901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117796786	117796786	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117796786delA								None (None upstream) : DDX18 (775469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118028927	118028928	+	IGR	DEL	AT	-	-	rs70947547		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118028927_118028928delAT								None (None upstream) : DDX18 (543327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118165419	118165420	+	IGR	INS	-	CTTT	CTTT	rs138636071	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118165419_118165420insCTTT								None (None upstream) : DDX18 (406835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118494232	118494232	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118494232delA								None (None upstream) : DDX18 (78023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118500265	118500266	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118500265_118500266insA								None (None upstream) : DDX18 (71989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118560626	118560626	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118560626delA								None (None upstream) : DDX18 (11629 downstream)																																			---	---	---	---
CCDC93	54520	broad.mit.edu	37	2	118748564	118748564	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118748564delA	uc002tlj.2	-						CCDC93_uc010fld.1_Intron	NM_019044	NP_061917			coiled-coil domain containing 93											large_intestine(1)|ovary(1)	2																		---	---	---	---
INSIG2	51141	broad.mit.edu	37	2	118861318	118861319	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118861318_118861319delTT	uc002tlk.2	+						INSIG2_uc010yye.1_Intron|INSIG2_uc002tll.2_Intron	NM_016133	NP_057217			insulin induced protein 2						ER-nuclear sterol response pathway	SREBP-SCAP-Insig complex				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	119577859	119577860	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119577859_119577860insA								INSIG2 (710263 upstream) : EN1 (21888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119584402	119584406	+	IGR	DEL	TTTTT	-	-	rs79465333		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119584402_119584406delTTTTT								INSIG2 (716806 upstream) : EN1 (15342 downstream)																																			---	---	---	---
EN1	2019	broad.mit.edu	37	2	119603829	119603829	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119603829delG	uc002tlm.2	-							NM_001426	NP_001417			engrailed homeobox 1						skeletal system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|lung(1)	2																		---	---	---	---
TMEM177	80775	broad.mit.edu	37	2	120451642	120451645	+	Intron	DEL	ACAC	-	-	rs147833710	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120451642_120451645delACAC	uc002tme.2	+											Homo sapiens cDNA FLJ32751 fis, clone TESTI2001621.							integral to membrane				ovary(1)	1	Colorectal(110;0.196)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	121307028	121307028	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121307028delT								LOC84931 (83103 upstream) : GLI2 (186171 downstream)																																			---	---	---	---
CLASP1	23332	broad.mit.edu	37	2	122394985	122394985	+	Intron	DEL	A	-	-	rs75305993	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122394985delA	uc002tnc.2	-						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	122471192	122471193	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122471192_122471193insT	uc002tnj.1	+											Homo sapiens cDNA FLJ40945 fis, clone UTERU2008747.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	122816574	122816574	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122816574delT								TSN (291148 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	122870615	122870615	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122870615delT								TSN (345189 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123114446	123114446	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123114446delA								TSN (589020 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123621710	123621710	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123621710delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123842843	123842854	+	IGR	DEL	TGTGTGTGTGTA	-	-	rs58140708		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123842843_123842854delTGTGTGTGTGTA								None (None upstream) : CNTNAP5 (940010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124164889	124164889	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124164889delT								None (None upstream) : CNTNAP5 (617975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124400831	124400831	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124400831delT								None (None upstream) : CNTNAP5 (382033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	125863947	125864012	+	IGR	DEL	AAGAGTGCCCTTTCAGACACCAAGTCTGATAGTGCTTAAGACAAAGATGGTGGTCTACAATCCAGA	-	-	rs58307494	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125863947_125864012delAAGAGTGCCCTTTCAGACACCAAGTCTGATAGTGCTTAAGACAAAGATGGTGGTCTACAATCCAGA								CNTNAP5 (191086 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	125968663	125968665	+	IGR	DEL	AAA	-	-	rs149954215		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125968663_125968665delAAA								CNTNAP5 (295802 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126196035	126196035	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126196035delA								CNTNAP5 (523174 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126473788	126473789	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126473788_126473789delTT								CNTNAP5 (800927 upstream) : GYPC (939895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126576058	126576058	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126576058delG								CNTNAP5 (903197 upstream) : GYPC (837626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126778932	126778933	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126778932_126778933insA								None (None upstream) : GYPC (634751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127224967	127224967	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127224967delC								None (None upstream) : GYPC (188717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127546691	127546691	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127546691delA								GYPC (92446 upstream) : BIN1 (258916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127609718	127609718	+	IGR	DEL	T	-	-	rs11677887	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127609718delT								GYPC (155473 upstream) : BIN1 (195889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127926706	127926706	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127926706delA								BIN1 (61842 upstream) : CYP27C1 (14706 downstream)																																			---	---	---	---
MYO7B	4648	broad.mit.edu	37	2	128323095	128323095	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128323095delT	uc002top.2	+							NM_001080527	NP_001073996			myosin VIIB							apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	130250529	130250530	+	IGR	INS	-	G	G	rs114740370	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130250529_130250530insG								None (None upstream) : LOC389033 (429905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130299026	130299027	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130299026_130299027insA								None (None upstream) : LOC389033 (381408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130573266	130573267	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130573266_130573267insA								None (None upstream) : LOC389033 (107168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130602578	130602578	+	IGR	DEL	T	-	-	rs145218656	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130602578delT								None (None upstream) : LOC389033 (77857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130894649	130894649	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130894649delC								POTEF (7854 upstream) : CCDC74B (2213 downstream)																																			---	---	---	---
FAM128B	80097	broad.mit.edu	37	2	130948157	130948157	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130948157delG	uc002tqu.2	+	3	588	c.435delG	c.(433-435)AAGfs	p.K145fs		NM_025029	NP_079305	Q6NZ67	MZT2B_HUMAN	hypothetical protein LOC80097	145						centrosome|gamma-tubulin ring complex|spindle	protein binding				0	Colorectal(110;0.1)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	131000154	131000154	+	IGR	DEL	T	-	-	rs77841472		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131000154delT								TUBA3E (44120 upstream) : CCDC115 (95662 downstream)																																			---	---	---	---
FAM128A	653784	broad.mit.edu	37	2	132250354	132250355	+	5'Flank	INS	-	G	G	rs148632212	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132250354_132250355insG	uc002tsw.3	-						LOC150776_uc010zax.1_5'Flank|LOC150776_uc010zay.1_5'Flank|LOC150776_uc010zaz.1_5'Flank|LOC150776_uc010fna.2_5'Flank|LOC150776_uc002tsy.3_5'Flank|FAM128A_uc002tsv.3_5'Flank|FAM128A_uc002tsx.1_5'Flank	NM_001085365	NP_001078834			hypothetical protein LOC653784							centrosome|gamma-tubulin ring complex|spindle					0				BRCA - Breast invasive adenocarcinoma(221;0.13)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	132375435	132375436	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132375435_132375436delTT								CCDC74A (84198 upstream) : C2orf27A (104628 downstream)																																			---	---	---	---
C2orf27B	408029	broad.mit.edu	37	2	132553833	132553833	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132553833delT	uc002ttg.1	-							NM_214461	NP_999626			hypothetical protein LOC408029												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	132743367	132743368	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132743367_132743368insA								C2orf27B (184133 upstream) : NCRNA00164 (161796 downstream)																																			---	---	---	---
NCRNA00164	554226	broad.mit.edu	37	2	132939034	132939035	+	Intron	INS	-	A	A	rs151177463	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132939034_132939035insA	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0																		---	---	---	---
NCRNA00164	554226	broad.mit.edu	37	2	133016676	133016677	+	5'Flank	INS	-	TGTC	TGTC	rs67307110		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133016676_133016677insTGTC	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	133022861	133022862	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133022861_133022862insA								NCRNA00164 (7319 upstream) : GPR39 (151285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133024157	133024158	+	IGR	DEL	AC	-	-	rs72064311		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133024157_133024158delAC								NCRNA00164 (8615 upstream) : GPR39 (149989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133065809	133065809	+	Intron	DEL	T	-	-	rs35536200		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133065809delT	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	133151513	133151514	+	IGR	INS	-	A	A	rs147624182	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133151513_133151514insA								NCRNA00164 (135971 upstream) : GPR39 (22633 downstream)																																			---	---	---	---
GPR39	2863	broad.mit.edu	37	2	133307600	133307601	+	Intron	INS	-	CTC	CTC	rs139680583	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133307600_133307601insCTC	uc002ttl.2	+							NM_001508	NP_001499			G protein-coupled receptor 39							integral to plasma membrane	G-protein coupled receptor activity|metal ion binding				0																		---	---	---	---
GPR39	2863	broad.mit.edu	37	2	133319151	133319158	+	Intron	DEL	ACACACAC	-	-	rs72360408		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133319151_133319158delACACACAC	uc002ttl.2	+							NM_001508	NP_001499			G protein-coupled receptor 39							integral to plasma membrane	G-protein coupled receptor activity|metal ion binding				0																		---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	134016745	134016745	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134016745delC	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																		---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	134111867	134111868	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134111867_134111868delTT	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																		---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	134151513	134151514	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134151513_134151514insA	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	134574561	134574561	+	IGR	DEL	A	-	-	rs113272181		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134574561delA								NCKAP5 (248530 upstream) : MGAT5 (437269 downstream)																																			---	---	---	---
MGAT5	4249	broad.mit.edu	37	2	135102666	135102666	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135102666delT	uc002ttv.1	+							NM_002410	NP_002401			N-acetylglucosaminyltransferase V						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)														---	---	---	---
TMEM163	81615	broad.mit.edu	37	2	135351850	135351850	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135351850delG	uc002ttx.2	-						TMEM163_uc002tty.2_Intron	NM_030923	NP_112185			transmembrane protein 163							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(221;0.154)														---	---	---	---
TMEM163	81615	broad.mit.edu	37	2	135465468	135465469	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135465468_135465469delTT	uc002ttx.2	-						TMEM163_uc002tty.2_Intron	NM_030923	NP_112185			transmembrane protein 163							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(221;0.154)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	135556003	135556005	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135556003_135556005delAAA								TMEM163 (30669 upstream) : ACMSD (40181 downstream)																																			---	---	---	---
RAB3GAP1	22930	broad.mit.edu	37	2	135876641	135876644	+	Intron	DEL	CCTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135876641_135876644delCCTC	uc002tuj.2	+						RAB3GAP1_uc010fnf.2_Intron|RAB3GAP1_uc010fng.2_Intron|RAB3GAP1_uc010fnh.1_Intron	NM_012233	NP_036365			RAB3 GTPase-activating protein							centrosome|nucleus|soluble fraction	Rab GTPase activator activity|Rab GTPase binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.117)														---	---	---	---
R3HDM1	23518	broad.mit.edu	37	2	136402887	136402887	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136402887delA	uc002tuo.2	+						R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron|R3HDM1_uc010zbh.1_Intron	NM_015361	NP_056176			R3H domain containing 1								nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)														---	---	---	---
UBXN4	23190	broad.mit.edu	37	2	136528108	136528108	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136528108delT	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	136574442	136574445	+	Intron	DEL	TTTT	-	-	rs67715501		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136574442_136574445delTTTT	uc002tuu.1	-							NM_002299	NP_002290			lactase-phlorizin hydrolase preproprotein						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	136594278	136594279	+	Frame_Shift_Del	DEL	AT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136594278_136594279delAT	uc002tuu.1	-	1	472_473	c.461_462delAT	c.(460-462)TATfs	p.Y154fs		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	154	Extracellular (Potential).|4 X approximate repeats.|1.				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)														---	---	---	---
DARS	1615	broad.mit.edu	37	2	136664813	136664817	+	3'UTR	DEL	TTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136664813_136664817delTTTTT	uc002tux.1	-	16					DARS_uc010fnj.1_3'UTR	NM_001349	NP_001340			aspartyl-tRNA synthetase						aspartyl-tRNA aminoacylation|protein complex assembly	cytosol|nuclear membrane|plasma membrane|soluble fraction	aminoacylase activity|aspartate-tRNA ligase activity|ATP binding|nucleic acid binding|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)													---	---	---	---
DARS	1615	broad.mit.edu	37	2	136673772	136673772	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136673772delA	uc002tux.1	-						DARS_uc010fnj.1_Intron	NM_001349	NP_001340			aspartyl-tRNA synthetase						aspartyl-tRNA aminoacylation|protein complex assembly	cytosol|nuclear membrane|plasma membrane|soluble fraction	aminoacylase activity|aspartate-tRNA ligase activity|ATP binding|nucleic acid binding|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)													---	---	---	---
DARS	1615	broad.mit.edu	37	2	136702146	136702147	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136702146_136702147delAA	uc002tux.1	-						DARS_uc010fnj.1_Intron	NM_001349	NP_001340			aspartyl-tRNA synthetase						aspartyl-tRNA aminoacylation|protein complex assembly	cytosol|nuclear membrane|plasma membrane|soluble fraction	aminoacylase activity|aspartate-tRNA ligase activity|ATP binding|nucleic acid binding|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	136894204	136894204	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136894204delT								CXCR4 (18479 upstream) : THSD7B (628911 downstream)																																			---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137664000	137664000	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137664000delT	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	138327575	138327575	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138327575delT	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	138496481	138496482	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138496481_138496482insT								THSD7B (61194 upstream) : HNMT (225108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	139015860	139015861	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139015860_139015861insG								HNMT (241927 upstream) : SPOPL (243489 downstream)																																			---	---	---	---
SPOPL	339745	broad.mit.edu	37	2	139287045	139287046	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139287045_139287046delTG	uc002tvh.2	+							NM_001001664	NP_001001664			speckle-type POZ protein-like							nucleus				skin(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0296)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	140205093	140205095	+	IGR	DEL	CTC	-	-	rs112564861		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140205093_140205095delCTC								NXPH2 (667282 upstream) : LRP1B (783901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140366637	140366638	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140366637_140366638insA								NXPH2 (828826 upstream) : LRP1B (622358 downstream)																																			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141447956	141447956	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141447956delT	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	142171807	142171809	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142171807_142171809delAAA	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	143485140	143485141	+	IGR	INS	-	TG	TG	rs138842807	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143485140_143485141insTG								LRP1B (595870 upstream) : KYNU (150054 downstream)																																			---	---	---	---
KYNU	8942	broad.mit.edu	37	2	143744891	143744891	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143744891delG	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)													---	---	---	---
KYNU	8942	broad.mit.edu	37	2	143754213	143754214	+	Intron	INS	-	G	G	rs139873483	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143754213_143754214insG	uc002tvl.2	+						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)													---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144276716	144276716	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144276716delA	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	144573053	144573056	+	IGR	DEL	ACTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144573053_144573056delACTC								ARHGAP15 (47133 upstream) : GTDC1 (130527 downstream)																																			---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	145025676	145025676	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145025676delG	uc002tvp.2	-						GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.2_Intron|GTDC1_uc010fnn.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637			glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)														---	---	---	---
ZEB2	9839	broad.mit.edu	37	2	145146458	145146458	+	3'UTR	DEL	A	-	-	rs72393406		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145146458delA	uc002tvu.2	-	10					ZEB2_uc002tvv.2_3'UTR|ZEB2_uc010zbm.1_3'UTR|ZEB2_uc010fnp.2_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	146046257	146046257	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146046257delA								ZEB2 (768326 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146062041	146062041	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146062041delT								ZEB2 (784110 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146387070	146387070	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146387070delT								None (None upstream) : PABPC1P2 (957555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146656726	146656727	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146656726_146656727insT								None (None upstream) : PABPC1P2 (687898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146847604	146847604	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146847604delT								None (None upstream) : PABPC1P2 (497021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	147659368	147659369	+	IGR	INS	-	CT	CT	rs144954667	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147659368_147659369insCT								PABPC1P2 (310811 upstream) : ACVR2A (942717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	147728491	147728492	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147728491_147728492insT								PABPC1P2 (379934 upstream) : ACVR2A (873594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	148052382	148052383	+	IGR	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148052382_148052383insCA								PABPC1P2 (703825 upstream) : ACVR2A (549703 downstream)																																			---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148637257	148637258	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148637257_148637258insT	uc002twg.2	+						ACVR2A_uc010zbn.1_Intron|ACVR2A_uc002twh.2_Intron	NM_001616	NP_001607			activin A receptor, type IIA precursor						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)														---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148683686	148683686	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
EPC2	26122	broad.mit.edu	37	2	149440133	149440133	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149440133delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	150084906	150084906	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150084906delG								LYPD6B (13134 upstream) : LYPD6 (102207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	150336534	150336534	+	IGR	DEL	T	-	-	rs111657029		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150336534delT								LYPD6 (6397 upstream) : MMADHC (89616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151115490	151115490	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151115490delA								MMADHC (671160 upstream) : RND3 (209222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151226835	151226835	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151226835delA								MMADHC (782505 upstream) : RND3 (97877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151421671	151421671	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151421671delA								RND3 (77491 upstream) : RBM43 (683058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151918238	151918239	+	IGR	INS	-	AGGA	AGGA	rs139643835	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151918238_151918239insAGGA								RND3 (574058 upstream) : RBM43 (186490 downstream)																																			---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152292282	152292283	+	Intron	DEL	TT	-	-	rs75364982	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152292282_152292283delTT	uc002txm.2	+						RIF1_uc002txl.2_Intron|RIF1_uc010fnv.1_Intron|RIF1_uc002txn.2_Intron|RIF1_uc002txo.2_Intron|RIF1_uc010zby.1_Intron	NM_018151	NP_060621			RAP1 interacting factor 1						cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152368722	152368722	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152368722delT	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	152404054	152404054	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152404054delA	uc010fnx.2	-						NEB_uc002txr.2_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	152473997	152474003	+	Intron	DEL	AAAAAAG	-	-	rs4303716	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152473997_152474003delAAAAAAG	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)														---	---	---	---
ARL5A	26225	broad.mit.edu	37	2	152652590	152652590	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152652590delA	uc010zcc.1	-											Homo sapiens ARFLP5 mRNA, complete cds.						small GTPase mediated signal transduction	intracellular	GTP binding				0				BRCA - Breast invasive adenocarcinoma(221;0.153)														---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152695482	152695482	+	3'UTR	DEL	T	-	-	rs111950042		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152695482delT	uc002tya.2	-	14					CACNB4_uc002txy.2_3'UTR|CACNB4_uc002txz.2_3'UTR|CACNB4_uc010fnz.2_3'UTR	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)													---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152874358	152874358	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152874358delT	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)													---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152936642	152936644	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152936642_152936644delTTT	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)													---	---	---	---
FMNL2	114793	broad.mit.edu	37	2	153192409	153192409	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153192409delC	uc002tye.2	+							NM_052905	NP_443137			formin-like 2						actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
FMNL2	114793	broad.mit.edu	37	2	153432761	153432762	+	Intron	INS	-	TT	TT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153432761_153432762insTT	uc002tye.2	+							NM_052905	NP_443137			formin-like 2						actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
PRPF40A	55660	broad.mit.edu	37	2	153509692	153509692	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153509692delA	uc002tyh.3	-	26					PRPF40A_uc002tyg.3_3'UTR	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	154406753	154406753	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154406753delT								RPRM (71431 upstream) : GALNT13 (321673 downstream)																																			---	---	---	---
GALNT13	114805	broad.mit.edu	37	2	155188938	155188938	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155188938delA	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron|GALNT13_uc010foc.1_Intron|GALNT13_uc010fod.2_Intron	NM_052917	NP_443149			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
GALNT13	114805	broad.mit.edu	37	2	155265469	155265469	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155265469delC	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron|GALNT13_uc010foc.1_Intron|GALNT13_uc010fod.2_Intron	NM_052917	NP_443149			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KCNJ3	3760	broad.mit.edu	37	2	155682255	155682256	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155682255_155682256insT	uc002tyv.1	+						KCNJ3_uc010zce.1_Intron	NM_002239	NP_002230			potassium inwardly-rectifying channel J3						synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			upper_aerodigestive_tract(1)|pancreas(1)	2					Halothane(DB01159)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	156050196	156050196	+	IGR	DEL	T	-	-	rs112584129		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156050196delT								KCNJ3 (337182 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156127170	156127170	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156127170delA								KCNJ3 (414156 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156208105	156208105	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156208105delA								KCNJ3 (495091 upstream) : NR4A2 (972841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156791609	156791609	+	IGR	DEL	T	-	-	rs16839799	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156791609delT								None (None upstream) : NR4A2 (389337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	157473569	157473569	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157473569delT								GPD2 (3322 upstream) : GALNT5 (640771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	157693575	157693575	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157693575delT								GPD2 (223328 upstream) : GALNT5 (420765 downstream)																																			---	---	---	---
GALNT5	11227	broad.mit.edu	37	2	158120687	158120688	+	Intron	DEL	AC	-	-	rs147126798		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158120687_158120688delAC	uc002tzg.2	+						GALNT5_uc010zci.1_Intron	NM_014568	NP_055383			N-acetylgalactosaminyltransferase 5						glycosaminoglycan biosynthetic process	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(3)|skin(1)	4																		---	---	---	---
ACVR1	90	broad.mit.edu	37	2	158643545	158643546	+	Intron	DEL	AA	-	-	rs74898722		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158643545_158643546delAA	uc002tzm.3	-						ACVR1_uc002tzn.3_Intron|ACVR1_uc010fog.2_Intron	NM_001111067	NP_001104537			activin A receptor, type I precursor						BMP signaling pathway|G1/S transition of mitotic cell cycle|negative regulation of activin receptor signaling pathway|negative regulation of apoptosis|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	activin receptor complex	activin binding|ATP binding|follistatin binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta binding			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	158755368	158755369	+	IGR	DEL	TG	-	-	rs77571157		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158755368_158755369delTG								ACVR1 (22994 upstream) : UPP2 (96322 downstream)																																			---	---	---	---
PKP4	8502	broad.mit.edu	37	2	159323055	159323055	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159323055delA	uc002tzv.2	+						PKP4_uc002tzt.1_Intron|PKP4_uc002tzu.2_Intron|PKP4_uc002tzw.2_Intron|PKP4_uc002tzx.2_Intron|PKP4_uc002tzy.1_Intron	NM_003628	NP_003619			plakophilin 4 isoform a						cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7															HNSCC(62;0.18)			---	---	---	---
TANC1	85461	broad.mit.edu	37	2	160031215	160031215	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160031215delA	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron|TANC1_uc002uai.1_5'Flank	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
WDSUB1	151525	broad.mit.edu	37	2	160102044	160102045	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160102044_160102045delAA	uc002uaj.3	-						WDSUB1_uc002uak.3_Intron|WDSUB1_uc002ual.3_Intron|WDSUB1_uc002uam.3_Intron|WDSUB1_uc010foo.2_Intron	NM_152528	NP_689741			WD repeat, sterile alpha motif and U-box domain							ubiquitin ligase complex	ubiquitin-protein ligase activity				0																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160345824	160345824	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160345824delA	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																		---	---	---	---
LY75	4065	broad.mit.edu	37	2	160642188	160642189	+	Intron	INS	-	A	A	rs140068875	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160642188_160642189insA	uc002ubb.3	-						LY75_uc010fos.2_Intron|CD302_uc002uba.2_Intron|CD302_uc010zco.1_Intron	NM_002349	NP_002340			lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)														---	---	---	---
LY75	4065	broad.mit.edu	37	2	160689641	160689643	+	Intron	DEL	TTT	-	-	rs67186154		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160689641_160689643delTTT	uc002ubc.3	-						LY75_uc002ubb.3_Intron|LY75_uc010fos.2_Intron	NM_002349	NP_002340			lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)														---	---	---	---
LY75	4065	broad.mit.edu	37	2	160732257	160732257	+	Intron	DEL	A	-	-	rs75237280		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160732257delA	uc002ubc.3	-						LY75_uc002ubb.3_Intron|LY75_uc010fos.2_Intron|LY75_uc010fot.1_Intron	NM_002349	NP_002340			lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)														---	---	---	---
ITGB6	3694	broad.mit.edu	37	2	160968845	160968845	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160968845delT	uc002ubh.2	-						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	161016460	161016460	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161016460delT	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	161063999	161063999	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161063999delA	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																		---	---	---	---
RBMS1	5937	broad.mit.edu	37	2	161162482	161162482	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161162482delA	uc002ubo.2	-						RBMS1_uc002ubj.2_Intron|RBMS1_uc002ubk.2_Intron|RBMS1_uc002ubl.2_Intron|RBMS1_uc002ubn.2_Intron|RBMS1_uc002ubi.3_Intron|RBMS1_uc002ubm.2_Intron|RBMS1_uc002ubp.2_Intron|RBMS1_uc010fox.2_Intron	NM_016836	NP_058520			RNA binding motif, single stranded interacting						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	162272776	162272776	+	5'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	162415090	162415091	+	IGR	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162415090_162415091insCA								TBR1 (133517 upstream) : SLC4A10 (65754 downstream)																																			---	---	---	---
DPP4	1803	broad.mit.edu	37	2	162903784	162903784	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162903784delA	uc002ubz.2	-						DPP4_uc010fpb.2_Intron|DPP4_uc002uca.1_Intron|DPP4_uc002ucb.1_Intron	NM_001935	NP_001926			dipeptidylpeptidase IV						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)													---	---	---	---
FIGN	55137	broad.mit.edu	37	2	164553614	164553614	+	Intron	DEL	C	-	-	rs67571143		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164553614delC	uc002uck.1	-							NM_018086	NP_060556			fidgetin							nuclear matrix	ATP binding|nucleoside-triphosphatase activity			large_intestine(2)|ovary(1)|skin(1)	4																		---	---	---	---
GRB14	2888	broad.mit.edu	37	2	165365366	165365366	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165365366delA	uc002ucl.2	-						GRB14_uc010zcv.1_Intron|GRB14_uc002ucm.2_Intron	NM_004490	NP_004481			growth factor receptor-bound protein 14						blood coagulation|leukocyte migration	cytosol|endosome membrane|Golgi membrane|microsome|plasma membrane	SH3/SH2 adaptor activity			ovary(5)|upper_aerodigestive_tract(1)|lung(1)	7																		---	---	---	---
GRB14	2888	broad.mit.edu	37	2	165430142	165430143	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165430142_165430143insT	uc002ucl.2	-						GRB14_uc002ucm.2_Intron	NM_004490	NP_004481			growth factor receptor-bound protein 14						blood coagulation|leukocyte migration	cytosol|endosome membrane|Golgi membrane|microsome|plasma membrane	SH3/SH2 adaptor activity			ovary(5)|upper_aerodigestive_tract(1)|lung(1)	7																		---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165570665	165570666	+	Intron	DEL	AC	-	-	rs10563101		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165570665_165570666delAC	uc010zcw.1	-						COBLL1_uc002ucp.2_Intron|COBLL1_uc002ucq.2_Intron|COBLL1_uc010zcx.1_Intron|COBLL1_uc002ucs.1_Intron|COBLL1_uc002uco.2_Intron	NM_014900	NP_055715			COBL-like 1											ovary(2)|pancreas(1)	3																		---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165600059	165600059	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165600059delT	uc010zcw.1	-						COBLL1_uc002ucp.2_Intron|COBLL1_uc002ucq.2_Intron|COBLL1_uc010zcx.1_Intron|COBLL1_uc002ucs.1_Intron|COBLL1_uc002uct.2_3'UTR	NM_014900	NP_055715			COBL-like 1											ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	165876772	165876775	+	IGR	DEL	CCCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165876772_165876775delCCCT								SLC38A11 (64737 upstream) : SCN3A (67257 downstream)																																			---	---	---	---
SCN2A	6326	broad.mit.edu	37	2	166144025	166144025	+	Intron	DEL	T	-	-	rs111865347		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166144025delT	uc002udc.2	+							NM_001040142	NP_001035232			sodium channel, voltage-gated, type II, alpha						myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)													---	---	---	---
SCN2A	6326	broad.mit.edu	37	2	166243209	166243209	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166243209delT	uc002udc.2	+						SCN2A_uc002udd.2_Intron|SCN2A_uc002ude.2_Intron	NM_001040142	NP_001035232			sodium channel, voltage-gated, type II, alpha						myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	166311790	166311791	+	IGR	DEL	AA	-	-	rs71393672		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166311790_166311791delAA								SCN2A (62972 upstream) : CSRNP3 (14366 downstream)																																			---	---	---	---
SCN1A	6323	broad.mit.edu	37	2	166852768	166852768	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166852768delA	uc010zcz.1	-							NM_006920	NP_008851			sodium channel, voltage-gated, type I, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)													---	---	---	---
SCN9A	6335	broad.mit.edu	37	2	167168775	167168777	+	Intron	DEL	AGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167168775_167168777delAGG	uc010fpl.2	-							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)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	168507774	168507785	+	IGR	DEL	GTGTGTGTGCGC	-	-	rs112769219	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168507774_168507785delGTGTGTGTGCGC								XIRP2 (391515 upstream) : B3GALT1 (167397 downstream)																																			---	---	---	---
STK39	27347	broad.mit.edu	37	2	168997409	168997409	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168997409delA	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	169503919	169503919	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169503919delT	uc002ueb.1	+						LASS6_uc002uec.1_Intron	NM_203463	NP_982288			longevity assurance homolog 6							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1																		---	---	---	---
LASS6	253782	broad.mit.edu	37	2	169524094	169524095	+	Intron	INS	-	TT	TT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169524094_169524095insTT	uc002ueb.1	+						LASS6_uc002uec.1_Intron	NM_203463	NP_982288			longevity assurance homolog 6							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1																		---	---	---	---
LASS6	253782	broad.mit.edu	37	2	169624750	169624750	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169624750delT	uc002ueb.1	+						LASS6_uc002uec.1_Intron	NM_203463	NP_982288			longevity assurance homolog 6							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1																		---	---	---	---
LRP2	4036	broad.mit.edu	37	2	169986156	169986156	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169986156delT	uc002ues.2	-							NM_004525	NP_004516			low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170129802	170129802	+	Intron	DEL	A	-	-	rs76310810		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170129802delA	uc002ues.2	-						LRP2_uc010zdf.1_Intron	NM_004525	NP_004516			low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170151228	170151237	+	Intron	DEL	AAAAAAAAAA	-	-	rs10535757		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170151228_170151237delAAAAAAAAAA	uc002ues.2	-						LRP2_uc010zdf.1_Intron	NM_004525	NP_004516			low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
KBTBD10	10324	broad.mit.edu	37	2	170344243	170344243	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170344243delT	uc010zdh.1	+						BBS5_uc002uet.2_Intron|BBS5_uc010fpw.2_Intron	NM_152384	NP_689597			Bardet-Biedl syndrome 5						striated muscle contraction	centrosome|nucleolus|plasma membrane|pseudopodium|ruffle					0																		---	---	---	---
KBTBD10	10324	broad.mit.edu	37	2	170382076	170382076	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170382076delT	uc002ueu.1	+						KBTBD10_uc010zdh.1_Intron	NM_006063	NP_006054			kelch repeat and BTB (POZ) domain containing 10						striated muscle contraction	centrosome|nucleolus|plasma membrane|pseudopodium|ruffle					0																		---	---	---	---
FASTKD1	79675	broad.mit.edu	37	2	170396776	170396776	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170396776delA	uc002uev.3	-						FASTKD1_uc002uew.3_Intron|FASTKD1_uc002uex.3_Intron	NM_024622	NP_078898			FAST kinase domains 1						apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(4)	4																		---	---	---	---
UBR3	130507	broad.mit.edu	37	2	170804034	170804035	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170804034_170804035delTT	uc010zdi.1	+						UBR3_uc002ufr.3_Intron|UBR3_uc010fqa.2_5'Flank|UBR3_uc002uft.3_5'Flank	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																		---	---	---	---
UBR3	130507	broad.mit.edu	37	2	170878140	170878140	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170878140delT	uc010zdi.1	+						UBR3_uc002ufr.3_Intron|UBR3_uc010fqa.2_Intron|UBR3_uc002uft.3_Intron|UBR3_uc010zdj.1_Intron|UBR3_uc002ufu.3_Intron	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																		---	---	---	---
UBR3	130507	broad.mit.edu	37	2	170938525	170938525	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	171210781	171210782	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171210781_171210782delTT	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																		---	---	---	---
MYO3B	140469	broad.mit.edu	37	2	171413037	171413038	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171413037_171413038delTT	uc002ufy.2	+						MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482			myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19																		---	---	---	---
METTL8	79828	broad.mit.edu	37	2	172182461	172182462	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172182461_172182462delAA	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																		---	---	---	---
METTL8	79828	broad.mit.edu	37	2	172231361	172231362	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172231361_172231362insT	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																		---	---	---	---
METTL8	79828	broad.mit.edu	37	2	172239234	172239234	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172239234delA	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																		---	---	---	---
DYNC1I2	1781	broad.mit.edu	37	2	172550553	172550554	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172550553_172550554delTT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	172638338	172638339	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172638338_172638339insT								DYNC1I2 (33419 upstream) : SLC25A12 (1576 downstream)																																			---	---	---	---
HAT1	8520	broad.mit.edu	37	2	172823128	172823128	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172823128delA	uc002uhi.2	+						HAT1_uc010fqi.2_Intron|HAT1_uc002uhj.2_Intron	NM_003642	NP_003633			histone acetyltransferase 1						chromatin silencing at telomere|DNA packaging	cytoplasm|nuclear matrix|nucleoplasm	histone acetyltransferase activity|protein binding			large_intestine(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
PDK1	5163	broad.mit.edu	37	2	173481843	173481843	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173481843delA	uc010zea.1	+							NM_002610				pyruvate dehydrogenase kinase 1 precursor						glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|small GTPase mediated signal transduction	mitochondrial matrix	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			lung(3)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.12)											Autosomal_Dominant_Polycystic_Kidney_Disease				---	---	---	---
RAPGEF4	11069	broad.mit.edu	37	2	173755864	173755864	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173755864delA	uc002uhv.3	+						RAPGEF4_uc002uhu.2_Intron|RAPGEF4_uc002uhw.3_Intron|RAPGEF4_uc010zec.1_Intron|RAPGEF4_uc010zed.1_Intron|RAPGEF4_uc010zee.1_Intron|RAPGEF4_uc010fqo.2_Intron	NM_007023	NP_008954			Rap guanine nucleotide exchange factor (GEF) 4						blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	174242686	174242688	+	IGR	DEL	TTT	-	-	rs71403372		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174242686_174242688delTTT								CDCA7 (8968 upstream) : SP3 (530571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174418085	174418085	+	IGR	DEL	C	-	-	rs1405230	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174418085delC								CDCA7 (184367 upstream) : SP3 (355174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174505699	174505700	+	IGR	INS	-	CT	CT	rs147845927	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174505699_174505700insCT								CDCA7 (271981 upstream) : SP3 (267559 downstream)																																			---	---	---	---
SP3	6670	broad.mit.edu	37	2	174783522	174783522	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174783522delA	uc002uig.2	-						SP3_uc002uie.2_Intron|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	174849465	174849465	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174849465delT								SP3 (19402 upstream) : OLA1 (87711 downstream)																																			---	---	---	---
OLA1	29789	broad.mit.edu	37	2	175031851	175031851	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175031851delA	uc002uih.2	-						OLA1_uc002uii.2_Intron|OLA1_uc010fqq.2_Intron|OLA1_uc002uij.2_Intron|OLA1_uc002uik.2_Intron|OLA1_uc010fqr.2_Intron	NM_013341	NP_037473			Obg-like ATPase 1 isoform 1						ATP catabolic process	cytoplasm	ATP binding|GTP binding|hydrolase activity|protein binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	175380498	175380498	+	IGR	DEL	T	-	-	rs113580732		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175380498delT								GPR155 (28687 upstream) : WIPF1 (43805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176159353	176159353	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176159353delT								ATP5G3 (112863 upstream) : KIAA1715 (631057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176170191	176170192	+	IGR	DEL	TC	-	-	rs67132850		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176170191_176170192delTC								ATP5G3 (123701 upstream) : KIAA1715 (620218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176208273	176208274	+	IGR	INS	-	G	G	rs137979691	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176208273_176208274insG								ATP5G3 (161783 upstream) : KIAA1715 (582136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176364730	176364731	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176364730_176364731delAA								ATP5G3 (318240 upstream) : KIAA1715 (425679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176637498	176637498	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176637498delG								ATP5G3 (591008 upstream) : KIAA1715 (152912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176708091	176708091	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176708091delT								ATP5G3 (661601 upstream) : KIAA1715 (82319 downstream)																																			---	---	---	---
HOXD12	3238	broad.mit.edu	37	2	176964374	176964374	+	5'Flank	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176964374delG	uc010zev.1	+						HOXD12_uc010zew.1_5'Flank	NM_021193	NP_067016			homeobox D12							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	177220645	177220645	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177220645delT								MTX2 (17894 upstream) : MIR1246 (245063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	177275008	177275009	+	IGR	INS	-	T	T	rs150602742	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177275008_177275009insT								MTX2 (72257 upstream) : MIR1246 (190699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	177317176	177317176	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177317176delA								MTX2 (114425 upstream) : MIR1246 (148532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	177676265	177676265	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177676265delA								MIR1246 (210485 upstream) : HNRNPA3 (401157 downstream)																																			---	---	---	---
AGPS	8540	broad.mit.edu	37	2	178402955	178402955	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178402955delT	uc002ull.2	+	20					AGPS_uc010zfb.1_3'UTR	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)															---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179258982	179258982	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179258982delT	uc002ulx.2	+						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)															---	---	---	---
PRKRA	8575	broad.mit.edu	37	2	179313319	179313319	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179313319delA	uc002umf.2	-						PRKRA_uc002umd.2_Intron|PRKRA_uc002ume.2_Intron|PRKRA_uc002umg.2_Intron|DFNB59_uc002umi.3_5'Flank	NM_003690	NP_003681			protein kinase, interferon-inducible double						immune response|negative regulation of cell proliferation|production of siRNA involved in RNA interference|response to virus	perinuclear region of cytoplasm	double-stranded RNA binding|enzyme activator activity|protein homodimerization activity			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)															---	---	---	---
DFNB59	494513	broad.mit.edu	37	2	179321040	179321041	+	Intron	DEL	AA	-	-	rs11448490		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179321040_179321041delAA	uc002umi.3	+						DFNB59_uc002umj.3_Intron	NM_001042702	NP_001036167			deafness, autosomal recessive 59						sensory perception of sound						0			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179403334	179403334	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179403334delA	uc010zfg.1	-	303	91742	c.91518delT	c.(91516-91518)TTTfs	p.F30506fs	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.F24201fs|TTN_uc010zfi.1_Frame_Shift_Del_p.F24134fs|TTN_uc010zfj.1_Frame_Shift_Del_p.F24009fs	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	31433							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	179535860	179535860	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179535860delT	uc010zfg.1	-	151	31586	c.31362delA	c.(31360-31362)AAAfs	p.K10454fs	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.K7115fs|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_5'UTR	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	11381							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179558767	179558767	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179558767delT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron	NM_133378	NP_596869			titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179559936	179559936	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179559936delA	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)															---	---	---	---
CCDC141	285025	broad.mit.edu	37	2	179827892	179827892	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179827892delA	uc002ung.2	-											SubName: Full=Putative uncharacterized protein CCDC141; SubName: Full=Putative uncharacterized protein FLJ39502;								protein binding			ovary(7)|pancreas(2)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	180177668	180177668	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180177668delC								SESTD1 (48318 upstream) : ZNF385B (129052 downstream)																																			---	---	---	---
ZNF385B	151126	broad.mit.edu	37	2	180682392	180682393	+	Intron	INS	-	TG	TG	rs143388441	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180682392_180682393insTG	uc002unn.3	-							NM_152520	NP_689733			zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)															---	---	---	---
ZNF385B	151126	broad.mit.edu	37	2	180690630	180690630	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180690630delC	uc002unn.3	-							NM_152520	NP_689733			zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	180953209	180953209	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180953209delA								CWC22 (81369 upstream) : UBE2E3 (891903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	181201616	181201617	+	IGR	DEL	TT	-	-	rs111416880		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181201616_181201617delTT								CWC22 (329776 upstream) : UBE2E3 (643495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	181361454	181361456	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181361454_181361456delTTT								CWC22 (489614 upstream) : UBE2E3 (483656 downstream)																																			---	---	---	---
UBE2E3	10477	broad.mit.edu	37	2	181886359	181886360	+	Intron	INS	-	TTCC	TTCC	rs56152201		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181886359_181886360insTTCC	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																		---	---	---	---
UBE2E3	10477	broad.mit.edu	37	2	181887629	181887630	+	Intron	INS	-	G	G	rs139755943	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181887629_181887630insG	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																		---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183085832	183085832	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183085832delC	uc002uos.2	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc002uoq.1_Intron|PDE1A_uc010zfq.1_Intron|PDE1A_uc002uor.2_Intron|PDE1A_uc002uou.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	183645957	183645957	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183645957delT								DNAJC10 (2702 upstream) : FRZB (52780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	185874512	185874513	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185874512_185874513delTT								ZNF804A (70300 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	188080668	188080668	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188080668delT								ZSWIM2 (366771 upstream) : CALCRL (127183 downstream)																																			---	---	---	---
CALCRL	10203	broad.mit.edu	37	2	188224010	188224010	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188224010delA	uc002upv.3	-						CALCRL_uc010frt.2_Intron	NM_005795	NP_005786			calcitonin receptor-like precursor							integral to plasma membrane				lung(3)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)															---	---	---	---
CALCRL	10203	broad.mit.edu	37	2	188245317	188245317	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188245317delA	uc002upv.3	-						CALCRL_uc010frt.2_Intron	NM_005795	NP_005786			calcitonin receptor-like precursor							integral to plasma membrane				lung(3)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)															---	---	---	---
CALCRL	10203	broad.mit.edu	37	2	188250275	188250275	+	Frame_Shift_Del	DEL	A	-	-	rs13391909	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188250275delA	uc002upv.3	-	4	596	c.48delT	c.(46-48)TTTfs	p.F16fs	CALCRL_uc010frt.2_Frame_Shift_Del_p.F16fs	NM_005795	NP_005786	Q16602	CALRL_HUMAN	calcitonin receptor-like precursor	16						integral to plasma membrane				lung(3)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)															---	---	---	---
GULP1	51454	broad.mit.edu	37	2	189309141	189309141	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189309141delA	uc010fru.2	+						GULP1_uc002uqc.3_Intron|GULP1_uc002uqd.2_Intron|GULP1_uc010zfw.1_Intron|GULP1_uc002uqe.2_Intron|GULP1_uc002uqf.2_Intron|GULP1_uc002uqg.2_Intron	NM_016315	NP_057399			GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	190200483	190200483	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190200483delA								COL5A2 (155878 upstream) : WDR75 (105676 downstream)																																			---	---	---	---
WDR75	84128	broad.mit.edu	37	2	190329787	190329788	+	Intron	INS	-	T	T	rs113619469		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190329787_190329788insT	uc002uql.1	+						WDR75_uc002uqm.1_Intron|WDR75_uc002uqn.1_Intron|WDR75_uc002uqo.1_Intron	NM_032168	NP_115544			WD repeat domain 75							nucleolus				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	190841116	190841116	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190841116delG								PMS1 (98762 upstream) : MSTN (79311 downstream)																																			---	---	---	---
HIBCH	26275	broad.mit.edu	37	2	191129008	191129009	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191129008_191129009delTT	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	191179681	191179681	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191179681delT	uc002uru.2	-						HIBCH_uc002urv.2_Intron	NM_014362	NP_055177			3-hydroxyisobutyryl-Coenzyme A hydrolase isoform						branched chain family amino acid catabolic process	mitochondrial matrix	3-hydroxyisobutyryl-CoA hydrolase activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	191431442	191431444	+	IGR	DEL	AAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191431442_191431444delAAG								TMEM194B (31974 upstream) : NAB1 (82404 downstream)																																			---	---	---	---
STAT4	6775	broad.mit.edu	37	2	192013065	192013066	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192013065_192013066insT	uc002usm.1	-						STAT4_uc010zgm.1_Intron|STAT4_uc010zgn.1_Intron|STAT4_uc010zgo.1_Intron|STAT4_uc002usn.1_Intron|STAT4_uc002uso.2_Intron|STAT4_uc002usp.3_Intron|STAT4_uc010zgl.1_Intron	NM_003151	NP_003142			signal transducer and activator of transcription						JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(3)|skin(2)|lung(1)|ovary(1)|prostate(1)|pancreas(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)															---	---	---	---
MYO1B	4430	broad.mit.edu	37	2	192234257	192234257	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192234257delT	uc010fsg.2	+						MYO1B_uc002usq.2_Intron|MYO1B_uc002usr.2_Intron	NM_001130158	NP_001123630			myosin IB isoform 1							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)															---	---	---	---
MYO1B	4430	broad.mit.edu	37	2	192278713	192278713	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192278713delT	uc010fsg.2	+						MYO1B_uc002usq.2_Intron|MYO1B_uc002usr.2_Intron|MYO1B_uc002usu.2_Intron|MYO1B_uc002usv.2_Intron	NM_001130158	NP_001123630			myosin IB isoform 1							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)															---	---	---	---
TMEFF2	23671	broad.mit.edu	37	2	192933700	192933701	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192933700_192933701delTT	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)															---	---	---	---
TMEFF2	23671	broad.mit.edu	37	2	193056769	193056769	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193056769delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	193077595	193077596	+	IGR	DEL	TT	-	-	rs78149951		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193077595_193077596delTT								TMEFF2 (17951 upstream) : PCGEM1 (536975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193176298	193176298	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193176298delC								TMEFF2 (116654 upstream) : PCGEM1 (438273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193185973	193185973	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193185973delT								TMEFF2 (126329 upstream) : PCGEM1 (428598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193265799	193265800	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193265799_193265800delTT								TMEFF2 (206155 upstream) : PCGEM1 (348771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194556928	194556928	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194556928delT								PCGEM1 (915307 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195265125	195265125	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195265125delA	uc002utf.1	+											Homo sapiens, clone IMAGE:5242593, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	195344936	195344936	+	IGR	DEL	A	-	-	rs34302583		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195344936delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195379496	195379496	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195379496delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195604088	195604088	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195604088delA								None (None upstream) : SLC39A10 (917444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196163674	196163675	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196163674_196163675delCT								None (None upstream) : SLC39A10 (357857 downstream)																																			---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196617946	196617946	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196617946delT	uc002utj.3	-						DNAH7_uc002uti.3_Intron	NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196752769	196752769	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196752769delT	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196890151	196890151	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196890151delA	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
HECW2	57520	broad.mit.edu	37	2	197157708	197157708	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197157708delT	uc002utm.1	-						HECW2_uc002utl.1_Intron	NM_020760	NP_065811			HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18																		---	---	---	---
HECW2	57520	broad.mit.edu	37	2	197439160	197439160	+	Intron	DEL	A	-	-	rs80015553		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197439160delA	uc002utm.1	-							NM_020760	NP_065811			HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18																		---	---	---	---
CCDC150	284992	broad.mit.edu	37	2	197584490	197584491	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197584490_197584491delAA	uc002utp.1	+						CCDC150_uc010zgs.1_Intron|CCDC150_uc010zgt.1_Intron|CCDC150_uc002utq.1_Intron|CCDC150_uc002utr.1_Intron	NM_001080539	NP_001074008			coiled-coil domain containing 150												0																		---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	197996831	197996831	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197996831delA	uc002uuc.2	-						ANKRD44_uc002uua.1_Intron|ANKRD44_uc002uub.2_Intron|ANKRD44_uc010zgw.1_Intron	NM_153697	NP_710181			ankyrin repeat domain 44								protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
HSPD1	3329	broad.mit.edu	37	2	198360213	198360215	+	Intron	DEL	ATT	-	-	rs13432424		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198360213_198360215delATT	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)															---	---	---	---
MOBKL3	25843	broad.mit.edu	37	2	198400624	198400627	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198400624_198400627delTTTT	uc002uun.3	+						MOBKL3_uc002uum.3_Intron|MOBKL3_uc010fsn.2_Intron|MOBKL3_uc010fso.2_Intron|MOBKL3_uc010zgz.1_Intron	NM_015387	NP_056202			Mps One Binder kinase activator-like 3 isoform						transport	Golgi cisterna membrane|perinuclear region of cytoplasm	metal ion binding|protein binding				0			Epithelial(96;0.225)															---	---	---	---
PLCL1	5334	broad.mit.edu	37	2	198894460	198894460	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198894460delA	uc010fsp.2	+						PLCL1_uc002uuv.3_Intron	NM_001114661	NP_001108133			RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	199156888	199156888	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199156888delC								PLCL1 (142282 upstream) : SATB2 (977336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	199602003	199602007	+	IGR	DEL	TTTTT	-	-	rs35713774		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199602003_199602007delTTTTT								PLCL1 (587397 upstream) : SATB2 (532217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	200084144	200084144	+	IGR	DEL	A	-	-	rs34568040		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200084144delA								None (None upstream) : SATB2 (50080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	200092066	200092066	+	IGR	DEL	T	-	-	rs35567874		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200092066delT								None (None upstream) : SATB2 (42158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	200121945	200121945	+	IGR	DEL	T	-	-	rs116637237	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200121945delT								None (None upstream) : SATB2 (12279 downstream)																																			---	---	---	---
SATB2	23314	broad.mit.edu	37	2	200139489	200139489	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200139489delA	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																		---	---	---	---
C2orf69	205327	broad.mit.edu	37	2	200790166	200790167	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200790166_200790167insA	uc010zhb.1	+	2	898_899	c.715_716insA	c.(715-717)GAAfs	p.E239fs		NM_153689	NP_710156	Q8N8R5	CB069_HUMAN	hypothetical protein LOC205327 precursor	239						extracellular region				central_nervous_system(1)	1																		---	---	---	---
C2orf60	129450	broad.mit.edu	37	2	200800573	200800573	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200800573delA	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	200867301	200867301	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200867301delA								C2orf47 (38456 upstream) : SPATS2L (303303 downstream)																																			---	---	---	---
SPATS2L	26010	broad.mit.edu	37	2	201295160	201295161	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201295160_201295161insA	uc002uvn.3	+						SPATS2L_uc010fst.2_Intron|SPATS2L_uc002uvo.3_Intron|SPATS2L_uc002uvp.3_Intron|SPATS2L_uc002uvq.3_Intron|SPATS2L_uc002uvr.3_Intron|SPATS2L_uc010zhc.1_Intron	NM_015535	NP_056350			SPATS2-like protein isoform a							cytoplasm|nucleolus				ovary(2)|pancreas(1)	3																		---	---	---	---
AOX1	316	broad.mit.edu	37	2	201464493	201464494	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201464493_201464494insT	uc002uvx.2	+							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)													---	---	---	---
AOX1	316	broad.mit.edu	37	2	201495240	201495240	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)													---	---	---	---
AOX1	316	broad.mit.edu	37	2	201517742	201517742	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201517742delA	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)													---	---	---	---
CLK1	1195	broad.mit.edu	37	2	201721344	201721344	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201721344delA	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																		---	---	---	---
NIF3L1	60491	broad.mit.edu	37	2	201758150	201758150	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201758150delT	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	201855303	201855303	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201855303delT	uc002uws.3	-						FAM126B_uc002uwu.2_Intron|FAM126B_uc002uwv.2_Intron	NM_173822	NP_776183			hypothetical protein LOC285172							intracellular				ovary(1)	1																		---	---	---	---
FAM126B	285172	broad.mit.edu	37	2	201903652	201903653	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201903652_201903653delAA	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																		---	---	---	---
CASP10	843	broad.mit.edu	37	2	202082648	202082648	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202082648delT	uc002uxl.1	+						CASP10_uc002uxj.1_3'UTR|CASP10_uc002uxk.1_3'UTR|CASP10_uc010fta.1_3'UTR|CASP10_uc002uxm.1_Intron|CASP10_uc010ftb.1_RNA	NM_032974	NP_116756			caspase 10 isoform b preproprotein						apoptosis|induction of apoptosis by extracellular signals|proteolysis	cytosol|plasma membrane	cysteine-type endopeptidase activity|identical protein binding|protein binding			skin(3)|ovary(1)|pancreas(1)|breast(1)	6																		---	---	---	---
CASP10	843	broad.mit.edu	37	2	202086944	202086945	+	Intron	DEL	TT	-	-	rs67564130		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202086944_202086945delTT	uc002uxl.1	+						CASP10_uc002uxm.1_Intron	NM_032974	NP_116756			caspase 10 isoform b preproprotein						apoptosis|induction of apoptosis by extracellular signals|proteolysis	cytosol|plasma membrane	cysteine-type endopeptidase activity|identical protein binding|protein binding			skin(3)|ovary(1)|pancreas(1)|breast(1)	6																		---	---	---	---
TRAK2	66008	broad.mit.edu	37	2	202262685	202262686	+	Intron	DEL	TC	-	-	rs3839051		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202262685_202262686delTC	uc002uyb.3	-						TRAK2_uc002uyc.2_Intron	NM_015049	NP_055864			trafficking protein, kinesin binding 2							early endosome|plasma membrane	GABA receptor binding				0																		---	---	---	---
TRAK2	66008	broad.mit.edu	37	2	202306406	202306406	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202306406delT	uc002uyb.3	-						TRAK2_uc002uyc.2_Intron	NM_015049	NP_055864			trafficking protein, kinesin binding 2							early endosome|plasma membrane	GABA receptor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	202906378	202906378	+	IGR	DEL	A	-	-	rs113436236		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202906378delA								FZD7 (3218 upstream) : SUMO1 (164525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	203054920	203054920	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203054920delA	uc002uyy.1	+	7	3400	c.739delA	c.(739-741)AAAfs	p.K247fs						RecName: Full=Uncharacterized protein KIAA2012;																														---	---	---	---
SUMO1	7341	broad.mit.edu	37	2	203079026	203079026	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203079026delA	uc002uyz.1	-						SUMO1_uc002uza.1_Intron	NM_001005781	NP_001005781			SMT3 suppressor of mif two 3 homolog 1 isoform a						DNA repair|interferon-gamma-mediated signaling pathway|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|palate development|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein complex assembly|protein sumoylation|regulation of interferon-gamma-mediated signaling pathway|regulation of protein localization	cytoplasm|nuclear membrane|nuclear pore|nuclear speck	ubiquitin protein ligase binding				0																		---	---	---	---
SUMO1	7341	broad.mit.edu	37	2	203096349	203096349	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203096349delA	uc002uyz.1	-						SUMO1_uc002uza.1_Intron	NM_001005781	NP_001005781			SMT3 suppressor of mif two 3 homolog 1 isoform a						DNA repair|interferon-gamma-mediated signaling pathway|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|palate development|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein complex assembly|protein sumoylation|regulation of interferon-gamma-mediated signaling pathway|regulation of protein localization	cytoplasm|nuclear membrane|nuclear pore|nuclear speck	ubiquitin protein ligase binding				0																		---	---	---	---
NOP58	51602	broad.mit.edu	37	2	203149027	203149027	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203149027delT	uc002uzb.2	+						NOP58_uc010zhv.1_Intron	NM_015934	NP_057018			NOP58 ribonucleoprotein homolog						cell growth|rRNA processing|snRNP protein import into nucleus	box C/D snoRNP complex|Cajal body|cytoplasm|pre-snoRNP complex	protein binding|snoRNA binding				0																		---	---	---	---
BMPR2	659	broad.mit.edu	37	2	203397633	203397634	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203397633_203397634delTT	uc002uzf.3	+						BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195			bone morphogenetic protein receptor type II						anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9																		---	---	---	---
ICA1L	130026	broad.mit.edu	37	2	203680781	203680781	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203680781delT	uc002uzh.1	-						ICA1L_uc002uzi.1_Intron	NM_138468	NP_612477			islet cell autoantigen 1,69kDa-like isoform 1												0																		---	---	---	---
NBEAL1	65065	broad.mit.edu	37	2	204018651	204018652	+	Intron	INS	-	T	T	rs76640292	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204018651_204018652insT	uc002uzt.3	+						NBEAL1_uc002uzs.3_Intron	NM_001114132	NP_001107604			neurobeachin-like 1 isoform 3								binding			ovary(1)|skin(1)	2																		---	---	---	---
NBEAL1	65065	broad.mit.edu	37	2	204034460	204034460	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204034460delT	uc002uzt.3	+						NBEAL1_uc002uzs.3_Intron	NM_001114132	NP_001107604			neurobeachin-like 1 isoform 3								binding			ovary(1)|skin(1)	2																		---	---	---	---
CYP20A1	57404	broad.mit.edu	37	2	204134813	204134814	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204134813_204134814delAA	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																		---	---	---	---
ABI2	10152	broad.mit.edu	37	2	204251754	204251754	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204251754delT	uc002vaa.2	+						ABI2_uc010zig.1_Intron|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	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	204292195	204292197	+	3'UTR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204292195_204292197delTTT	uc002vaa.2	+	11					ABI2_uc002uzz.2_3'UTR|ABI2_uc010zih.1_3'UTR|ABI2_uc010zii.1_3'UTR|ABI2_uc010zij.1_3'UTR|ABI2_uc002vab.2_3'UTR|ABI2_uc010zik.1_3'UTR|ABI2_uc010zil.1_3'UTR|ABI2_uc010zim.1_3'UTR|ABI2_uc002vac.2_3'UTR|ABI2_uc010zin.1_3'UTR	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	204761437	204761437	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204761437delA								CTLA4 (22754 upstream) : ICOS (40034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	204984692	204984693	+	IGR	DEL	TT	-	-	rs67581003		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204984692_204984693delTT								ICOS (158396 upstream) : PARD3B (425823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	206508775	206508776	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206508775_206508776delGT								PARD3B (28238 upstream) : NRP2 (38448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	206534532	206534532	+	IGR	DEL	G	-	-	rs2540812	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206534532delG								PARD3B (53995 upstream) : NRP2 (12692 downstream)																																			---	---	---	---
INO80D	54891	broad.mit.edu	37	2	206874786	206874787	+	Intron	INS	-	ACACACACAC	ACACACACAC	rs144790541	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206874786_206874787insACACACACAC	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																		---	---	---	---
NDUFS1	4719	broad.mit.edu	37	2	206997836	206997837	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206997836_206997837delAA	uc002vbe.2	-						NDUFS1_uc010ziq.1_Intron|NDUFS1_uc010zir.1_Intron|NDUFS1_uc010zis.1_Intron|NDUFS1_uc010zit.1_Intron|NDUFS1_uc010ziu.1_Intron	NM_005006	NP_004997			NADH dehydrogenase (ubiquinone) Fe-S protein 1,						apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	207304000	207304000	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207304000delT								ZDBF2 (124852 upstream) : ADAM23 (4368 downstream)																																			---	---	---	---
ADAM23	8745	broad.mit.edu	37	2	207446610	207446610	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207446610delT	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)														---	---	---	---
LOC200726	200726	broad.mit.edu	37	2	207512390	207512391	+	Intron	INS	-	AGAG	AGAG	rs5838038		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207512390_207512391insAGAG	uc010fuh.1	+							NM_001102659	NP_001096129			hypothetical protein LOC200726												0				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.115)|Lung(261;0.133)														---	---	---	---
CREB1	1385	broad.mit.edu	37	2	208442484	208442484	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208442484delT	uc002vcc.2	+						CREB1_uc002vcd.2_Intron	NM_134442	NP_604391			cAMP responsive element binding protein 1						activation of phospholipase C activity|axon guidance|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|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		protein dimerization activity|transcription cofactor activity		EWSR1/CREB1(42)	soft_tissue(42)|breast(1)|central_nervous_system(1)	44				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Bromocriptine(DB01200)|Naloxone(DB01183)			T	EWSR1	clear cell sarcoma|angiomatoid fibrous histiocytoma								---	---	---	---
CCNYL1	151195	broad.mit.edu	37	2	208573830	208573830	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208573830delT	uc002vci.2	+						CCNYL1_uc002vch.2_5'Flank	NM_001142300	NP_001135772			cyclin Y-like 1 isoform 1						regulation of cyclin-dependent protein kinase activity		protein kinase binding				0				LUSC - Lung squamous cell carcinoma(261;0.0731)|Epithelial(149;0.139)|Lung(261;0.14)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	208971409	208971409	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208971409delC								PLEKHM3 (81125 upstream) : CRYGD (14923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	209022190	209022190	+	IGR	DEL	T	-	-	rs76626322		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209022190delT								CRYGB (11313 upstream) : CRYGA (3275 downstream)																																			---	---	---	---
CRYGA	1418	broad.mit.edu	37	2	209025576	209025577	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209025576_209025577insC	uc002vcq.3	-	3	493_494	c.476_477insG	c.(475-477)GGTfs	p.G159fs		NM_014617	NP_055432	P11844	CRGA_HUMAN	crystallin, gamma A	159	Beta/gamma crystallin 'Greek key' 4.				visual perception		structural constituent of eye lens				0				Epithelial(149;0.067)|LUSC - Lung squamous cell carcinoma(261;0.0708)|Lung(261;0.135)														---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210393866	210393866	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210393866delA	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)													---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210545254	210545255	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210545254_210545255insT	uc002vde.1	+						MAP2_uc002vdc.1_Intron|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Intron	NM_002374	NP_002365			microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210562575	210562575	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210562575delT	uc002vde.1	+						MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Intron	NM_002374	NP_002365			microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
MYL1	4632	broad.mit.edu	37	2	211180075	211180075	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211180075delC	uc002vec.2	-							NM_079420	NP_524144			fast skeletal myosin alkali light chain 1						muscle filament sliding|muscle organ development	cytosol|muscle myosin complex|sarcomere	calcium ion binding|structural constituent of muscle			ovary(1)	1				Epithelial(149;0.00573)|Lung(261;0.0422)|LUSC - Lung squamous cell carcinoma(261;0.0444)|all cancers(144;0.057)														---	---	---	---
CPS1	1373	broad.mit.edu	37	2	211370854	211370854	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211370854delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	211570580	211570580	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211570580delA								CPS1 (26751 upstream) : ERBB4 (669862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	211753859	211753860	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211753859_211753860insT								CPS1 (210030 upstream) : ERBB4 (486582 downstream)																																			---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212352903	212352903	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212352903delC	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	212469214	212469214	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212469214delT	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	213027823	213027824	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213027823_213027824insA	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	213403254	213403254	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213403254delT	uc002veg.1	-	1	99	c.1delA	c.(1-3)ATGfs	p.M1fs	ERBB4_uc002veh.1_Frame_Shift_Del_p.M1fs|ERBB4_uc010zji.1_Frame_Shift_Del_p.M1fs|ERBB4_uc010zjj.1_Frame_Shift_Del_p.M1fs|ERBB4_uc010fut.1_Frame_Shift_Del_p.M1fs	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	1					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	213748811	213748812	+	IGR	INS	-	TGTG	TGTG	rs139389966	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213748811_213748812insTGTG								ERBB4 (345459 upstream) : IKZF2 (115601 downstream)																																			---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214207509	214207509	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214207509delT	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron|SPAG16_uc002vep.1_Intron|SPAG16_uc002ves.1_Intron	NM_024532	NP_078808			sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)														---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214715413	214715413	+	Intron	DEL	T	-	-	rs142268680		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214715413delT	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808			sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)														---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	215056711	215056711	+	Intron	DEL	A	-	-	rs73081037	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215056711delA	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)														---	---	---	---
VWC2L	402117	broad.mit.edu	37	2	215343193	215343193	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215343193delA	uc002vet.2	+						VWC2L_uc010zjl.1_Intron	NM_001080500	NP_001073969			von Willebrand factor C domain-containing							extracellular region					0																		---	---	---	---
BARD1	580	broad.mit.edu	37	2	215602671	215602672	+	Intron	INS	-	A	A	rs147608815	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215602671_215602672insA	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				---	---	---	---
ATIC	471	broad.mit.edu	37	2	216196913	216196914	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216196913_216196914insT	uc002vex.3	+						ATIC_uc010zjo.1_Intron|ATIC_uc002vey.3_Intron	NM_004044	NP_004035			5-aminoimidazole-4-carboxamide ribonucleotide						IMP biosynthetic process|purine base metabolic process	cytosol	IMP cyclohydrolase activity|phosphoribosylaminoimidazolecarboxamide formyltransferase activity|protein homodimerization activity		ATIC/ALK(24)	haematopoietic_and_lymphoid_tissue(22)|ovary(2)|lung(2)|soft_tissue(2)|skin(1)	29		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Tetrahydrofolic acid(DB00116)			T	ALK	ALCL								---	---	---	---
FN1	2335	broad.mit.edu	37	2	216243237	216243237	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216243237delA	uc002vfa.2	-						FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_Intron|FN1_uc010zjp.1_Intron|FN1_uc002vfk.1_5'Flank|FN1_uc010fva.1_5'Flank|FN1_uc010fvb.1_5'Flank|FN1_uc010fvc.1_Intron|FN1_uc010fvd.1_Intron	NM_212482	NP_997647			fibronectin 1 isoform 1 preproprotein						acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	216328174	216328174	+	IGR	DEL	A	-	-	rs34905717		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216328174delA								FN1 (27383 upstream) : MREG (479141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	216463615	216463616	+	IGR	INS	-	ACACACACAC	ACACACACAC	rs146436460	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216463615_216463616insACACACACAC								FN1 (162824 upstream) : MREG (343699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	216693510	216693510	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216693510delT	uc002vfm.1	-						uc002vfn.1_5'Flank					Homo sapiens cDNA FLJ34546 fis, clone HLUNG2008959.																												OREG0015174	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	2	216705241	216705241	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216705241delA	uc002vfm.1	-											Homo sapiens cDNA FLJ34546 fis, clone HLUNG2008959.																														---	---	---	---
PECR	55825	broad.mit.edu	37	2	216884749	216884749	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)													---	---	---	---
MARCH4	57574	broad.mit.edu	37	2	217139260	217139260	+	Intron	DEL	A	-	-	rs112433986		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217139260delA	uc002vgb.2	-							NM_020814	NP_065865			membrane-associated ring finger (C3HC4) 4							Golgi membrane|Golgi stack|integral to membrane|trans-Golgi network	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)														---	---	---	---
MARCH4	57574	broad.mit.edu	37	2	217172262	217172262	+	Intron	DEL	T	-	-	rs67744243		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217172262delT	uc002vgb.2	-							NM_020814	NP_065865			membrane-associated ring finger (C3HC4) 4							Golgi membrane|Golgi stack|integral to membrane|trans-Golgi network	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	217481339	217481340	+	IGR	DEL	GT	-	-	rs111458346		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217481339_217481340delGT								RPL37A (115153 upstream) : IGFBP2 (16787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217833080	217833080	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217833080delT								TNP1 (108298 upstream) : DIRC3 (315668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	218639389	218639389	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218639389delG								DIRC3 (18073 upstream) : TNS1 (25123 downstream)																																			---	---	---	---
TNS1	7145	broad.mit.edu	37	2	218834724	218834725	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218834724_218834725delAA	uc010fvk.1	-						TNS1_uc002vgv.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	219016281	219016281	+	IGR	DEL	A	-	-	rs76144481		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219016281delA								CXCR2 (14306 upstream) : CXCR1 (11289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	219022680	219022680	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219022680delT								CXCR2 (20705 upstream) : CXCR1 (4890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	219065979	219065979	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219065979delA								CXCR1 (34263 upstream) : ARPC2 (15895 downstream)																																			---	---	---	---
ARPC2	10109	broad.mit.edu	37	2	219100229	219100229	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219100229delT	uc002vhd.2	+						ARPC2_uc002vhe.2_Intron|ARPC2_uc002vhf.2_5'UTR	NM_152862	NP_690601			actin related protein 2/3 complex subunit 2						cellular component movement	Arp2/3 protein complex|cell projection|Golgi apparatus	actin binding|structural constituent of cytoskeleton			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;1.21e-06)|all cancers(144;0.000212)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0103)														---	---	---	---
CTDSP1	58190	broad.mit.edu	37	2	219265994	219265995	+	Intron	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219265994_219265995insTG	uc002vhy.2	+						CTDSP1_uc002vhx.2_Intron|CTDSP1_uc002vhz.2_5'Flank|uc010zkd.1_5'Flank|MIR26B_hsa-mir-26b|MI0000084_5'Flank	NM_021198	NP_067021			CTD (carboxy-terminal domain, RNA polymerase II,						protein dephosphorylation|regulation of transcription from RNA polymerase II promoter	nucleus	CTD phosphatase activity|metal ion binding|protein binding			ovary(1)	1		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	219272180	219272180	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219272180delC								CTDSP1 (1517 upstream) : VIL1 (11658 downstream)																																			---	---	---	---
VIL1	7429	broad.mit.edu	37	2	219306118	219306118	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219306118delA	uc002via.2	+						VIL1_uc010zke.1_Intron|VIL1_uc002vib.2_Intron	NM_007127	NP_009058			villin 1						actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	219705208	219705208	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219705208delA								PRKAG3 (8696 upstream) : WNT6 (19338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	219832127	219832127	+	IGR	DEL	A	-	-	rs76602847		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219832127delA								CDK5R2 (5251 upstream) : LOC151300 (8879 downstream)																																			---	---	---	---
ATG9A	79065	broad.mit.edu	37	2	220091409	220091409	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220091409delA	uc002vke.1	-						ATG9A_uc002vkd.1_Intron|ATG9A_uc002vkf.1_Intron	NM_001077198	NP_001070666			APG9 autophagy 9-like 1						autophagic vacuole assembly|protein transport	autophagic vacuole membrane|cytoplasmic vesicle|Golgi apparatus|integral to membrane|late endosome membrane				skin(1)	1		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
TMEM198	130612	broad.mit.edu	37	2	220411501	220411504	+	Intron	DEL	TTTT	-	-	rs141021062		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220411501_220411504delTTTT	uc002vme.2	+						TMEM198_uc002vmf.2_Intron	NM_001005209	NP_001005209			transmembrane protein 198							integral to membrane				ovary(1)	1		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)														---	---	---	---
SLC4A3	6508	broad.mit.edu	37	2	220505024	220505024	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220505024delC	uc002vmp.3	+						SLC4A3_uc002vmo.3_Intron|SLC4A3_uc010fwm.2_Intron	NM_005070	NP_005061			solute carrier family 4, anion exchanger, member						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	221214060	221214060	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221214060delT								SLC4A3 (707359 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221246066	221246066	+	IGR	DEL	T	-	-	rs146655990		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221246066delT								SLC4A3 (739365 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221627509	221627509	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221627509delA								None (None upstream) : EPHA4 (655240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221833115	221833115	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221833115delT								None (None upstream) : EPHA4 (449634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221981462	221981462	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221981462delA								None (None upstream) : EPHA4 (301287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222209260	222209260	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222209260delT								None (None upstream) : EPHA4 (73489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222875419	222875419	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222875419delT								EPHA4 (436497 upstream) : PAX3 (189188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222908747	222908747	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222908747delT								EPHA4 (469825 upstream) : PAX3 (155860 downstream)																																			---	---	---	---
SGPP2	130367	broad.mit.edu	37	2	223328689	223328690	+	Intron	INS	-	GT	GT	rs150701979	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223328689_223328690insGT	uc010zlo.1	+						SGPP2_uc010zlp.1_Intron	NM_152386	NP_689599			sphingosine-1-phosphate phosphotase 2						sphingosine metabolic process	endoplasmic reticulum membrane|integral to membrane	dihydrosphingosine-1-phosphate phosphatase activity|sphingosine-1-phosphate phosphatase activity			central_nervous_system(1)|skin(1)	2		Renal(207;0.0376)		Epithelial(121;2.08e-09)|all cancers(144;9.25e-07)|LUSC - Lung squamous cell carcinoma(224;0.011)|Lung(261;0.0143)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	223636883	223636884	+	IGR	DEL	TG	-	-	rs113912430		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223636883_223636884delTG								MOGAT1 (62234 upstream) : ACSL3 (88848 downstream)																																			---	---	---	---
ACSL3	2181	broad.mit.edu	37	2	223789443	223789443	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223789443delA	uc002vni.2	+						ACSL3_uc002vnj.2_Intron	NM_004457	NP_004448			acyl-CoA synthetase long-chain family member 3						long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|fatty-acyl-CoA synthase activity|long-chain fatty acid-CoA ligase activity|protein binding			ovary(2)	2		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)			T	ETV1	prostate								---	---	---	---
Unknown	0	broad.mit.edu	37	2	224059792	224059792	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224059792delC								KCNE4 (139439 upstream) : SCG2 (401868 downstream)																																			---	---	---	---
WDFY1	57590	broad.mit.edu	37	2	224749570	224749571	+	Intron	INS	-	TTC	TTC	rs142075274	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224749570_224749571insTTC	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)														---	---	---	---
WDFY1	57590	broad.mit.edu	37	2	224791365	224791368	+	Intron	DEL	GTGC	-	-	rs58786494		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224791365_224791368delGTGC	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	224905385	224905385	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224905385delT	uc002vnu.2	-						SERPINE2_uc010zlr.1_5'Flank|SERPINE2_uc002vnv.2_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	225090257	225090258	+	IGR	INS	-	CC	CC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225090257_225090258insCC								SERPINE2 (186221 upstream) : FAM124B (153158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	225303400	225303402	+	IGR	DEL	CTT	-	-	rs10534246		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225303400_225303402delCTT								FAM124B (36689 upstream) : CUL3 (31467 downstream)																																			---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225706624	225706624	+	Intron	DEL	A	-	-	rs80175418		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225706624delA	uc010fwz.1	-						DOCK10_uc002vob.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)														---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225778227	225778228	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225778227_225778228delGT	uc010fwz.1	-						DOCK10_uc002vob.2_Intron|DOCK10_uc002vod.1_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	225936885	225936886	+	IGR	INS	-	TG	TG	rs143811274	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225936885_225936886insTG								DOCK10 (29555 upstream) : KIAA1486 (328716 downstream)																																			---	---	---	---
KIAA1486	57624	broad.mit.edu	37	2	226506198	226506199	+	Intron	INS	-	T	T	rs55641842		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226506198_226506199insT	uc002voe.2	+						KIAA1486_uc010fxa.1_Intron|KIAA1486_uc002vof.1_Intron	NM_020864	NP_065915			hypothetical protein LOC57624											ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	226703643	226703644	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226703643_226703644insA								KIAA1486 (108172 upstream) : IRS1 (892390 downstream)																																			---	---	---	---
COL4A4	1286	broad.mit.edu	37	2	227942416	227942416	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227942416delA	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	227985652	227985652	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227985652delA	uc010zlt.1	-							NM_000092	NP_000083			alpha 4 type IV collagen precursor						axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	228460068	228460068	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228460068delT								AGFG1 (34130 upstream) : C2orf83 (14739 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	228460111	228460111	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228460111delT								AGFG1 (34173 upstream) : C2orf83 (14696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	228620811	228620812	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228620811_228620812delTT								SLC19A3 (38066 upstream) : CCL20 (57746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	228667176	228667176	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228667176delA								SLC19A3 (84431 upstream) : CCL20 (11382 downstream)																																			---	---	---	---
WDR69	164781	broad.mit.edu	37	2	228788462	228788462	+	Intron	DEL	A	-	-	rs78456977		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228788462delA	uc002vpn.1	+						WDR69_uc010zlw.1_Intron|WDR69_uc002vpo.1_Intron	NM_178821	NP_849143			WD repeat domain 69											breast(1)	1		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;1.22e-10)|all cancers(144;8.11e-08)|Lung(261;0.011)|LUSC - Lung squamous cell carcinoma(224;0.0148)														---	---	---	---
SPHKAP	80309	broad.mit.edu	37	2	228846310	228846310	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228846310delT	uc002vpq.2	-	12					SPHKAP_uc002vpp.2_3'UTR|SPHKAP_uc010zlx.1_3'UTR	NM_001142644	NP_001136116			sphingosine kinase type 1-interacting protein							cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	229334781	229334782	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229334781_229334782insA								SPHKAP (288420 upstream) : PID1 (553908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229505631	229505631	+	IGR	DEL	A	-	-	rs7563197		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229505631delA								SPHKAP (459270 upstream) : PID1 (383059 downstream)																																			---	---	---	---
DNER	92737	broad.mit.edu	37	2	230422453	230422453	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230422453delA	uc002vpv.2	-						DNER_uc010zly.1_Intron	NM_139072	NP_620711			delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)														---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230643753	230643753	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230643753delT	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.1_Intron	NM_004238	NP_004229			thyroid hormone receptor interactor 12						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)														---	---	---	---
SLC16A14	151473	broad.mit.edu	37	2	230902403	230902403	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230902403delT	uc002vqd.1	-						FBXO36_uc010fxi.1_Intron	NM_152527	NP_689740			solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			ovary(4)|skin(2)	6		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)														---	---	---	---
SP140L	93349	broad.mit.edu	37	2	231193355	231193355	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231193355delT	uc010fxm.1	+						SP140_uc010zma.1_Intron	NM_138402	NP_612411			SP140 nuclear body protein-like							nucleus	DNA binding|metal ion binding			central_nervous_system(1)	1																		---	---	---	---
SP140L	93349	broad.mit.edu	37	2	231260130	231260130	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231260130delA	uc010fxm.1	+						SP140L_uc010fxo.1_Intron	NM_138402	NP_612411			SP140 nuclear body protein-like							nucleus	DNA binding|metal ion binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	231744859	231744860	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231744859_231744860delTT								ITM2C (897 upstream) : GPR55 (27174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	232043655	232043655	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232043655delA								PSMD1 (6182 upstream) : ARMC9 (19687 downstream)																																			---	---	---	---
ARMC9	80210	broad.mit.edu	37	2	232065557	232065557	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232065557delA	uc002vrq.3	+						ARMC9_uc002vrp.3_Intron	NM_025139	NP_079415			armadillo repeat containing 9								binding			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)														---	---	---	---
ARMC9	80210	broad.mit.edu	37	2	232121096	232121096	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232121096delT	uc002vrq.3	+						ARMC9_uc002vrp.3_Intron	NM_025139	NP_079415			armadillo repeat containing 9								binding			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)														---	---	---	---
ARMC9	80210	broad.mit.edu	37	2	232129810	232129811	+	Intron	DEL	AA	-	-	rs77609981		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232129810_232129811delAA	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	232344724	232344724	+	IGR	DEL	T	-	-	rs66513453		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232344724delT								NCL (15519 upstream) : C2orf52 (28413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	232386673	232386673	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232386673delT								C2orf52 (7623 upstream) : NMUR1 (1199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	232509782	232509785	+	IGR	DEL	CTTT	-	-	rs144976269		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232509782_232509785delCTTT								C2orf57 (50790 upstream) : PTMA (63450 downstream)																																			---	---	---	---
COPS7B	64708	broad.mit.edu	37	2	232656425	232656425	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232656425delT	uc002vsg.1	+						COPS7B_uc010fxy.1_Intron|COPS7B_uc002vsh.1_Intron|COPS7B_uc002vsi.1_Intron|COPS7B_uc002vsj.1_Intron|COPS7B_uc002vsk.1_5'Flank	NM_022730	NP_073567			COP9 constitutive photomorphogenic homolog						cullin deneddylation	cytoplasm|signalosome				ovary(1)|liver(1)|skin(1)	3		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;1.36e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00136)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)														---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	233172218	233172218	+	Intron	DEL	T	-	-	rs34030272		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233172218delT	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	233455295	233455304	+	IGR	DEL	GTGTGTGTGT	-	-	rs71985927		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233455295_233455304delGTGTGTGTGT								EIF4E2 (6946 upstream) : EFHD1 (15463 downstream)																																			---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233756672	233756689	+	Intron	DEL	GCAGGGATGGCAGGGACG	-	-	rs150626527		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233756672_233756689delGCAGGGATGGCAGGGACG	uc002vts.2	-						NGEF_uc010zmm.1_Intron|NGEF_uc010fyg.1_Intron	NM_019850	NP_062824			neuronal guanine nucleotide exchange factor						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)														---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	233970516	233970517	+	Intron	DEL	GA	-	-	rs116307041	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233970516_233970517delGA	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	233989932	233989932	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233989932delG	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	234079896	234079896	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234079896delA	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)														---	---	---	---
ATG16L1	55054	broad.mit.edu	37	2	234200699	234200699	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234200699delT	uc002vty.2	+						ATG16L1_uc002vtx.1_Intron|ATG16L1_uc002vua.2_Intron|ATG16L1_uc002vub.2_Intron|ATG16L1_uc002vtz.2_Intron|ATG16L1_uc002vud.3_Intron	NM_030803	NP_110430			APG16 autophagy 16-like isoform 1						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)														---	---	---	---
DGKD	8527	broad.mit.edu	37	2	234305619	234305619	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234305619delG	uc002vui.1	+						DGKD_uc002vuj.1_Intron	NM_152879	NP_690618			diacylglycerol kinase, delta 130kDa isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	234506245	234506245	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234506245delT								USP40 (30817 upstream) : UGT1A8 (20046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	234808357	234808357	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234808357delT								MSL3L2 (31302 upstream) : TRPM8 (17686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235291718	235291718	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235291718delA								SPP2 (305942 upstream) : ARL4C (109970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235315449	235315449	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235315449delT								SPP2 (329673 upstream) : ARL4C (86239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235487159	235487160	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235487159_235487160delAC								ARL4C (81466 upstream) : SH3BP4 (373468 downstream)																																			---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236791974	236791975	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236791974_236791975insT	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	236804544	236804547	+	Intron	DEL	AAAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236804544_236804547delAAAG	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	236953412	236953413	+	Intron	DEL	CA	-	-	rs34701466		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236953412_236953413delCA	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	237551339	237551339	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237551339delC								CXCR7 (60347 upstream) : COPS8 (442745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	238144344	238144345	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238144344_238144345insT								COPS8 (136857 upstream) : COL6A3 (88310 downstream)																																			---	---	---	---
LRRFIP1	9208	broad.mit.edu	37	2	238618927	238618927	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238618927delT	uc002vxe.2	+						LRRFIP1_uc002vxc.2_Intron|LRRFIP1_uc010znm.1_Intron|LRRFIP1_uc002vxd.2_Intron|LRRFIP1_uc002vxf.2_Intron	NM_001137552	NP_001131024			leucine rich repeat (in FLII) interacting						negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|cytoskeleton|nucleus	DNA binding|double-stranded RNA binding|protein binding			breast(3)	3		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	238761138	238761139	+	IGR	DEL	TT	-	-	rs34721995		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238761138_238761139delTT								RBM44 (9688 upstream) : RAMP1 (7048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	239132916	239132917	+	IGR	INS	-	A	A	rs140678665	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239132916_239132917insA								ILKAP (20592 upstream) : LOC151174 (837 downstream)																																			---	---	---	---
PER2	8864	broad.mit.edu	37	2	239168597	239168597	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239168597delT	uc002vyc.2	-						PER2_uc010znv.1_Intron	NM_022817	NP_073728			period 2						circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			upper_aerodigestive_tract(1)|breast(1)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)														---	---	---	---
TRAF3IP1	26146	broad.mit.edu	37	2	239235149	239235149	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239235149delT	uc002vye.2	+						TRAF3IP1_uc002vyf.2_Intron	NM_015650	NP_056465			TNF receptor-associated factor 3 interacting							cytoplasm|cytoskeleton	protein binding			ovary(1)	1		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)														---	---	---	---
TRAF3IP1	26146	broad.mit.edu	37	2	239270892	239270893	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239270892_239270893delTT	uc002vye.2	+						TRAF3IP1_uc002vyf.2_Intron	NM_015650	NP_056465			TNF receptor-associated factor 3 interacting							cytoplasm|cytoskeleton	protein binding			ovary(1)	1		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	239864606	239864606	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239864606delT								TWIST2 (32369 upstream) : HDAC4 (105259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	239961625	239961626	+	IGR	INS	-	ACAT	ACAT	rs78703038		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239961625_239961626insACAT								TWIST2 (129388 upstream) : HDAC4 (8239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	240587723	240587723	+	IGR	DEL	A	-	-	rs76915488		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240587723delA								HDAC4 (264377 upstream) : NDUFA10 (312435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	240731646	240731646	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240731646delT								HDAC4 (408300 upstream) : NDUFA10 (168512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	241362370	241362370	+	IGR	DEL	A	-	-	rs76162500		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241362370delA								OTOS (282297 upstream) : GPC1 (12745 downstream)																																			---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241757461	241757462	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241757461_241757462insG	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)														---	---	---	---
MTERFD2	130916	broad.mit.edu	37	2	242038497	242038499	+	Intron	DEL	TTT	-	-	rs67371529		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242038497_242038499delTTT	uc002wan.1	-						MTERFD2_uc010zoj.1_Intron|MTERFD2_uc010zok.1_Intron	NM_182501	NP_872307			MTERF domain containing 2											ovary(1)	1		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)														---	---	---	---
HDLBP	3069	broad.mit.edu	37	2	242176393	242176400	+	Intron	DEL	GGGGGGGG	-	-	rs72214250	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242176393_242176400delGGGGGGGG	uc002waz.2	-						HDLBP_uc002wba.2_Intron|HDLBP_uc002wbb.2_Intron	NM_203346	NP_976221			high density lipoprotein binding protein						cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)														---	---	---	---
FARP2	9855	broad.mit.edu	37	2	242433013	242433013	+	Intron	DEL	T	-	-	rs113589065		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242433013delT	uc002wbi.1	+							NM_014808	NP_055623			FERM, RhoGEF and pleckstrin domain protein 2						axon guidance|neuron remodeling|Rac protein signal transduction|regulation of Rho protein signal transduction	cytoskeleton|cytosol|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)														---	---	---	---
BOK	666	broad.mit.edu	37	2	242511585	242511586	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242511585_242511586delAC	uc002wbq.2	+						BOK_uc002wbr.2_5'Flank	NM_032515	NP_115904			BCL2-related ovarian killer						activation of caspase activity|cell proliferation|signal transduction by p53 class mediator resulting in induction of apoptosis	mitochondrial membrane|nucleus				ovary(1)	1		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.04e-33)|all cancers(36;7.87e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.52e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.64e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0835)														---	---	---	---
GAL3ST2	64090	broad.mit.edu	37	2	242716014	242716014	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242716014delC	uc002wcj.1	+							NM_022134	NP_071417			galactose-3-O-sulfotransferase 2						biosynthetic process	Golgi cisterna membrane|integral to membrane	galactosylceramide sulfotransferase 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;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)														---	---	---	---
NEU4	129807	broad.mit.edu	37	2	242751353	242751353	+	Intron	DEL	G	-	-	rs74594321		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242751353delG	uc010fzr.2	+						uc002wck.1_Intron|NEU4_uc002wcl.2_Intron|NEU4_uc002wcm.2_Intron|NEU4_uc002wcn.1_5'Flank|NEU4_uc002wco.1_5'Flank|NEU4_uc002wcp.1_5'Flank	NM_080741	NP_542779			sialidase 4							lysosomal lumen|organelle inner membrane	exo-alpha-sialidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	475305	475305	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:475305delT								CHL1 (24210 upstream) : CNTN6 (659315 downstream)																																			---	---	---	---
CNTN6	27255	broad.mit.edu	37	3	1151997	1151997	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1151997delT	uc003boz.2	+						CNTN6_uc010hbo.2_Intron|CNTN6_uc011asj.1_Intron|CNTN6_uc003bpa.2_Intron	NM_014461	NP_055276			contactin 6 precursor						axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)														---	---	---	---
CNTN6	27255	broad.mit.edu	37	3	1262335	1262335	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1262335delT	uc003boz.2	+						CNTN6_uc010hbo.2_Intron|CNTN6_uc011asj.1_Intron|CNTN6_uc003bpa.2_Intron	NM_014461	NP_055276			contactin 6 precursor						axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	2004475	2004475	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2004475delG								CNTN6 (559198 upstream) : CNTN4 (136075 downstream)																																			---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2889025	2889025	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2889025delA	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	2980020	2980020	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2980020delT	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	3103806	3103807	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3103806_3103807delAA								CNTN4 (4162 upstream) : IL5RA (7594 downstream)																																			---	---	---	---
CRBN	51185	broad.mit.edu	37	3	3204001	3204001	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3204001delT	uc003bpq.2	-						CRBN_uc003bpr.2_Intron|CRBN_uc010hbw.2_Intron|CRBN_uc011aso.1_Intron	NM_016302	NP_057386			cereblon						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	3320089	3320089	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3320089delT								CRBN (98699 upstream) : SUMF1 (502947 downstream)																																			---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	3973579	3973580	+	Intron	INS	-	C	C	rs2442821		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3973579_3973580insC	uc003bps.1	-							NM_182760				sulfatase modifying factor 1 isoform 1							endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)														---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	4419019	4419019	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4419019delA	uc003bpz.1	-						SUMF1_uc003bps.1_Intron|SUMF1_uc011ass.1_Intron|SUMF1_uc010hby.1_Intron|SUMF1_uc011ast.1_Intron	NM_182760	NP_877437			sulfatase modifying factor 1 isoform 1							endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)														---	---	---	---
ITPR1	3708	broad.mit.edu	37	3	4620164	4620165	+	Intron	INS	-	TG	TG	rs143203883	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4620164_4620165insTG	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)														---	---	---	---
ITPR1	3708	broad.mit.edu	37	3	4646657	4646658	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4646657_4646658delTT	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	5082533	5082533	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5082533delT								BHLHE40 (55670 upstream) : ARL8B (81397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5689511	5689511	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5689511delA								EDEM1 (427862 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6399542	6399542	+	IGR	DEL	A	-	-	rs11325381		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6399542delA								None (None upstream) : GRM7 (503260 downstream)																																			---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7235353	7235354	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7235353_7235354delCT	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7342850	7342851	+	Intron	INS	-	T	T	rs140844063	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7342850_7342851insT	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7349043	7349044	+	Intron	INS	-	AAAGA	AAAGA	rs138019894	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7349043_7349044insAAAGA	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7409411	7409411	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7409411delA	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7453721	7453722	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7453721_7453722delCT	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7468170	7468170	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7468170delT	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	7832964	7832965	+	IGR	INS	-	A	A	rs111704262		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7832964_7832965insA								GRM7 (49746 upstream) : LMCD1 (710546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	7921691	7921691	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7921691delA								GRM7 (138473 upstream) : LMCD1 (621820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	8160958	8160958	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8160958delA								GRM7 (377740 upstream) : LMCD1 (382553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	8161725	8161726	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8161725_8161726insT								GRM7 (378507 upstream) : LMCD1 (381785 downstream)																																			---	---	---	---
LMCD1	29995	broad.mit.edu	37	3	8558278	8558278	+	Intron	DEL	A	-	-	rs112341331		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8558278delA	uc003bqq.2	+						LMCD1_uc011atd.1_Intron|LMCD1_uc011ate.1_Intron	NM_014583	NP_055398			LIM and cysteine-rich domains 1						positive regulation of calcineurin-NFAT signaling pathway|regulation of cardiac muscle hypertrophy|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus	transcription corepressor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(96;0.124)														---	---	---	---
C3orf32	51066	broad.mit.edu	37	3	8741525	8741526	+	Intron	INS	-	G	G	rs138848676	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8741525_8741526insG	uc003bqz.2	-							NM_015931	NP_057015			hypothetical protein LOC51066											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	9539307	9539307	+	IGR	DEL	T	-	-	rs71796158		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9539307delT								SETD5 (19471 upstream) : LHFPL4 (739 downstream)																																			---	---	---	---
LHFPL4	375323	broad.mit.edu	37	3	9597768	9597769	+	5'Flank	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9597768_9597769delTC	uc003bry.2	-							NM_198560	NP_940962			lipoma HMGIC fusion partner-like 4							integral to membrane				ovary(2)|skin(1)	3	Medulloblastoma(99;0.227)																	---	---	---	---
MTMR14	64419	broad.mit.edu	37	3	9714262	9714262	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9714262delT	uc003brz.2	+						MTMR14_uc003bsa.2_Intron|MTMR14_uc003bsb.2_Intron|MTMR14_uc011ath.1_Intron|MTMR14_uc010hcl.2_Intron|MTMR14_uc003bsc.2_Intron	NM_001077525	NP_001070993			jumpy isoform 2							perinuclear region of cytoplasm|ruffle	phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(99;0.227)																	---	---	---	---
MTMR14	64419	broad.mit.edu	37	3	9729243	9729244	+	Intron	DEL	AA	-	-	rs34956746		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9729243_9729244delAA	uc003brz.2	+						MTMR14_uc003bsa.2_Intron|MTMR14_uc003bsb.2_Intron|MTMR14_uc011ath.1_Intron|MTMR14_uc010hcl.2_Intron|MTMR14_uc003bsc.2_Intron	NM_001077525	NP_001070993			jumpy isoform 2							perinuclear region of cytoplasm|ruffle	phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(99;0.227)																	---	---	---	---
MTMR14	64419	broad.mit.edu	37	3	9740553	9740554	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9740553_9740554delAA	uc003brz.2	+						MTMR14_uc003bsa.2_Intron|MTMR14_uc003bsb.2_Intron|MTMR14_uc011ath.1_Intron|MTMR14_uc010hcl.2_Intron|MTMR14_uc003bsc.2_Intron	NM_001077525	NP_001070993			jumpy isoform 2							perinuclear region of cytoplasm|ruffle	phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(99;0.227)																	---	---	---	---
OGG1	4968	broad.mit.edu	37	3	9798357	9798358	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9798357_9798358delTC	uc003bsi.2	+						OGG1_uc003bsh.2_Intron|OGG1_uc003bsj.2_Intron|OGG1_uc003bsk.2_Intron|OGG1_uc003bsl.2_Intron|OGG1_uc003bsm.2_Intron|OGG1_uc003bsn.2_Intron|OGG1_uc003bso.2_Intron|OGG1_uc003bsp.1_Intron|OGG1_uc010hcm.1_Intron|OGG1_uc003bsq.1_Intron|OGG1_uc003bsr.1_Intron	NM_002542	NP_002533			8-oxoguanine DNA-glycosylase 1 isoform 1a						depurination|nucleotide-excision repair|regulation of protein import into nucleus, translocation|regulation of transcription, DNA-dependent|response to oxidative stress|response to radiation	mitochondrion|nuclear matrix|nuclear speck	damaged DNA binding|endonuclease activity|oxidized purine base lesion DNA N-glycosylase activity|protein binding				0	Medulloblastoma(99;0.227)												BER_DNA_glycosylases					---	---	---	---
CRELD1	78987	broad.mit.edu	37	3	9984680	9984680	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9984680delC	uc003bug.2	+						CIDEC_uc003bto.2_Intron|CRELD1_uc003buf.2_Intron|CRELD1_uc003buh.2_Intron|CRELD1_uc003bui.2_Intron|CRELD1_uc003buj.2_Intron	NM_001077415	NP_001070883			cysteine-rich with EGF-like domains 1 isoform 3						cardiac septum development|endocardial cushion development	integral to membrane	calcium ion binding			ovary(1)	1																		---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10118757	10118757	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10118757delA	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_Intron	NM_033084	NP_149075			Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)				D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
TATDN2	9797	broad.mit.edu	37	3	10298163	10298163	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10298163delT	uc003bvg.2	+						TATDN2_uc003bvf.2_Intron|TATDN2_uc011atr.1_Intron|TATDN2_uc011ats.1_Intron|TATDN2_uc011att.1_Intron	NM_014760	NP_055575			TatD DNase domain containing 2							nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding			pancreas(2)	2																		---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10379188	10379188	+	Intron	DEL	G	-	-	rs63241661		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10379188delG	uc003bvt.2	-						ATP2B2_uc003bvv.2_Intron|ATP2B2_uc003bvw.2_Intron|ATP2B2_uc003bvs.2_5'Flank|ATP2B2_uc010hdo.2_Intron	NM_001001331	NP_001001331			plasma membrane calcium ATPase 2 isoform 1						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10427117	10427117	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10427117delA	uc003bvt.2	-						ATP2B2_uc003bvv.2_Intron|ATP2B2_uc003bvw.2_Intron|ATP2B2_uc010hdo.2_Intron	NM_001001331	NP_001001331			plasma membrane calcium ATPase 2 isoform 1						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	10988558	10988558	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10988558delT								SLC6A11 (8414 upstream) : SLC6A1 (45862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	11084938	11084938	+	IGR	DEL	A	-	-	rs113171997		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11084938delA								SLC6A1 (4004 upstream) : HRH1 (93841 downstream)																																			---	---	---	---
ATG7	10533	broad.mit.edu	37	3	11332379	11332379	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11332379delT	uc003bwc.2	+						ATG7_uc003bwd.2_Intron|ATG7_uc011aum.1_Intron	NM_006395	NP_006386			APG7 autophagy 7-like isoform a						autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1																		---	---	---	---
ATG7	10533	broad.mit.edu	37	3	11479435	11479435	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11479435delA	uc003bwc.2	+						ATG7_uc003bwd.2_Intron|ATG7_uc011aum.1_Intron	NM_006395	NP_006386			APG7 autophagy 7-like isoform a						autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1																		---	---	---	---
VGLL4	9686	broad.mit.edu	37	3	11599950	11599951	+	3'UTR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11599950_11599951delTT	uc003bwf.2	-	6					VGLL4_uc010hdx.1_3'UTR|VGLL4_uc003bwg.2_3'UTR|VGLL4_uc010hdv.1_3'UTR|VGLL4_uc010hdw.1_3'UTR|VGLL4_uc011aun.1_3'UTR	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	11982873	11982874	+	IGR	DEL	TT	-	-	rs35601741		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11982873_11982874delTT								C3orf31 (94521 upstream) : SYN2 (62988 downstream)																																			---	---	---	---
SYN2	6854	broad.mit.edu	37	3	12104827	12104827	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12104827delA	uc003bwm.2	+						SYN2_uc003bwl.1_Intron	NM_133625	NP_598328			synapsin II isoform IIa						neurotransmitter secretion	synaptic vesicle	ATP binding|ligase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PPARG	5468	broad.mit.edu	37	3	12463465	12463465	+	Intron	DEL	C	-	-	rs11293844	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12463465delC	uc003bwx.2	+						PPARG_uc003bwr.2_Intron|PPARG_uc003bws.2_Intron|PPARG_uc003bwu.2_Intron|PPARG_uc003bwv.2_Intron	NM_015869	NP_056953			peroxisome proliferative activated receptor						activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation	cytosol|nucleoplasm	activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|kidney(1)	2					Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197)			T	PAX8	follicular thyroid		Insulin resistance ; lipodystrophy|familial partial L;diabetes mellitus|insulin-resistantI|with acanthosis nigricans and hypertension						---	---	---	---
RAF1	5894	broad.mit.edu	37	3	12650848	12650848	+	Intron	DEL	A	-	-	rs3730270		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12650848delA	uc003bxf.3	-						RAF1_uc011aut.1_5'Flank|RAF1_uc011auu.1_Intron	NM_002880	NP_002871			v-raf-1 murine leukemia viral oncogene homolog						activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity		ESRP1/RAF1(4)|SRGAP3/RAF1(4)	central_nervous_system(4)|prostate(4)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|liver(1)|ovary(1)	14					Sorafenib(DB00398)			T	SRGAP3	pilocytic astrocytoma				Noonan_syndrome				---	---	---	---
RAF1	5894	broad.mit.edu	37	3	12659890	12659890	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12659890delA	uc003bxf.3	-						RAF1_uc011auu.1_Intron	NM_002880	NP_002871			v-raf-1 murine leukemia viral oncogene homolog						activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity		ESRP1/RAF1(4)|SRGAP3/RAF1(4)	central_nervous_system(4)|prostate(4)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|liver(1)|ovary(1)	14					Sorafenib(DB00398)			T	SRGAP3	pilocytic astrocytoma				Noonan_syndrome				---	---	---	---
IQSEC1	9922	broad.mit.edu	37	3	13013812	13013812	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13013812delA	uc011auw.1	-						IQSEC1_uc003bxu.3_Intron	NM_001134382	NP_001127854			IQ motif and Sec7 domain 1 isoform a						regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	13150010	13150010	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13150010delT								IQSEC1 (35393 upstream) : NUP210 (207727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	13244659	13244661	+	IGR	DEL	ACT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13244659_13244661delACT								IQSEC1 (130042 upstream) : NUP210 (113076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	13516804	13516805	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13516804_13516805insT								NUP210 (54995 upstream) : HDAC11 (4419 downstream)																																			---	---	---	---
WNT7A	7476	broad.mit.edu	37	3	13909461	13909461	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13909461delG	uc003bye.1	-							NM_004625	NP_004616			wingless-type MMTV integration site family,						activation of JUN kinase activity|anterior/posterior pattern formation|canonical Wnt receptor signaling pathway|cell proliferation in forebrain|cellular response to transforming growth factor beta stimulus|central nervous system vasculogenesis|cerebellar granule cell differentiation|dorsal/ventral pattern formation|embryonic axis specification|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic leg morphogenesis|lens fiber cell development|negative regulation of neurogenesis|palate development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of JNK cascade|positive regulation of synaptogenesis|positive regulation of transcription from RNA polymerase II promoter|regulation of axon diameter|satellite cell activation|satellite cell maintenance involved in skeletal muscle regeneration|sex differentiation|uterus development|Wnt receptor signaling pathway involved in wound healing, spreading of epidermal cells|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	cytokine activity|frizzled binding|receptor agonist activity|signal transducer activity			ovary(2)|breast(1)	3																		---	---	---	---
TPRXL	348825	broad.mit.edu	37	3	14054635	14054636	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14054635_14054636insT	uc011avd.1	+							NR_002223				RecName: Full=Putative protein TPRXL;												0																		---	---	---	---
CHCHD4	131474	broad.mit.edu	37	3	14156769	14156770	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14156769_14156770delAA	uc003byj.3	-						CHCHD4_uc003byi.3_Intron	NM_001098502	NP_001091972			coiled-coil-helix-coiled-coil-helix domain						protein transport|transmembrane transport	mitochondrial intermembrane space					0																		---	---	---	---
XPC	7508	broad.mit.edu	37	3	14190590	14190591	+	Intron	DEL	TT	-	-	rs111520695		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14190590_14190591delTT	uc011ave.1	-						XPC_uc011avf.1_Intron|XPC_uc011avg.1_Intron	NM_004628	NP_004619			xeroderma pigmentosum, complementation group C						nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal	cytoplasm|nucleoplasm|XPC complex	bubble DNA binding|damaged DNA binding|loop DNA binding|protein binding|single-stranded DNA binding			ovary(2)|breast(1)	3								Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		NER	Xeroderma_Pigmentosum				---	---	---	---
SLC6A6	6533	broad.mit.edu	37	3	14519503	14519503	+	Intron	DEL	C	-	-	rs3214656		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14519503delC	uc010heg.2	+						SLC6A6_uc003byq.2_Intron|SLC6A6_uc003byr.2_Intron	NM_001134367	NP_001127839			solute carrier family 6 (neurotransmitter						cellular amino acid metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity|taurine:sodium symporter activity			ovary(1)	1																		---	---	---	---
C3orf19	51244	broad.mit.edu	37	3	14703402	14703410	+	Intron	DEL	ATAATTACA	-	-	rs66468540		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14703402_14703410delATAATTACA	uc003byw.2	+						C3orf19_uc010hei.1_Intron|C3orf19_uc010hej.2_Intron	NM_016474	NP_057558			hypothetical protein LOC51244												0																		---	---	---	---
NR2C2	7182	broad.mit.edu	37	3	15026340	15026340	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15026340delT	uc003bzj.3	+						NR2C2_uc003bzi.2_Intron	NM_003298	NP_003289			nuclear receptor subfamily 2, group C, member 2						cell differentiation|nervous system development|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	15201466	15201466	+	IGR	DEL	T	-	-	rs67569761		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15201466delT								ZFYVE20 (60811 upstream) : DVWA (5403 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	15422540	15422541	+	IGR	INS	-	G	G	rs143330287	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15422540_15422541insG								SH3BP5 (39639 upstream) : METTL6 (243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	15905226	15905226	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15905226delA								ANKRD28 (4173 upstream) : MIR563 (10052 downstream)																																			---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16531415	16531415	+	Intron	DEL	A	-	-	rs112940969		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16531415delA	uc003cay.2	-							NM_015150	NP_055965			raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	16574927	16574927	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16574927delT	uc003caz.1	+											Homo sapiens cDNA clone IMAGE:5273537.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	16584923	16584924	+	IGR	DEL	TT	-	-	rs35555538		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16584923_16584924delTT								RFTN1 (29701 upstream) : DAZL (43379 downstream)																																			---	---	---	---
PLCL2	23228	broad.mit.edu	37	3	16966424	16966424	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16966424delT	uc011awc.1	+						PLCL2_uc010het.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																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17300086	17300086	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17300086delA	uc003cbf.2	-						TBC1D5_uc010heu.2_Intron|TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron|TBC1D5_uc010hew.1_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	17703387	17703387	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17703387delC	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	17829456	17829456	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17829456delT								TBC1D5 (45216 upstream) : SATB1 (559810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	18184782	18184782	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18184782delC	uc003cbg.2	+											Homo sapiens cDNA clone IMAGE:5584035.																														---	---	---	---
SATB1	6304	broad.mit.edu	37	3	18438657	18438657	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18438657delT	uc003cbh.2	-						SATB1_uc003cbi.2_Intron|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																		---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19191842	19191842	+	Intron	DEL	T	-	-	rs79648308		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19191842delT	uc003cbk.1	+						KCNH8_uc011awe.1_Intron|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																		---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19566084	19566085	+	Intron	INS	-	A	A	rs141537260	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19566084_19566085insA	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																		---	---	---	---
EFHB	151651	broad.mit.edu	37	3	19946899	19946900	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19946899_19946900delAA	uc003cbl.3	-						EFHB_uc003cbm.2_Intron	NM_144715	NP_653316			EF hand domain family, member B						signal transduction	proteinaceous extracellular matrix	calcium ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	20758250	20758251	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20758250_20758251delCA								SGOL1 (530567 upstream) : VENTXP7 (688967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	20976834	20976835	+	IGR	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20976834_20976835insCA								SGOL1 (749151 upstream) : VENTXP7 (470383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	21121627	21121627	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21121627delT								SGOL1 (893944 upstream) : VENTXP7 (325591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	21370259	21370260	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21370259_21370260insTG								None (None upstream) : VENTXP7 (76958 downstream)																																			---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	21660906	21660907	+	Intron	DEL	GT	-	-	rs71859430		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21660906_21660907delGT	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	22144389	22144389	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22144389delA	uc010hfb.1	-											Homo sapiens cDNA: FLJ22419 fis, clone HRC08593.							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	22563577	22563578	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22563577_22563578delCA								ZNF385D (149454 upstream) : UBE2E2 (681075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	22669055	22669055	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22669055delA								ZNF385D (254932 upstream) : UBE2E2 (575598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	22929958	22929959	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22929958_22929959delAA								ZNF385D (515835 upstream) : UBE2E2 (314694 downstream)																																			---	---	---	---
UBE2E2	7325	broad.mit.edu	37	3	23478056	23478057	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23478056_23478057delTT	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	23747666	23747666	+	IGR	DEL	A	-	-	rs74358011		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23747666delA								UBE2E2 (115370 upstream) : UBE2E1 (99773 downstream)																																			---	---	---	---
NR1D2	9975	broad.mit.edu	37	3	23994448	23994448	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23994448delT	uc003ccs.2	+						NR1D2_uc010hfd.2_Intron|NR1D2_uc011awk.1_Intron	NM_005126	NP_005117			nuclear receptor subfamily 1, group D, member 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding			urinary_tract(1)|kidney(1)|skin(1)	3																		---	---	---	---
LOC152024	152024	broad.mit.edu	37	3	24138195	24138196	+	RNA	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24138195_24138196insT	uc003ccu.3	-	4		c.2552_2553insA								Homo sapiens hypothetical protein LOC152024, mRNA (cDNA clone IMAGE:4829078).												0																		---	---	---	---
THRB	7068	broad.mit.edu	37	3	24418935	24418936	+	Intron	INS	-	G	G	rs140962886	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24418935_24418936insG	uc003ccx.3	-						THRB_uc010hfe.2_Intron|THRB_uc003ccy.3_Intron|THRB_uc003ccz.3_Intron|THRB_uc003cdc.2_Intron|THRB_uc003cdd.2_Intron|THRB_uc003cde.1_Intron	NM_001128176	NP_001121648			thyroid hormone receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(2)|pancreas(1)	3					Levothyroxine(DB00451)|Liothyronine(DB00279)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	24669339	24669339	+	IGR	DEL	A	-	-	rs7647235	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24669339delA								THRB (132886 upstream) : RARB (546484 downstream)																																			---	---	---	---
RARB	5915	broad.mit.edu	37	3	25542906	25542907	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25542906_25542907insA	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)													---	---	---	---
RARB	5915	broad.mit.edu	37	3	25621873	25621873	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25621873delA	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)													---	---	---	---
RARB	5915	broad.mit.edu	37	3	25634977	25634977	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25634977delT	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)													---	---	---	---
TOP2B	7155	broad.mit.edu	37	3	25670433	25670433	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25670433delT	uc011awn.1	-	15	1854	c.1811delA	c.(1810-1812)AATfs	p.N604fs	TOP2B_uc003cdj.2_Frame_Shift_Del_p.N599fs	NM_001068	NP_001059	Q02880	TOP2B_HUMAN	DNA topoisomerase II, beta isozyme	604					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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	26146707	26146708	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26146707_26146708delTT								OXSM (310683 upstream) : LRRC3B (517592 downstream)																																			---	---	---	---
LRRC3B	116135	broad.mit.edu	37	3	26719261	26719261	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26719261delT	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	26805634	26805634	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26805634delT								LRRC3B (53371 upstream) : NEK10 (346761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27125230	27125230	+	IGR	DEL	A	-	-	rs36114733		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27125230delA								LRRC3B (372967 upstream) : NEK10 (27165 downstream)																																			---	---	---	---
NEK10	152110	broad.mit.edu	37	3	27395443	27395443	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27395443delA	uc003cdt.1	-							NM_199347	NP_955379			NIMA-related kinase 10 isoform 3								ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1)	13																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	27626809	27626809	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27626809delA								SLC4A7 (100971 upstream) : EOMES (131079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27742992	27742993	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27742992_27742993delTT								SLC4A7 (217154 upstream) : EOMES (14895 downstream)																																			---	---	---	---
EOMES	8320	broad.mit.edu	37	3	27761564	27761564	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27761564delA	uc003cdx.2	-						EOMES_uc003cdy.3_Intron|EOMES_uc010hfn.2_Intron|EOMES_uc011axc.1_Intron	NM_005442	NP_005433			eomesodermin						CD8-positive, alpha-beta T cell differentiation involved in immune response|cell differentiation involved in embryonic placenta development|endoderm formation|mesoderm formation|mesodermal to mesenchymal transition involved in gastrulation|positive regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|breast(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	27946105	27946105	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27946105delA								EOMES (181899 upstream) : CMC1 (337019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	28076453	28076453	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28076453delA								EOMES (312247 upstream) : CMC1 (206671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	28624575	28624575	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28624575delT								ZCWPW2 (57945 upstream) : RBMS3 (698368 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	28873951	28873951	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28873951delG								ZCWPW2 (307321 upstream) : RBMS3 (448992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	28881173	28881173	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28881173delA								ZCWPW2 (314543 upstream) : RBMS3 (441770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	29144315	29144315	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29144315delA								ZCWPW2 (577685 upstream) : RBMS3 (178628 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	29188630	29188631	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29188630_29188631delAA								ZCWPW2 (622000 upstream) : RBMS3 (134312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	29265950	29265950	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29265950delT								ZCWPW2 (699320 upstream) : RBMS3 (56993 downstream)																																			---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	30045454	30045454	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30045454delT	uc003cel.2	+	15					RBMS3_uc003cem.2_3'UTR|RBMS3_uc010hfr.2_3'UTR	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	30317543	30317543	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30317543delA								RBMS3 (270924 upstream) : TGFBR2 (330451 downstream)																																			---	---	---	---
GADL1	339896	broad.mit.edu	37	3	30769515	30769515	+	3'UTR	DEL	T	-	-	rs72077676		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30769515delT	uc003cep.2	-	15						NM_207359	NP_997242			glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
GADL1	339896	broad.mit.edu	37	3	30904546	30904547	+	Intron	DEL	CT	-	-	rs60151925		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30904546_30904547delCT	uc003cep.2	-						GADL1_uc003ceq.1_Intron	NM_207359	NP_997242			glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	30988430	30988430	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30988430delC								GADL1 (52277 upstream) : STT3B (586061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	31054782	31054783	+	IGR	INS	-	GT	GT	rs139082979	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31054782_31054783insGT								GADL1 (118629 upstream) : STT3B (519708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	31066059	31066064	+	IGR	DEL	TTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31066059_31066064delTTTTTT								GADL1 (129906 upstream) : STT3B (508427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	31278785	31278786	+	IGR	DEL	AC	-	-	rs62236305		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31278785_31278786delAC								GADL1 (342632 upstream) : STT3B (295705 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	31482388	31482388	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31482388delT								GADL1 (546235 upstream) : STT3B (92103 downstream)																																			---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31710397	31710397	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31710397delT	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)														---	---	---	---
GPD1L	23171	broad.mit.edu	37	3	32186315	32186316	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32186315_32186316delAC	uc003cew.2	+							NM_015141	NP_055956			glycerol-3-phosphate dehydrogenase 1-like						glycerol-3-phosphate catabolic process	glycerol-3-phosphate dehydrogenase complex	glycerol-3-phosphate dehydrogenase|NAD binding|protein homodimerization activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	32671832	32671832	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32671832delG								DYNC1LI1 (59482 upstream) : CNOT10 (54866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	32677112	32677112	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32677112delA								DYNC1LI1 (64762 upstream) : CNOT10 (49586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	33143652	33143652	+	IGR	DEL	A	-	-	rs112223243		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33143652delA								GLB1 (4958 upstream) : CRTAP (11798 downstream)																																			---	---	---	---
SUSD5	26032	broad.mit.edu	37	3	33255778	33255778	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33255778delT	uc003cfo.1	-							NM_015551	NP_056366			sushi domain containing 5 precursor						cell adhesion	integral to membrane	hyaluronic acid binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
FBXL2	25827	broad.mit.edu	37	3	33406075	33406076	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33406075_33406076insA	uc003cfp.2	+						FBXL2_uc011axm.1_Intron|FBXL2_uc011axn.1_Intron|FBXL2_uc011axo.1_Intron|FBXL2_uc011axp.1_Intron|FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron|FBXL2_uc011axs.1_Intron	NM_012157	NP_036289			F-box and leucine-rich repeat protein 2						interspecies interaction between organisms|proteolysis	cytoplasm|membrane	protein binding|ubiquitin-protein ligase activity			large_intestine(1)	1																		---	---	---	---
FBXL2	25827	broad.mit.edu	37	3	33415742	33415742	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33415742delT	uc003cfp.2	+						FBXL2_uc011axm.1_Intron|FBXL2_uc011axn.1_Intron|FBXL2_uc011axo.1_Intron|FBXL2_uc011axp.1_Intron|FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron|FBXL2_uc011axs.1_Intron	NM_012157	NP_036289			F-box and leucine-rich repeat protein 2						interspecies interaction between organisms|proteolysis	cytoplasm|membrane	protein binding|ubiquitin-protein ligase activity			large_intestine(1)	1																		---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33641457	33641458	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33641457_33641458insA	uc003cfu.2	-						CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron|CLASP2_uc011axt.1_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	34116177	34116200	+	IGR	DEL	TGTGTGTGTGTGTGTGTGTGTGTG	-	-	rs56898016		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34116177_34116200delTGTGTGTGTGTGTGTGTGTGTGTG								PDCD6IP (204983 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34294068	34294068	+	IGR	DEL	T	-	-	rs75037947		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34294068delT								PDCD6IP (382874 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34596244	34596246	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34596244_34596246delTTT								PDCD6IP (685050 upstream) : None (None downstream)																																			---	---	---	---
ARPP21	10777	broad.mit.edu	37	3	35833708	35833708	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35833708delA	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc011axy.1_Intron|ARPP21_uc003cgf.2_Intron|ARPP21_uc003cgg.2_Intron	NM_016300	NP_057384			cyclic AMP-regulated phosphoprotein, 21 kD							cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	35896411	35896411	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35896411delA								ARPP21 (60424 upstream) : STAC (525686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36810381	36810382	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36810381_36810382delTT								DCLK3 (29029 upstream) : TRANK1 (57929 downstream)																																			---	---	---	---
GOLGA4	2803	broad.mit.edu	37	3	37370690	37370690	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37370690delT	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	37744079	37744079	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37744079delA	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)														---	---	---	---
DLEC1	9940	broad.mit.edu	37	3	38093246	38093246	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38093246delA	uc003cho.1	+						DLEC1_uc003chp.1_Intron|DLEC1_uc010hgv.1_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	38365597	38365597	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38365597delT								SLC22A14 (5738 upstream) : XYLB (22654 downstream)																																			---	---	---	---
EXOG	9941	broad.mit.edu	37	3	38536273	38536274	+	5'Flank	INS	-	CTT	CTT	rs10627090		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38536273_38536274insCTT	uc003cih.2	+						EXOG_uc010hhg.2_5'Flank|EXOG_uc011ayq.1_5'Flank|EXOG_uc003cij.2_5'Flank|EXOG_uc010hhd.2_5'Flank|EXOG_uc010hhe.2_5'Flank|EXOG_uc003cik.2_5'Flank|EXOG_uc010hhf.2_5'Flank|EXOG_uc003cii.2_5'Flank	NM_005107	NP_005098			endo/exonuclease (5'-3'), endonuclease G-like							mitochondrial inner membrane	endonuclease activity|metal ion binding|nucleic acid binding				0																		---	---	---	---
EXOG	9941	broad.mit.edu	37	3	38539074	38539074	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
EXOG	9941	broad.mit.edu	37	3	38540046	38540046	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38540046delA	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																		---	---	---	---
SCN5A	6331	broad.mit.edu	37	3	38671191	38671192	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38671191_38671192insT	uc003cio.2	-						SCN5A_uc003cin.2_Intron|SCN5A_uc003cil.3_Intron|SCN5A_uc010hhi.2_Intron|SCN5A_uc010hhk.2_Intron|SCN5A_uc011ayr.1_Intron	NM_198056	NP_932173			voltage-gated sodium channel type V alpha						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	38793536	38793539	+	Intron	DEL	TCTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38793536_38793539delTCTC	uc003ciq.2	-							NM_006514	NP_006505			sodium channel, voltage-gated, type X, alpha						sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	39007193	39007193	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39007193delT								SCN11A (15141 upstream) : WDR48 (86314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39272718	39272718	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39272718delT								XIRP1 (38641 upstream) : CX3CR1 (32268 downstream)																																			---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	40067874	40067875	+	Intron	DEL	AT	-	-	rs138136048		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40067874_40067875delAT	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	40817178	40817179	+	IGR	DEL	GC	-	-	rs146446946	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40817178_40817179delGC								ZNF621 (236135 upstream) : CTNNB1 (419222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	40908513	40908513	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40908513delT								ZNF621 (327470 upstream) : CTNNB1 (327888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	41140360	41140360	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41140360delA								ZNF621 (559317 upstream) : CTNNB1 (96041 downstream)																																			---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41329706	41329706	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41329706delA	uc003ckv.3	-							NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41391973	41391973	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41391973delA	uc003ckv.3	-							NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41805943	41805944	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41805943_41805944insA	uc003ckv.3	-							NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41902283	41902286	+	Intron	DEL	CTTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41902283_41902286delCTTC	uc003ckv.3	-						ULK4_uc003ckw.2_Intron	NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41939991	41939991	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41939991delT	uc003ckv.3	-						ULK4_uc003ckw.2_Intron|ULK4_uc003ckx.1_Intron	NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41993677	41993677	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41993677delA	uc003ckv.3	-						ULK4_uc003ckw.2_Intron|ULK4_uc003ckx.1_Intron	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)														---	---	---	---
SEC22C	9117	broad.mit.edu	37	3	42602009	42602010	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42602009_42602010delAA	uc003clj.2	-						SEC22C_uc003clh.2_Intron|SEC22C_uc011azo.1_Intron|SEC22C_uc010hic.2_Intron|SEC22C_uc003cli.2_Intron	NM_032970	NP_116752			SEC22 vesicle trafficking protein homolog C						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(284;0.222)														---	---	---	---
FAM198A	729085	broad.mit.edu	37	3	43077760	43077760	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43077760delC	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	43120465	43120466	+	IGR	INS	-	C	C	rs150332003	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43120465_43120466insC								FAM198A (18762 upstream) : C3orf39 (263 downstream)																																			---	---	---	---
ANO10	55129	broad.mit.edu	37	3	43425669	43425669	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43425669delA	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	43672376	43672376	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43672376delT								ANO10 (8816 upstream) : ABHD5 (59999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	43679077	43679077	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43679077delT								ANO10 (15517 upstream) : ABHD5 (53298 downstream)																																			---	---	---	---
C3orf23	285343	broad.mit.edu	37	3	44399534	44399534	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44399534delT	uc010him.2	+						C3orf23_uc003cnd.3_Intron|C3orf23_uc003cne.3_Intron|C3orf23_uc003cnb.3_Intron|C3orf23_uc003cnc.3_Intron	NM_173826	NP_776187			hypothetical protein LOC285343 isoform 1							mitochondrion				upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(197;0.0468)|Kidney(197;0.0585)														---	---	---	---
ZNF167	55888	broad.mit.edu	37	3	44606301	44606302	+	Intron	INS	-	T	T	rs11381684		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44606301_44606302insT	uc010hin.2	+						ZNF167_uc003cnh.2_Intron|ZNF167_uc003cni.2_Intron|ZNF167_uc010hio.2_Intron|ZNF167_uc003cnj.2_Intron|ZNF167_uc003cnk.2_Intron	NM_018651	NP_061121			zinc finger protein 167 isoform 1						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(197;0.0486)|Kidney(197;0.0609)														---	---	---	---
ZNF167	55888	broad.mit.edu	37	3	44606821	44606821	+	Intron	DEL	T	-	-	rs79512510		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44606821delT	uc010hin.2	+						ZNF167_uc003cnh.2_Intron|ZNF167_uc003cni.2_Intron|ZNF167_uc010hio.2_Intron|ZNF167_uc003cnj.2_Intron|ZNF167_uc003cnk.2_Intron	NM_018651	NP_061121			zinc finger protein 167 isoform 1						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(197;0.0486)|Kidney(197;0.0609)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	44750690	44750691	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44750690_44750691delTT								ZNF35 (48408 upstream) : ZNF502 (3444 downstream)																																			---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44876908	44876908	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44876908delT	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)														---	---	---	---
ZDHHC3	51304	broad.mit.edu	37	3	44979483	44979483	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44979483delT	uc003cod.2	-						ZDHHC3_uc003cog.2_Intron|ZDHHC3_uc011bad.1_Intron	NM_016598	NP_057682			zinc finger, DHHC-type containing 3 isoform 2							Golgi membrane|integral to membrane	zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00943)|KIRC - Kidney renal clear cell carcinoma(197;0.053)|Kidney(197;0.0665)														---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45534598	45534598	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45534598delT	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155			leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)													---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45564232	45564232	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45564232delA	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155			leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	45610664	45610665	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45610664_45610665insC								LARS2 (20336 upstream) : LIMD1 (25658 downstream)																																			---	---	---	---
FYCO1	79443	broad.mit.edu	37	3	46028895	46028895	+	Intron	DEL	A	-	-	rs75357697		TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	46049353	46049353	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46049353delT								FYCO1 (12046 upstream) : XCR1 (12939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	46738614	46738614	+	IGR	DEL	A	-	-	rs35278467		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46738614delA								ALS2CL (3443 upstream) : TMIE (4209 downstream)																																			---	---	---	---
NBEAL2	23218	broad.mit.edu	37	3	47035857	47035859	+	Intron	DEL	ATG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47035857_47035859delATG	uc003cqp.2	+						NBEAL2_uc003cqq.1_Intron|NBEAL2_uc010hjm.1_5'Flank	NM_015175	NP_055990			neurobeachin-like 2								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)														---	---	---	---
KIF9	64147	broad.mit.edu	37	3	47292002	47292002	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47292002delT	uc010hjp.2	-						KIF9_uc003cqx.2_Intron|KIF9_uc003cqy.2_Intron|KIF9_uc011bat.1_Intron|KIF9_uc011bau.1_Intron	NM_001134878	NP_001128350			kinesin family member 9 isoform 2						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)														---	---	---	---
KIF9	64147	broad.mit.edu	37	3	47315092	47315092	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47315092delC	uc010hjp.2	-	5	920	c.316delG	c.(316-318)GCAfs	p.A106fs	KIF9_uc003cqx.2_Frame_Shift_Del_p.A106fs|KIF9_uc003cqy.2_Frame_Shift_Del_p.A106fs|KIF9_uc011bat.1_Intron|KIF9_uc011bau.1_RNA	NM_001134878	NP_001128350	Q9HAQ2	KIF9_HUMAN	kinesin family member 9 isoform 2	106	Kinesin-motor.				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)														---	---	---	---
KLHL18	23276	broad.mit.edu	37	3	47368745	47368745	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47368745delA	uc003crd.2	+						KLHL18_uc003crc.2_Intron|KLHL18_uc011bav.1_Intron|KLHL18_uc010hjq.1_5'Flank	NM_025010	NP_079286			kelch-like 18												0		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)														---	---	---	---
SMARCC1	6599	broad.mit.edu	37	3	47633045	47633045	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47633045delT	uc003crq.2	-						SMARCC1_uc011bbc.1_Intron|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	47963444	47963444	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47963444delT	uc003csb.2	-						MAP4_uc003csc.3_Intron|MAP4_uc011bbf.1_Intron|MAP4_uc003csf.3_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	48136913	48136913	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48136913delT								MAP4 (6144 upstream) : CDC25A (61755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	48161397	48161398	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48161397_48161398delTT								MAP4 (30628 upstream) : CDC25A (37270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	48169140	48169141	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48169140_48169141insA								MAP4 (38371 upstream) : CDC25A (29527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	48184539	48184539	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48184539delT								MAP4 (53770 upstream) : CDC25A (14129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	48237077	48237077	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48237077delA								CDC25A (7276 upstream) : CAMP (27785 downstream)																																			---	---	---	---
SPINK8	646424	broad.mit.edu	37	3	48368399	48368399	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48368399delA	uc003csq.1	-							NM_001080525	NP_001073994			serine peptidase inhibitor, Kazal type 8							extracellular region	serine-type endopeptidase inhibitor activity				0				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)														---	---	---	---
FBXW12	285231	broad.mit.edu	37	3	48423614	48423615	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48423614_48423615insT	uc003csr.2	+						FBXW12_uc010hjv.2_Intron|FBXW12_uc003css.2_Intron|FBXW12_uc010hjw.2_Intron	NM_207102	NP_996985			F-box and WD repeat domain containing 12 isoform												0				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
UQCRC1	7384	broad.mit.edu	37	3	48639957	48639958	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48639957_48639958delTT	uc003cub.1	-						UQCRC1_uc003cua.1_Intron|UQCRC1_uc003cuc.1_Intron|UQCRC1_uc003cud.1_Intron	NM_003365	NP_003356			ubiquinol-cytochrome c reductase core protein I						aerobic respiration|proteolysis		metalloendopeptidase activity|ubiquinol-cytochrome-c reductase activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)	Atovaquone(DB01117)													---	---	---	---
IP6K2	51447	broad.mit.edu	37	3	48748051	48748052	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48748051_48748052delTT	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																		---	---	---	---
SLC25A20	788	broad.mit.edu	37	3	48916233	48916238	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48916233_48916238delAAAAAA	uc003cva.3	-						SLC25A20_uc011bbw.1_Intron|SLC25A20_uc010hkj.2_Intron	NM_000387	NP_000378			carnitine/acylcarnitine translocase						carnitine shuttle|cellular lipid metabolic process|regulation of fatty acid oxidation	integral to membrane|mitochondrial inner membrane	acyl carnitine transporter activity				0				BRCA - Breast invasive adenocarcinoma(193;0.000168)|Kidney(197;0.00231)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	L-Carnitine(DB00583)													---	---	---	---
ARIH2	10425	broad.mit.edu	37	3	48973634	48973634	+	Intron	DEL	T	-	-	rs79755326		TCGA-BR-4292-01	TCGA-BR-4292-01									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	48991299	48991299	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48991299delA	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)														---	---	---	---
CCDC36	339834	broad.mit.edu	37	3	49280458	49280458	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49280458delT	uc003cwk.2	+						CCDC36_uc003cwl.3_Intron|CCDC36_uc011bck.1_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)														---	---	---	---
C3orf62	375341	broad.mit.edu	37	3	49308392	49308392	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49308392delA	uc003cwn.2	-	3					C3orf62_uc003cwm.2_3'UTR	NM_198562	NP_940964			hypothetical protein LOC375341												0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
C3orf62	375341	broad.mit.edu	37	3	49309180	49309180	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49309180delA	uc003cwn.2	-						C3orf62_uc003cwm.2_Intron|hsa-mir-4271|MI0015879_5'Flank	NM_198562	NP_940964			hypothetical protein LOC375341												0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
RHOA	387	broad.mit.edu	37	3	49420493	49420493	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49420493delA	uc003cwu.2	-						RHOA_uc010hku.2_Intron	NM_001664	NP_001655			ras homolog gene family, member A precursor						axon guidance|interspecies interaction between organisms|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of axonogenesis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of neuron differentiation|positive regulation of NF-kappaB import into nucleus|positive regulation of stress fiber assembly|regulation of cell migration|regulation of small GTPase mediated signal transduction|Rho protein signal transduction|spindle assembly involved in mitosis	cytoskeleton|cytosol|plasma membrane	GTP binding|GTPase activity|myosin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	Atorvastatin(DB01076)|Simvastatin(DB00641)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	49584581	49584581	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49584581delC								DAG1 (11535 upstream) : BSN (7341 downstream)																																			---	---	---	---
IP6K1	9807	broad.mit.edu	37	3	49817060	49817060	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49817060delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	50167085	50167085	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50167085delT	uc003cyi.1	-											Homo sapiens cDNA FLJ43511 fis, clone PERIC2003957.																														---	---	---	---
GNAT1	2779	broad.mit.edu	37	3	50230412	50230412	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50230412delG	uc003cym.2	+						GNAT1_uc003cyl.2_Intron	NM_144499	NP_653082			rod-type transducin alpha subunit						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)												OREG0015579	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	3	50353123	50353124	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50353123_50353124insT								HYAL1 (3311 upstream) : HYAL2 (2104 downstream)																																			---	---	---	---
CACNA2D2	9254	broad.mit.edu	37	3	50484576	50484576	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50484576delG	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)													---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51064762	51064762	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51064762delT	uc011bds.1	+							NM_004947	NP_004938			dedicator of cytokinesis 3							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51417604	51417604	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51417604delC	uc011bds.1	+	52	5572	c.5549delC	c.(5548-5550)ACCfs	p.T1850fs		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1850						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
GRM2	2912	broad.mit.edu	37	3	51746928	51746928	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51746928delG	uc010hlv.2	+	3	1129	c.890delG	c.(889-891)TGGfs	p.W297fs	GRM2_uc003dbo.3_Intron|GRM2_uc010hlu.2_RNA	NM_000839	NP_000830	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2 isoform a	297	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)													---	---	---	---
RRP9	9136	broad.mit.edu	37	3	51974545	51974545	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51974545delT	uc003dbw.1	-						PARP3_uc003dby.2_5'Flank|PARP3_uc003dbz.2_5'Flank	NM_004704	NP_004695			RNA, U3 small nucleolar interacting protein 2						rRNA processing	nucleolus|small nuclear ribonucleoprotein complex|small nucleolar ribonucleoprotein complex	RNA binding			breast(2)|ovary(1)	3				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	52044340	52044343	+	IGR	DEL	ATCC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52044340_52044343delATCC								RPL29 (14382 upstream) : DUSP7 (38596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	52082358	52082360	+	IGR	DEL	AAT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52082358_52082360delAAT								RPL29 (52400 upstream) : DUSP7 (579 downstream)																																			---	---	---	---
ALAS1	211	broad.mit.edu	37	3	52240857	52240857	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52240857delT	uc003dcy.1	+						ALAS1_uc003dcz.1_Intron|ALAS1_uc011bec.1_Intron	NM_000688	NP_000679			5-aminolevulinate synthase 1 precursor						heme biosynthetic process	mitochondrial matrix	5-aminolevulinate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(2)|upper_aerodigestive_tract(1)	3				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
ALAS1	211	broad.mit.edu	37	3	52241490	52241490	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52241490delT	uc003dcy.1	+						ALAS1_uc003dcz.1_Intron|ALAS1_uc011bec.1_Intron	NM_000688	NP_000679			5-aminolevulinate synthase 1 precursor						heme biosynthetic process	mitochondrial matrix	5-aminolevulinate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(2)|upper_aerodigestive_tract(1)	3				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
STAB1	23166	broad.mit.edu	37	3	52550871	52550871	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52550871delC	uc003dej.2	+						STAB1_uc003dek.1_5'Flank	NM_015136	NP_055951			stabilin 1 precursor						cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52668500	52668500	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52668500delA	uc003des.2	-						PBRM1_uc003dex.2_Intron|PBRM1_uc003deq.2_Intron|PBRM1_uc003der.2_Intron|PBRM1_uc003det.2_Intron|PBRM1_uc003deu.2_Intron|PBRM1_uc003dev.2_Intron|PBRM1_uc003dew.2_Intron|PBRM1_uc010hmk.1_Intron|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_Intron|PBRM1_uc003dfb.1_Intron	NM_181042	NP_060635			polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)				Mis|N|F|S|D|O		clear cell renal carcinoma|breast								---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52676243	52676243	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52676243delT	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								---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52692429	52692430	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52692429_52692430delTT	uc003des.2	-						PBRM1_uc003dex.2_Intron|PBRM1_uc003deq.2_Intron|PBRM1_uc003der.2_Intron|PBRM1_uc003det.2_Intron|PBRM1_uc003deu.2_Intron|PBRM1_uc003dev.2_Intron|PBRM1_uc003dew.2_Intron|PBRM1_uc010hmk.1_Intron|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_Intron|PBRM1_uc003dfb.1_Intron	NM_181042	NP_060635			polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)				Mis|N|F|S|D|O		clear cell renal carcinoma|breast								---	---	---	---
NEK4	6787	broad.mit.edu	37	3	52768925	52768925	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52768925delA	uc003dfq.3	-						NEK4_uc011bej.1_Intron	NM_003157	NP_003148			NIMA-related kinase 4						cell division|mitosis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)														---	---	---	---
TMEM110	375346	broad.mit.edu	37	3	52870876	52870877	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52870876_52870877insC	uc003dgc.3	-						MUSTN1_uc003dga.3_5'Flank|MUSTN1_uc003dgb.3_Intron	NM_198563	NP_940965			transmembrane protein 110							integral to membrane				large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.72e-05)|Kidney(197;0.000777)|KIRC - Kidney renal clear cell carcinoma(197;0.000915)|OV - Ovarian serous cystadenocarcinoma(275;0.0541)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	53098199	53098200	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53098199_53098200delTT								SFMBT1 (18129 upstream) : RFT1 (24303 downstream)																																			---	---	---	---
TKT	7086	broad.mit.edu	37	3	53260099	53260099	+	Intron	DEL	A	-	-	rs112475320		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53260099delA	uc003dgo.2	-						TKT_uc003dgp.2_Intron|TKT_uc011beo.1_Intron|TKT_uc003dgq.2_Intron|TKT_uc011beq.1_Intron|TKT_uc011ber.1_Intron|TKT_uc011bep.1_Intron	NM_001135055	NP_001128527			transketolase isoform 1						energy reserve metabolic process|xylulose biosynthetic process	cytosol	protein binding|transketolase activity			ovary(2)	2		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)	Thiamine(DB00152)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	53431445	53431445	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53431445delT								DCP1A (49808 upstream) : CACNA1D (97586 downstream)																																			---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53844946	53844947	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53844946_53844947insT	uc003dgv.3	+						CACNA1D_uc003dgu.3_Intron|CACNA1D_uc003dgy.3_Intron|CACNA1D_uc003dgw.3_Intron|CACNA1D_uc011bes.1_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	53975320	53975320	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53975320delT								SELK (49331 upstream) : CACNA2D3 (181373 downstream)																																			---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54367161	54367161	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54367161delT	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	54637284	54637285	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54637284_54637285delCA	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	54754580	54754580	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54754580delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	55127104	55127107	+	IGR	DEL	ATTT	-	-	rs36031755		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55127104_55127107delATTT								CACNA2D3 (18522 upstream) : WNT5A (372637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	55488540	55488540	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55488540delT								CACNA2D3 (379958 upstream) : WNT5A (11204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	56745902	56745902	+	IGR	DEL	C	-	-	rs77386094		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56745902delC								C3orf63 (28767 upstream) : ARHGEF3 (15544 downstream)																																			---	---	---	---
IL17RD	54756	broad.mit.edu	37	3	57174350	57174350	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57174350delT	uc003dil.2	-						IL17RD_uc003dik.2_Intron|IL17RD_uc010hna.2_Intron|IL17RD_uc011bex.1_Intron	NM_017563	NP_060033			interleukin 17 receptor D precursor							Golgi membrane|integral to membrane|plasma membrane	receptor activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)														---	---	---	---
APPL1	26060	broad.mit.edu	37	3	57274379	57274379	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57274379delT	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)														---	---	---	---
ASB14	142686	broad.mit.edu	37	3	57313073	57313073	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57313073delA	uc003diq.2	-						ASB14_uc003dip.1_5'Flank	NM_001142733	NP_001136205			ankyrin repeat and SOCS box-containing 14						intracellular signal transduction						0				KIRC - Kidney renal clear cell carcinoma(284;0.011)|Kidney(284;0.0127)														---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57357302	57357302	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57357302delA	uc003dit.2	-						DNAH12_uc010hnc.2_Intron	NM_178504	NP_848599			dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2																		---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57494742	57494742	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57494742delT	uc003dit.2	-						DNAH12_uc003diu.2_Intron	NM_178504	NP_848599			dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	57602079	57602081	+	IGR	DEL	AGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57602079_57602081delAGG								ARF4 (18864 upstream) : FAM116A (9101 downstream)																																			---	---	---	---
SLMAP	7871	broad.mit.edu	37	3	57850103	57850103	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57850103delA	uc003dje.1	+						SLMAP_uc003djc.1_Intron|SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron|SLMAP_uc003djg.1_5'Flank	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)														---	---	---	---
ACOX2	8309	broad.mit.edu	37	3	58494879	58494879	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58494879delT	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)														---	---	---	---
FAM107A	11170	broad.mit.edu	37	3	58597698	58597698	+	Intron	DEL	C	-	-	rs34148953		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58597698delC	uc003dko.2	-							NM_007177	NP_009108			downregulated in renal cell carcinoma						regulation of cell growth	nucleus	protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)														---	---	---	---
FAM107A	11170	broad.mit.edu	37	3	58602295	58602295	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58602295delC	uc003dko.2	-							NM_007177	NP_009108			downregulated in renal cell carcinoma						regulation of cell growth	nucleus	protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	59343152	59343152	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59343152delT								C3orf67 (307394 upstream) : FHIT (391886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59489003	59489003	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59489003delT								C3orf67 (453245 upstream) : FHIT (246035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59659098	59659099	+	IGR	INS	-	C	C	rs145622380	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59659098_59659099insC								C3orf67 (623340 upstream) : FHIT (75939 downstream)																																			---	---	---	---
FHIT	2272	broad.mit.edu	37	3	60188731	60188731	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60188731delA	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				---	---	---	---
FHIT	2272	broad.mit.edu	37	3	60265800	60265800	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60265800delA	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				---	---	---	---
FHIT	2272	broad.mit.edu	37	3	60408221	60408221	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60408221delA	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				---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	61669108	61669109	+	Intron	INS	-	T	T	rs139370560	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61669108_61669109insT	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron|PTPRG_uc003dla.3_Intron	NM_002841	NP_002832			protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)														---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	61978201	61978201	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61978201delT	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron	NM_002841	NP_002832			protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)														---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	62109662	62109663	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62109662_62109663insT	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron|ID2B_uc011bfh.1_RNA	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	63013600	63013600	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63013600delT	uc003dlo.2	+						LOC285401_uc010hnr.1_Intron					Homo sapiens, clone IMAGE:5557531, mRNA.												0																		---	---	---	---
SYNPR	132204	broad.mit.edu	37	3	63416037	63416038	+	Intron	INS	-	AC	AC	rs141211092	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63416037_63416038insAC	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	63555488	63555488	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63555488delT	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)														---	---	---	---
PSMD6	9861	broad.mit.edu	37	3	63999000	63999000	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63999000delC	uc003dma.1	-						PSMD6_uc003dlz.1_Intron|PSMD6_uc003dmb.1_Intron|PSMD6_uc003dmc.1_Intron|PSMD6_uc003dmd.1_Intron	NM_014814	NP_055629			proteasome (prosome, macropain) 26S 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|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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	64044389	64044389	+	IGR	DEL	T	-	-	rs72878958	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64044389delT								PSMD6 (34731 upstream) : PRICKLE2 (35138 downstream)																																			---	---	---	---
PRICKLE2	166336	broad.mit.edu	37	3	64088455	64088455	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64088455delA	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	64391117	64391117	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64391117delA								PRICKLE2 (179986 upstream) : ADAMTS9 (110216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	64447881	64447881	+	IGR	DEL	A	-	-	rs113537217		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64447881delA								PRICKLE2 (236750 upstream) : ADAMTS9 (53452 downstream)																																			---	---	---	---
ADAMTS9	56999	broad.mit.edu	37	3	64618505	64618505	+	Intron	DEL	A	-	-	rs67621736		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64618505delA	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc003dmh.1_Intron|ADAMTS9_uc003dmk.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	64850536	64850537	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64850536_64850537delTT	uc003dml.2	+											Homo sapiens cDNA FLJ25194 fis, clone REC04095.																														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65384174	65384174	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65384174delA	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hnx.1_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)														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65564680	65564680	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65564680delT	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)														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65924576	65924576	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65924576delT	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229			membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)														---	---	---	---
SLC25A26	115286	broad.mit.edu	37	3	66293635	66293635	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66293635delT	uc011bfq.1	+	4	927	c.199delT	c.(199-201)TTTfs	p.F67fs	SLC25A26_uc011bfs.1_5'UTR|SLC25A26_uc011bft.1_RNA|SLC25A26_uc011bfr.1_Frame_Shift_Del_p.F67fs|SLC25A26_uc003dmt.2_5'UTR	NM_173471	NP_775742	Q70HW3	SAMC_HUMAN	solute carrier family 25, member 26 isoform a	67	Solcar 1.|Helical; Name=2; (Potential).					integral to membrane|mitochondrial inner membrane|nucleus	S-adenosylmethionine transmembrane transporter activity			pancreas(1)	1		Lung NSC(201;0.00774)		BRCA - Breast invasive adenocarcinoma(55;0.00046)|KIRC - Kidney renal clear cell carcinoma(15;0.0515)|Kidney(15;0.0648)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	66687519	66687519	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66687519delA								LRIG1 (136674 upstream) : KBTBD8 (361208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	66889682	66889682	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66889682delA								LRIG1 (338837 upstream) : KBTBD8 (159045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	67080953	67080953	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67080953delT								KBTBD8 (19323 upstream) : SUCLG2 (344192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	67741424	67741424	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67741424delT	uc003dnb.2	+						uc003dnc.2_Intron					Homo sapiens mRNA; cDNA DKFZp686F1220 (from clone DKFZp686F1220).																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	67947629	67947629	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67947629delA	uc003dnc.2	+											Homo sapiens mRNA; cDNA DKFZp686F1220 (from clone DKFZp686F1220).																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	68681384	68681384	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68681384delT								FAM19A1 (86615 upstream) : FAM19A4 (99533 downstream)																																			---	---	---	---
C3orf64	285203	broad.mit.edu	37	3	69039500	69039507	+	Intron	DEL	TTTTTTTT	-	-	rs66964206		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69039500_69039507delTTTTTTTT	uc003dnl.2	-						C3orf64_uc003dnj.2_Intron|C3orf64_uc003dnk.2_Intron|C3orf64_uc011bfw.1_Intron|C3orf64_uc003dnm.1_Intron	NM_173654	NP_775925			AER61 glycosyltransferase							extracellular region	transferase activity, transferring glycosyl groups			ovary(1)	1		Lung NSC(201;0.126)		BRCA - Breast invasive adenocarcinoma(55;4.61e-05)|Epithelial(33;0.000291)|LUSC - Lung squamous cell carcinoma(21;0.0127)|KIRC - Kidney renal clear cell carcinoma(39;0.216)														---	---	---	---
LMOD3	56203	broad.mit.edu	37	3	69171665	69171667	+	5'UTR	DEL	TTT	-	-	rs35214408		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69171665_69171667delTTT	uc003dns.2	-	1					LMOD3_uc003dnt.2_5'UTR	NM_198271	NP_938012			leiomodin 3 (fetal)							cytoplasm|cytoskeleton	tropomyosin binding			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69328933	69328935	+	Intron	DEL	CTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69328933_69328935delCTC	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnx.1_Intron	NM_015123	NP_055938			FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69336796	69336797	+	Intron	DEL	TT	-	-	rs78688753		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69336796_69336797delTT	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnx.1_Intron	NM_015123	NP_055938			FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69366232	69366232	+	Intron	DEL	A	-	-	rs72087348		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69366232delA	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnx.1_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)														---	---	---	---
MITF	4286	broad.mit.edu	37	3	69906676	69906676	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69906676delT	uc003dnz.2	+						MITF_uc011bgb.1_Intron|MITF_uc003doa.2_Intron	NM_198159	NP_937802			microphthalmia-associated transcription factor						melanocyte differentiation|multicellular organismal development|protein complex assembly	nucleus|protein complex	DNA binding|protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription			ovary(2)	2		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)				A		melanoma 		Waardenburg syndrome type 2|Tietz syndrome						---	---	---	---
Unknown	0	broad.mit.edu	37	3	70983556	70983557	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70983556_70983557insA								MITF (966070 upstream) : FOXP1 (21180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	71676304	71676304	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71676304delT								FOXP1 (43164 upstream) : EIF4E3 (52138 downstream)																																			---	---	---	---
EIF4E3	317649	broad.mit.edu	37	3	71781556	71781556	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71781556delA	uc003dox.2	-						EIF4E3_uc011bgd.1_Intron|EIF4E3_uc010hoc.2_Intron	NM_173359	NP_775495			eukaryotic translation initiation factor 4E						regulation of translation	cytoplasm|mRNA cap binding complex	translation initiation factor activity				0		Prostate(10;0.0166)		BRCA - Breast invasive adenocarcinoma(55;2.56e-05)|Epithelial(33;2.9e-05)|Lung(16;9.28e-05)|LUSC - Lung squamous cell carcinoma(21;0.00227)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	71840487	71840488	+	IGR	INS	-	AAAC	AAAC	rs147907498	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71840487_71840488insAAAC								PROK2 (6130 upstream) : RYBP (583263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72018082	72018083	+	IGR	DEL	AA	-	-	rs72322976		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72018082_72018083delAA								PROK2 (183725 upstream) : RYBP (405668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72243968	72243968	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72243968delA								PROK2 (409611 upstream) : RYBP (179783 downstream)																																			---	---	---	---
SHQ1	55164	broad.mit.edu	37	3	72885640	72885640	+	Intron	DEL	A	-	-	rs78415242		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72885640delA	uc003dpf.2	-						SHQ1_uc010hod.2_Intron	NM_018130	NP_060600			SHQ1 homolog						ribonucleoprotein complex assembly	cytosol|nucleoplasm	protein binding			ovary(2)|large_intestine(1)	3		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)														---	---	---	---
SHQ1	55164	broad.mit.edu	37	3	72885934	72885934	+	Intron	DEL	A	-	-	rs36099891		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72885934delA	uc003dpf.2	-						SHQ1_uc010hod.2_Intron	NM_018130	NP_060600			SHQ1 homolog						ribonucleoprotein complex assembly	cytosol|nucleoplasm	protein binding			ovary(2)|large_intestine(1)	3		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)														---	---	---	---
GXYLT2	727936	broad.mit.edu	37	3	72973520	72973520	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72973520delT	uc003dpg.2	+							NM_001080393	NP_001073862			glycosyltransferase 8 domain containing 4						O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	74012794	74012794	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74012794delA								PDZRN3 (338722 upstream) : CNTN3 (298928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	74628516	74628516	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74628516delA								CNTN3 (58173 upstream) : FAM86D (842189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75332594	75332594	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75332594delG								CNTN3 (762251 upstream) : FAM86D (138111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75909582	75909582	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75909582delA								ZNF717 (74912 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76412365	76412366	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76412365_76412366delCA								ZNF717 (577695 upstream) : ROBO2 (676928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76488127	76488127	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76488127delT								ZNF717 (653457 upstream) : ROBO2 (601167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76845570	76845570	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76845570delA								None (None upstream) : ROBO2 (243724 downstream)																																			---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77571803	77571804	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77571803_77571804delTG	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	78334265	78334265	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78334265delT								ROBO2 (637604 upstream) : ROBO1 (312123 downstream)																																			---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79279678	79279678	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79279678delA	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	79847834	79847836	+	IGR	DEL	AAA	-	-	rs79389535		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79847834_79847836delAAA								ROBO1 (30775 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80038622	80038622	+	IGR	DEL	T	-	-	rs72039996		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80038622delT								ROBO1 (221563 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81043448	81043448	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81043448delA								None (None upstream) : GBE1 (495402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81076337	81076338	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81076337_81076338delGT								None (None upstream) : GBE1 (462512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81330608	81330609	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81330608_81330609insA								None (None upstream) : GBE1 (208241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	82182440	82182441	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82182440_82182441delAA	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	83395918	83395919	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83395918_83395919insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83400337	83400337	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83400337delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84624145	84624145	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84624145delA								None (None upstream) : CADM2 (383988 downstream)																																			---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85171175	85171175	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85171175delT	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	85825486	85825487	+	Intron	INS	-	ACAC	ACAC	rs141105558	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85825486_85825487insACAC	uc003dqj.2	+						CADM2_uc003dqk.2_Intron|CADM2_uc003dql.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85858727	85858727	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85858727delA	uc003dqj.2	+						CADM2_uc003dqk.2_Intron|CADM2_uc003dql.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	86202547	86202547	+	IGR	DEL	A	-	-	rs112091317		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86202547delA								CADM2 (84599 upstream) : VGLL3 (784578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	86217674	86217674	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86217674delT								CADM2 (99726 upstream) : VGLL3 (769451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	86404915	86404916	+	IGR	DEL	TA	-	-	rs143026577	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86404915_86404916delTA								CADM2 (286967 upstream) : VGLL3 (582209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	86482729	86482729	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86482729delA								CADM2 (364781 upstream) : VGLL3 (504396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87543848	87543849	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87543848_87543849delAG								POU1F1 (218111 upstream) : HTR1F (487877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	88750022	88750022	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88750022delT								C3orf38 (542909 upstream) : EPHA3 (406652 downstream)																																			---	---	---	---
EPHA3	2042	broad.mit.edu	37	3	89231178	89231178	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89231178delT	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	89383032	89383032	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89383032delA	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	89430825	89430825	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89430825delA	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	89448447	89448447	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89448447delT	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	89567439	89567442	+	IGR	DEL	TGTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89567439_89567442delTGTG								EPHA3 (36157 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	89974936	89974936	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89974936delA								EPHA3 (443654 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	90450383	90450384	+	IGR	INS	-	GG	GG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90450383_90450384insGG								EPHA3 (919101 upstream) : None (None downstream)																																			---	---	---	---
NSUN3	63899	broad.mit.edu	37	3	93787630	93787631	+	Intron	DEL	AC	-	-	rs148744382		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93787630_93787631delAC	uc003drl.1	+							NM_022072	NP_071355			NOL1/NOP2/Sun domain family, member 3								methyltransferase activity			skin(1)	1																		---	---	---	---
NSUN3	63899	broad.mit.edu	37	3	93813863	93813863	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93813863delT	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	94910217	94910218	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94910217_94910218delTT								LOC255025 (15138 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95218621	95218622	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95218621_95218622delTT								LOC255025 (323542 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95362592	95362592	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95362592delT								LOC255025 (467513 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95501643	95501644	+	IGR	INS	-	GT	GT	rs146079245	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95501643_95501644insGT								LOC255025 (606564 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96067783	96067783	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96067783delT								None (None upstream) : EPHA6 (465642 downstream)																																			---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	96757153	96757153	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96757153delC	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	97368608	97368609	+	Intron	INS	-	CA	CA	rs147744796	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97368608_97368609insCA	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	97577815	97577816	+	Intron	INS	-	T	T	rs144137188	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97577815_97577816insT	uc011bgq.1	+											SubName: Full=cDNA FLJ60082, weakly similar to Uro-adherence factor A; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	97908008	97908009	+	IGR	INS	-	C	C	rs146973134	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97908008_97908009insC								OR5H15 (19525 upstream) : OR5H6 (75120 downstream)																																			---	---	---	---
ST3GAL6	10402	broad.mit.edu	37	3	98460067	98460067	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98460067delT	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	98529907	98529907	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98529907delT	uc003dtd.2	-						DCBLD2_uc003dte.2_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	98918430	98918430	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98918430delT								DCBLD2 (297897 upstream) : COL8A1 (439024 downstream)																																			---	---	---	---
TBC1D23	55773	broad.mit.edu	37	3	100009611	100009611	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100009611delT	uc003dtt.2	+						TBC1D23_uc003dts.2_Intron	NM_018309	NP_060779			TBC1 domain family, member 23							intracellular	Rab GTPase activator activity			ovary(1)|liver(1)	2																		---	---	---	---
TBC1D23	55773	broad.mit.edu	37	3	100042414	100042414	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100042414delT	uc003dtt.2	+						TBC1D23_uc003dts.2_Intron|TBC1D23_uc003dtu.2_Intron	NM_018309	NP_060779			TBC1 domain family, member 23							intracellular	Rab GTPase activator activity			ovary(1)|liver(1)	2																		---	---	---	---
GPR128	84873	broad.mit.edu	37	3	100330087	100330088	+	Intron	INS	-	TTTCCTTC	TTTCCTTC	rs71981038		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100330087_100330088insTTTCCTTC	uc003duc.2	+							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																		---	---	---	---
GPR128	84873	broad.mit.edu	37	3	100378513	100378513	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	100511670	100511670	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100511670delA	uc003dun.2	-						ABI3BP_uc003duj.2_Intron|ABI3BP_uc003duk.2_Intron|ABI3BP_uc003dul.2_Intron|ABI3BP_uc011bhd.1_Intron|ABI3BP_uc003dum.2_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																		---	---	---	---
ABI3BP	25890	broad.mit.edu	37	3	100628230	100628230	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100628230delA	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	100716646	100716647	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100716646_100716647insT								ABI3BP (4312 upstream) : IMPG2 (228641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	100868099	100868100	+	IGR	DEL	TA	-	-	rs145170178		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100868099_100868100delTA								ABI3BP (155765 upstream) : IMPG2 (77188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	101332715	101332715	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101332715delT								PCNP (19436 upstream) : ZBTB11 (35570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	101363825	101363825	+	IGR	DEL	T	-	-	rs112341476		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101363825delT								PCNP (50546 upstream) : ZBTB11 (4460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	101628117	101628118	+	IGR	INS	-	T	T	rs139919670	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101628117_101628118insT								NFKBIZ (48252 upstream) : LOC152225 (31585 downstream)																																			---	---	---	---
ZPLD1	131368	broad.mit.edu	37	3	102060561	102060561	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102060561delT	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	102466044	102466051	+	IGR	DEL	AAGAAAGG	-	-	rs71793116	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102466044_102466051delAAGAAAGG								ZPLD1 (267359 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103175824	103175824	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103175824delT								ZPLD1 (977139 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103342562	103342563	+	IGR	INS	-	AAC	AAC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103342562_103342563insAAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104757042	104757042	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104757042delA								None (None upstream) : ALCAM (328671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	105077846	105077846	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105077846delA								None (None upstream) : ALCAM (7867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	105297585	105297585	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105297585delT								ALCAM (1842 upstream) : CBLB (79525 downstream)																																			---	---	---	---
CBLB	868	broad.mit.edu	37	3	105470205	105470206	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105470205_105470206delTG	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	105734963	105734964	+	IGR	DEL	AA	-	-	rs141531586		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105734963_105734964delAA								CBLB (146697 upstream) : LOC100302640 (820696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	106414485	106414487	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106414485_106414487delTTT								CBLB (826219 upstream) : LOC100302640 (141173 downstream)																																			---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106791487	106791489	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106791487_106791489delAAA	uc003dwf.3	-											Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106821226	106821227	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106821226_106821227delAC	uc003dwf.3	-											Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106860862	106860862	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106860862delA	uc003dwf.3	-						LOC100302640_uc011bhk.1_Intron					Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106869530	106869530	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106869530delA	uc003dwf.3	-						LOC100302640_uc011bhk.1_Intron					Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	107679074	107679074	+	IGR	DEL	C	-	-	rs7639149	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107679074delC								LOC285205 (31323 upstream) : CD47 (82867 downstream)																																			---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108103394	108103394	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108103394delA	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																		---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108746412	108746414	+	Intron	DEL	TTT	-	-	rs143920909		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108746412_108746414delTTT	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	108814683	108814683	+	Intron	DEL	A	-	-	rs78252612	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108814683delA	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244			MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	108871486	108871489	+	IGR	DEL	TGAT	-	-	rs140897777		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108871486_108871489delTGAT								MORC1 (34493 upstream) : C3orf66 (25523 downstream)																																			---	---	---	---
C3orf66	677779	broad.mit.edu	37	3	108901764	108901765	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108901764_108901765delTT	uc003dxn.2	+							NR_026767				Homo sapiens cDNA FLJ41232 fis, clone BRAMY2030799.												0																		---	---	---	---
DPPA2	151871	broad.mit.edu	37	3	109017963	109017963	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109017963delG	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	109168381	109168381	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109168381delT	uc003dxr.1	+							NM_001145553	NP_001139025			hypothetical protein LOC401082												0																		---	---	---	---
FLJ25363	401082	broad.mit.edu	37	3	109203553	109203554	+	Intron	DEL	AA	-	-	rs79817323		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109203553_109203554delAA	uc003dxr.1	+							NM_001145553	NP_001139025			hypothetical protein LOC401082												0																		---	---	---	---
FLJ25363	401082	broad.mit.edu	37	3	109206592	109206592	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	109863867	109863868	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109863867_109863868insA								FLJ25363 (649853 upstream) : PVRL3 (926997 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109864785	109864785	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109864785delT								FLJ25363 (650771 upstream) : PVRL3 (926080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109953315	109953315	+	IGR	DEL	A	-	-	rs1599482	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109953315delA								FLJ25363 (739301 upstream) : PVRL3 (837550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	110498043	110498043	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110498043delA								None (None upstream) : PVRL3 (292822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	111175740	111175742	+	IGR	DEL	TTT	-	-	rs71680371		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111175740_111175742delTTT								PVRL3 (263367 upstream) : CD96 (85184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	111249128	111249128	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111249128delA								PVRL3 (336755 upstream) : CD96 (11798 downstream)																																			---	---	---	---
CD96	10225	broad.mit.edu	37	3	111269439	111269439	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111269439delA	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				---	---	---	---
PHLDB2	90102	broad.mit.edu	37	3	111460389	111460390	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111460389_111460390delTG	uc003dyc.2	+						PLCXD2_uc003dya.2_Intron|PLCXD2_uc003dxz.2_Intron	NM_001134437	NP_001127909			pleckstrin homology-like domain, family B,							cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6																		---	---	---	---
PHLDB2	90102	broad.mit.edu	37	3	111673395	111673395	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111673395delT	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	111893726	111893735	+	Intron	DEL	AGTGAGGAAA	-	-	rs67704362		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111893726_111893735delAGTGAGGAAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	112847513	112847514	+	IGR	INS	-	AAG	AAG	rs149624968	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112847513_112847514insAAG								C3orf17 (108958 upstream) : BOC (82898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	112850044	112850045	+	IGR	INS	-	A	A	rs11449737		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112850044_112850045insA								C3orf17 (111489 upstream) : BOC (80367 downstream)																																			---	---	---	---
BOC	91653	broad.mit.edu	37	3	112970348	112970349	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112970348_112970349delTT	uc003dzx.2	+						BOC_uc010hqi.2_Intron|BOC_uc003dzy.2_Intron|BOC_uc003dzz.2_Intron|BOC_uc003dzw.1_3'UTR|BOC_uc003eaa.1_3'UTR	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	113091579	113091579	+	Intron	DEL	A	-	-	rs74350193		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113091579delA	uc003eae.1	-							NM_018338	NP_060808			WD repeat domain 52 isoform 2											central_nervous_system(1)	1																		---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114123936	114123936	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114123936delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	115065122	115065123	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115065122_115065123delTT								ZBTB20 (198995 upstream) : GAP43 (277028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	115115635	115115635	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115115635delA								ZBTB20 (249508 upstream) : GAP43 (226516 downstream)																																			---	---	---	---
GAP43	2596	broad.mit.edu	37	3	115377098	115377098	+	Intron	DEL	T	-	-	rs80248290	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115377098delT	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036			growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	116716492	116716492	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116716492delA								LOC285194 (280607 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	118076720	118076720	+	IGR	DEL	T	-	-	rs142068054		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118076720delT								None (None upstream) : IGSF11 (542761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	118294290	118294291	+	Intron	DEL	GG	-	-	rs5852164		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118294290_118294291delGG	uc011biu.1	-											Homo sapiens clone HA_003061 mRNA sequence.																														---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118802385	118802386	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118802385_118802386delAC	uc003eby.2	-						IGSF11_uc003ebz.2_Intron|IGSF11_uc010hqs.2_Intron	NM_152538	NP_689751			immunoglobulin superfamily, member 11 isoform a						cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0																		---	---	---	---
B4GALT4	8702	broad.mit.edu	37	3	118959089	118959089	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118959089delT	uc003ecg.2	-						B4GALT4_uc003ece.1_Intron|B4GALT4_uc003ech.2_Intron|B4GALT4_uc003eci.2_Intron|B4GALT4_uc011biy.1_Intron	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	119083625	119083626	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119083625_119083626insT	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	119104080	119104080	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119104080delT	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																		---	---	---	---
NR1I2	8856	broad.mit.edu	37	3	119522609	119522610	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119522609_119522610delTT	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	119595241	119595241	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119595241delA	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)													---	---	---	---
RABL3	285282	broad.mit.edu	37	3	120445119	120445119	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120445119delA	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)														---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	121058663	121058664	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121058663_121058664delAA	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	121099441	121099441	+	Intron	DEL	T	-	-	rs76801680		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121099441delT	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	121217164	121217164	+	Intron	DEL	A	-	-	rs76023468		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121217164delA	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)					---	---	---	---
POLQ	10721	broad.mit.edu	37	3	121224955	121224956	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121224955_121224956insA	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)					---	---	---	---
FBXO40	51725	broad.mit.edu	37	3	121334887	121334888	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121334887_121334888insG	uc003eeg.2	+							NM_016298	NP_057382			F-box protein 40						muscle cell differentiation	centrosome|nucleus	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(114;0.189)														---	---	---	---
HCLS1	3059	broad.mit.edu	37	3	121377299	121377299	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121377299delT	uc003eeh.3	-						HCLS1_uc011bjj.1_Intron|HCLS1_uc011bjk.1_Intron|HCLS1_uc011bjl.1_Intron	NM_005335	NP_005326			hematopoietic cell-specific Lyn substrate 1						erythrocyte differentiation|intracellular signal transduction|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of STAT protein|response to hormone stimulus	mitochondrion|nucleus|plasma membrane	DNA binding|sequence-specific DNA binding transcription factor activity				0				GBM - Glioblastoma multiforme(114;0.0912)														---	---	---	---
IQCB1	9657	broad.mit.edu	37	3	121517893	121517893	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121517893delT	uc010hre.1	-						IQCB1_uc003eek.2_Intron|IQCB1_uc010hrf.1_Intron	NM_001023570	NP_001018864			IQ motif containing B1 isoform a						cilium assembly|maintenance of organ identity|photoreceptor cell maintenance	centrosome|photoreceptor connecting cilium	calmodulin binding				0				GBM - Glioblastoma multiforme(114;0.0983)														---	---	---	---
CD86	942	broad.mit.edu	37	3	121825688	121825689	+	Intron	DEL	CA	-	-	rs72230382		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121825688_121825689delCA	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)													---	---	---	---
KPNA1	3836	broad.mit.edu	37	3	122219347	122219347	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122219347delT	uc003efd.1	-						KPNA1_uc010hrh.2_Intron|KPNA1_uc003efe.2_Intron	NM_002264	NP_002255			karyopherin alpha 1						DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|regulation of DNA recombination|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein binding|protein transporter activity				0				GBM - Glioblastoma multiforme(114;0.0898)														---	---	---	---
SEMA5B	54437	broad.mit.edu	37	3	122709461	122709462	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122709461_122709462delCA	uc003efz.1	-						SEMA5B_uc011bju.1_Intron|SEMA5B_uc003ega.1_Intron|SEMA5B_uc003egb.1_Intron|SEMA5B_uc010hro.1_Intron|SEMA5B_uc010hrp.1_Intron	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	122811188	122811188	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122811188delT	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	122821475	122821475	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122821475delT	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	122964979	122964979	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122964979delT	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)														---	---	---	---
ADCY5	111	broad.mit.edu	37	3	123022109	123022109	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123022109delG	uc003egh.1	-						ADCY5_uc003egg.1_Intron|ADCY5_uc003egi.1_Intron	NM_183357	NP_899200			adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	123173598	123173598	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123173598delA								ADCY5 (6206 upstream) : PTPLB (39765 downstream)																																			---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123542940	123542941	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123542940_123542941delTT	uc003ego.2	-						MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Intron|MYLK_uc003egu.1_Intron	NM_053025	NP_444253			myosin light chain kinase isoform 1						aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	123936385	123936385	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123936385delA	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	123996138	123996138	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123996138delT	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	124059376	124059378	+	Intron	DEL	AAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124059376_124059378delAAG	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	124258616	124258617	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124258616_124258617insT	uc003ehg.2	+						KALRN_uc003ehi.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	124499557	124499557	+	Intron	DEL	C	-	-	rs111552815		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124499557delC	uc003eho.2	-						ITGB5_uc010hrx.2_Intron	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)														---	---	---	---
MUC13	56667	broad.mit.edu	37	3	124629206	124629206	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124629206delC	uc003ehq.1	-							NM_033049	NP_149038			mucin 13, epithelial transmembrane							extracellular region|integral to membrane|plasma membrane					0																		---	---	---	---
MUC13	56667	broad.mit.edu	37	3	124631783	124631790	+	Intron	DEL	AAAAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124631783_124631790delAAAAAAAA	uc003ehq.1	-							NM_033049	NP_149038			mucin 13, epithelial transmembrane							extracellular region|integral to membrane|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	124658685	124658686	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124658685_124658686insT								MUC13 (5105 upstream) : HEG1 (25869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	124678785	124678785	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124678785delA								MUC13 (25205 upstream) : HEG1 (5770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	124793622	124793622	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124793622delA								HEG1 (18820 upstream) : SLC12A8 (7860 downstream)																																			---	---	---	---
SLC12A8	84561	broad.mit.edu	37	3	124816067	124816067	+	Intron	DEL	A	-	-	rs10707707		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124816067delA	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	125085687	125085687	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125085687delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	125382898	125382898	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125382898delT								OSBPL11 (68517 upstream) : MIR548I1 (126349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	125486701	125486702	+	IGR	DEL	CT	-	-	rs143781607	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125486701_125486702delCT								OSBPL11 (172320 upstream) : MIR548I1 (22545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	125522010	125522011	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125522010_125522011insA								MIR548I1 (12615 upstream) : LOC100125556 (113433 downstream)																																			---	---	---	---
ALDH1L1	10840	broad.mit.edu	37	3	125851982	125851982	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125851982delT	uc003eim.1	-						ALDH1L1_uc010hse.1_Intron|ALDH1L1_uc011bki.1_Intron|ALDH1L1_uc003eio.2_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)											OREG0015764	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ALDH1L1	10840	broad.mit.edu	37	3	125882974	125882974	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	125993665	125993666	+	IGR	INS	-	A	A	rs139049883	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125993665_125993666insA								ALDH1L1 (94180 upstream) : KLF15 (67812 downstream)																																			---	---	---	---
UROC1	131669	broad.mit.edu	37	3	126221797	126221798	+	Intron	INS	-	TGTG	TGTG	rs144044419	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126221797_126221798insTGTG	uc003eiz.1	-						UROC1_uc010hsi.1_Intron	NM_144639	NP_653240			urocanase domain containing 1 isoform 1						histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)														---	---	---	---
PLXNA1	5361	broad.mit.edu	37	3	126735391	126735391	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126735391delC	uc003ejg.2	+	15	2981	c.2977delC	c.(2977-2979)CCCfs	p.P993fs		NM_032242	NP_115618	Q9UIW2	PLXA1_HUMAN	plexin A1	1016	IPT/TIG 2.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)|skin(1)	3				GBM - Glioblastoma multiforme(114;0.155)														---	---	---	---
C3orf27	23434	broad.mit.edu	37	3	128295804	128295804	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128295804delC	uc003ekq.2	-							NM_007354	NP_031380			putative GR6 protein												0				GBM - Glioblastoma multiforme(114;0.176)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	128437028	128437029	+	IGR	DEL	CA	-	-	rs71975170	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128437028_128437029delCA								RPN1 (37110 upstream) : RAB7A (7950 downstream)																																			---	---	---	---
COPG	22820	broad.mit.edu	37	3	128974023	128974023	+	Intron	DEL	T	-	-	rs63166061		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128974023delT	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																		---	---	---	---
RPL32P3	132241	broad.mit.edu	37	3	129103544	129103545	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129103544_129103545delTG	uc003ema.2	-						RPL32P3_uc003emb.2_Intron	NR_003111				Homo sapiens cDNA FLJ36158 fis, clone TESTI2025757, weakly similar to Human mRNA for ribosomal protein L32.												0																		---	---	---	---
IFT122	55764	broad.mit.edu	37	3	129183764	129183764	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	129334706	129334707	+	IGR	INS	-	GAGCAGAGGAGGGTGAGAGGC	GAGCAGAGGAGGGTGAGAGGC	rs150751109	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129334706_129334707insGAGCAGAGGAGGGTGAGAGGC								PLXND1 (9124 upstream) : TMCC1 (31930 downstream)																																			---	---	---	---
TMCC1	23023	broad.mit.edu	37	3	129565983	129565983	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129565983delA	uc003emz.3	-						TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395			transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	130038304	130038304	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130038304delA								COL6A4P2 (45656 upstream) : COL29A1 (26055 downstream)																																			---	---	---	---
COL29A1	256076	broad.mit.edu	37	3	130178570	130178570	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130178570delT	uc010htj.1	+						COL29A1_uc010hti.1_Intron|COL29A1_uc010htk.1_Intron	NM_153264	NP_694996			collagen, type XXIX, alpha 1						axon guidance|cell adhesion	collagen					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	130224104	130224104	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130224104delA								COL29A1 (20416 upstream) : COL6A6 (55074 downstream)																																			---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130367861	130367863	+	Intron	DEL	TTT	-	-	rs72391450		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130367861_130367863delTTT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	130547277	130547277	+	IGR	DEL	A	-	-	rs3211035		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130547277delA								PIK3R4 (81581 upstream) : ATP2C1 (22168 downstream)																																			---	---	---	---
ATP2C1	27032	broad.mit.edu	37	3	130699886	130699886	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130699886delT	uc003enl.2	+						ATP2C1_uc011blg.1_Intron|ATP2C1_uc011blh.1_Intron|ATP2C1_uc011bli.1_Intron|ATP2C1_uc003enk.2_Intron|ATP2C1_uc003enm.2_Intron|ATP2C1_uc003enn.2_Intron|ATP2C1_uc003eno.2_Intron|ATP2C1_uc003enp.2_Intron|ATP2C1_uc003enq.2_Intron|ATP2C1_uc003enr.2_Intron|ATP2C1_uc003ens.2_Intron|ATP2C1_uc003ent.2_Intron|ATP2C1_uc003enu.2_Intron	NM_014382	NP_055197			calcium-transporting ATPase 2C1 isoform 1a						actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)									Hailey-Hailey_disease				---	---	---	---
ATP2C1	27032	broad.mit.edu	37	3	130725683	130725683	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130725683delT	uc011bli.1	+						ATP2C1_uc011blh.1_Intron|ATP2C1_uc003enm.2_Intron|ATP2C1_uc003enn.2_Intron|ATP2C1_uc003enp.2_Intron|ATP2C1_uc003enr.2_Intron|ATP2C1_uc003ens.2_Intron|ATP2C1_uc003ent.2_Intron	NM_001001487	NP_001001487			calcium-transporting ATPase 2C1 isoform 1b						actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)									Hailey-Hailey_disease				---	---	---	---
Unknown	0	broad.mit.edu	37	3	131144744	131144744	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131144744delT								NUDT16 (39815 upstream) : MRPL3 (36302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	131168200	131168200	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131168200delT								NUDT16 (63271 upstream) : MRPL3 (12846 downstream)																																			---	---	---	---
MRPL3	11222	broad.mit.edu	37	3	131203425	131203426	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131203425_131203426insA	uc003eoh.2	-						MRPL3_uc011blo.1_Intron|MRPL3_uc011blp.1_Intron	NM_007208	NP_009139			mitochondrial ribosomal protein L3						translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0																		---	---	---	---
CPNE4	131034	broad.mit.edu	37	3	131295569	131295569	+	Intron	DEL	T	-	-	rs72140188		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131295569delT	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	131655809	131655810	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131655809_131655810delAA	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	131663470	131663470	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131663470delA	uc003eok.2	-						CPNE4_uc011blq.1_Intron|CPNE4_uc003eol.2_Intron|CPNE4_uc003eom.2_Intron	NM_130808	NP_570720			copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
ACPP	55	broad.mit.edu	37	3	132068579	132068580	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132068579_132068580delAA	uc010htp.2	+						ACPP_uc003eon.3_Intron|ACPP_uc003eop.3_Intron	NM_001099	NP_001090			acid phosphatase, prostate short isoform							extracellular region|lysosomal membrane	5'-nucleotidase activity|acid phosphatase activity			ovary(1)	1																		---	---	---	---
DNAJC13	23317	broad.mit.edu	37	3	132179281	132179282	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132179281_132179282delTT	uc003eor.2	+						DNAJC13_uc010htq.1_Intron	NM_015268	NP_056083			DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2																		---	---	---	---
NPHP3	27031	broad.mit.edu	37	3	132418048	132418048	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132418048delT	uc003epe.1	-						NPHP3_uc003epd.1_Intron	NM_153240	NP_694972			nephrocystin 3						maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1																		---	---	---	---
TMEM108	66000	broad.mit.edu	37	3	132759352	132759353	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132759352_132759353delTT	uc003eph.2	+						TMEM108_uc003epi.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	133168989	133168991	+	Intron	DEL	GAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133168989_133168991delGAA	uc003epn.1	+						uc003epo.2_Intron	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	133361872	133361874	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133361872_133361874delTTT	uc003eps.2	-							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	133539542	133539544	+	IGR	DEL	TCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133539542_133539544delTCT								SRPRB (19 upstream) : RAB6B (3538 downstream)																																			---	---	---	---
SLCO2A1	6578	broad.mit.edu	37	3	133701664	133701664	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133701664delA	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	135387084	135387084	+	IGR	DEL	T	-	-	rs113404850		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135387084delT								EPHB1 (407779 upstream) : PPP2R3A (297483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	135635120	135635120	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135635120delT								EPHB1 (655815 upstream) : PPP2R3A (49447 downstream)																																			---	---	---	---
MSL2	55167	broad.mit.edu	37	3	135895504	135895504	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135895504delA	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	135989348	135989349	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135989348_135989349delTT	uc003eqy.1	+						PCCB_uc003eqz.1_Intron|PCCB_uc011bmc.1_Intron|PCCB_uc011bmd.1_Intron	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	136130863	136130863	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136130863delA	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron	NM_005862	NP_005853			stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	137261237	137261237	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137261237delG								IL20RB (531317 upstream) : SOX14 (222342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137283861	137283861	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137283861delT								IL20RB (553941 upstream) : SOX14 (199718 downstream)																																			---	---	---	---
DZIP1L	199221	broad.mit.edu	37	3	137798559	137798559	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137798559delT	uc003erq.2	-						DZIP1L_uc003err.1_Intron	NM_173543	NP_775814			DAZ interacting protein 1-like							intracellular	zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137959892	137959893	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137959892_137959893delAA	uc003esa.1	+						ARMC8_uc003erw.2_Intron|ARMC8_uc003erx.2_Intron|ARMC8_uc003ery.2_Intron|ARMC8_uc003erz.2_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron|ARMC8_uc003esc.1_Intron	NM_015396	NP_056211			armadillo repeat containing 8 isoform 2								binding				0																		---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137988856	137988856	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137988856delT	uc003esa.1	+						TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron|ARMC8_uc003esc.1_Intron|ARMC8_uc003esf.1_Intron	NM_015396	NP_056211			armadillo repeat containing 8 isoform 2								binding				0																		---	---	---	---
CEP70	80321	broad.mit.edu	37	3	138221382	138221382	+	Intron	DEL	A	-	-	rs35132741		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138221382delA	uc003esl.2	-						CEP70_uc011bmk.1_Intron|CEP70_uc011bml.1_Intron|CEP70_uc011bmm.1_Intron|CEP70_uc003esm.2_Intron	NM_024491	NP_077817			centrosomal protein 70 kDa						G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding			skin(1)	1																		---	---	---	---
CEP70	80321	broad.mit.edu	37	3	138255844	138255847	+	Intron	DEL	AAAA	-	-	rs148750633		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138255844_138255847delAAAA	uc003esl.2	-						CEP70_uc011bmk.1_Intron|CEP70_uc011bml.1_Intron|CEP70_uc011bmm.1_Intron|CEP70_uc003esm.2_Intron|CEP70_uc003esn.2_3'UTR	NM_024491	NP_077817			centrosomal protein 70 kDa						G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding			skin(1)	1																		---	---	---	---
PIK3CB	5291	broad.mit.edu	37	3	138474573	138474573	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	138560084	138560084	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138560084delA								PIK3CB (81899 upstream) : FOXL2 (102983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	138968953	138968954	+	IGR	DEL	CT	-	-	rs138854147		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138968953_138968954delCT								PISRT1 (16589 upstream) : MRPS22 (93844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	139499779	139499779	+	IGR	DEL	C	-	-	rs35524164		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139499779delC								NMNAT3 (102939 upstream) : CLSTN2 (154248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	139522495	139522496	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139522495_139522496delTG								NMNAT3 (125655 upstream) : CLSTN2 (131531 downstream)																																			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	140238438	140238438	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140238438delT	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)			---	---	---	---
SLC25A36	55186	broad.mit.edu	37	3	140682088	140682089	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140682088_140682089delAA	uc003etr.2	+						SLC25A36_uc003etp.2_3'UTR|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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	141486406	141486407	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141486406_141486407insT								RNF7 (21164 upstream) : GRK7 (10636 downstream)																																			---	---	---	---
GRK7	131890	broad.mit.edu	37	3	141509407	141509410	+	Intron	DEL	TTTT	-	-	rs10540138		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141509407_141509410delTTTT	uc011bnd.1	+							NM_139209	NP_631948			G-protein-coupled receptor kinase 7 precursor						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	141742191	141742191	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141742191delT	uc003eun.3	-						TFDP2_uc003eul.3_Intron|TFDP2_uc011bnf.1_Intron|TFDP2_uc011bng.1_Intron|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																		---	---	---	---
TFDP2	7029	broad.mit.edu	37	3	141838002	141838003	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141838002_141838003insA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	142713091	142713091	+	IGR	DEL	A	-	-	rs112422321		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142713091delA								PAQR9 (30913 upstream) : SR140 (7281 downstream)																																			---	---	---	---
SLC9A9	285195	broad.mit.edu	37	3	143371652	143371653	+	Intron	INS	-	AT	AT	rs150971314	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143371652_143371653insAT	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	143860840	143860841	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143860840_143860841delTC								C3orf58 (149631 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144169465	144169466	+	IGR	INS	-	TGTG	TGTG	rs147981040	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144169465_144169466insTGTG								C3orf58 (458256 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144196818	144196818	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144196818delT								C3orf58 (485609 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144862285	144862285	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144862285delA								None (None upstream) : PLOD2 (924943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144938250	144938251	+	IGR	INS	-	CA	CA	rs144255024	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144938250_144938251insCA								None (None upstream) : PLOD2 (848977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	145211466	145211466	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145211466delT								None (None upstream) : PLOD2 (575762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	145671215	145671215	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145671215delT								None (None upstream) : PLOD2 (116013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146569077	146569077	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146569077delA								PLSCR5 (245074 upstream) : ZIC4 (534760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146696335	146696336	+	IGR	INS	-	AC	AC	rs147173324	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146696335_146696336insAC								PLSCR5 (372332 upstream) : ZIC4 (407501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146876384	146876385	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146876384_146876385insA								PLSCR5 (552381 upstream) : ZIC4 (227452 downstream)																																			---	---	---	---
ZIC1	7545	broad.mit.edu	37	3	147129058	147129059	+	Intron	DEL	AC	-	-	rs111509390		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147129058_147129059delAC	uc003ewe.2	+							NM_003412	NP_003403			zinc finger protein of the cerebellum 1						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	147462721	147462721	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147462721delA								ZIC1 (328217 upstream) : AGTR1 (952937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147675586	147675586	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147675586delT								ZIC1 (541082 upstream) : AGTR1 (740072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147919527	147919530	+	IGR	DEL	TCTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147919527_147919530delTCTC								ZIC1 (785023 upstream) : AGTR1 (496128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148385273	148385273	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148385273delA								None (None upstream) : AGTR1 (30385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148656800	148656800	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148656800delT								CPA3 (41930 upstream) : GYG1 (52575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148689002	148689002	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148689002delA								CPA3 (74132 upstream) : GYG1 (20373 downstream)																																			---	---	---	---
HPS3	84343	broad.mit.edu	37	3	148849060	148849061	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148849060_148849061insT	uc003ewu.1	+						HPS3_uc003ewt.1_Intron|HPS3_uc011bnq.1_Intron	NM_032383	NP_115759			Hermansky-Pudlak syndrome 3 protein							cytoplasm				ovary(5)|large_intestine(1)	6			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)											Hermansky-Pudlak_syndrome				---	---	---	---
CP	1356	broad.mit.edu	37	3	148899609	148899609	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148899609delT	uc003ewy.3	-						CP_uc011bnr.1_Intron|CP_uc003eww.3_5'Flank|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)													---	---	---	---
WWTR1	25937	broad.mit.edu	37	3	149422636	149422637	+	5'Flank	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149422636_149422637delAA	uc003exh.2	-							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)															---	---	---	---
C3orf16	389161	broad.mit.edu	37	3	149495263	149495264	+	Intron	INS	-	AACAAC	AACAAC	rs145748362	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149495263_149495264insAACAAC	uc003exl.2	-						C3orf16_uc011bnt.1_Intron	NM_001144960	NP_001138432			hypothetical protein LOC389161												0																		---	---	---	---
RNF13	11342	broad.mit.edu	37	3	149638898	149638898	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149638898delT	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	150185358	150185358	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150185358delC								TSC22D2 (7745 upstream) : SERP1 (74423 downstream)																																			---	---	---	---
EIF2A	83939	broad.mit.edu	37	3	150282062	150282063	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150282062_150282063delTT	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)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150845633	150845633	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150845633delG	uc003eyp.2	+	4	456	c.418delG	c.(418-420)GAGfs	p.E140fs	MED12L_uc011bnz.1_Frame_Shift_Del_p.E140fs|MED12L_uc003eym.1_Frame_Shift_Del_p.E140fs|MED12L_uc003eyn.2_Frame_Shift_Del_p.E140fs|MED12L_uc003eyo.2_Frame_Shift_Del_p.E140fs	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	140					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	150876701	150876701	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150876701delA	uc003eyp.2	+						MED12L_uc011bnz.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	151010370	151010370	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151010370delT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
IGSF10	285313	broad.mit.edu	37	3	151160336	151160337	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151160336_151160337delTT	uc011bod.1	-						IGSF10_uc011bob.1_5'Flank|IGSF10_uc011boc.1_5'Flank	NM_178822	NP_849144			immunoglobulin superfamily, member 10 precursor						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	151291345	151291345	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151291345delT								IGSF10 (114848 upstream) : AADACL2 (160359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	152491044	152491045	+	IGR	DEL	TT	-	-	rs74405025		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152491044_152491045delTT								MBNL1 (307476 upstream) : P2RY1 (61691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	152932098	152932098	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152932098delT								RAP2B (45837 upstream) : C3orf79 (270186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	153344866	153344867	+	IGR	DEL	TG	-	-	rs35716753		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153344866_153344867delTG								C3orf79 (124383 upstream) : SGEF (494282 downstream)																																			---	---	---	---
SGEF	26084	broad.mit.edu	37	3	153842092	153842092	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153842092delA	uc011bog.1	+						SGEF_uc011boh.1_Intron	NM_015595	NP_056410			Src homology 3 domain-containing guanine						regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	154206904	154206905	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154206904_154206905delAA								GPR149 (59400 upstream) : MME (535008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154673690	154673690	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154673690delA								GPR149 (526186 upstream) : MME (68223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154727710	154727710	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154727710delA								GPR149 (580206 upstream) : MME (14203 downstream)																																			---	---	---	---
MME	4311	broad.mit.edu	37	3	154834153	154834153	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154834153delT	uc010hvr.1	+						MME_uc003fab.1_Intron|MME_uc003fac.1_Intron|MME_uc003fad.1_Intron|MME_uc003fae.1_Intron	NM_007289	NP_009220			membrane metallo-endopeptidase						cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)													---	---	---	---
PLCH1	23007	broad.mit.edu	37	3	155232467	155232467	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155232467delT	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432			phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	155445686	155445686	+	IGR	DEL	T	-	-	rs63042562		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155445686delT								PLCH1 (23689 upstream) : C3orf33 (34715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	155576012	155576012	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155576012delT								SLC33A1 (3845 upstream) : GMPS (12313 downstream)																																			---	---	---	---
KCNAB1	7881	broad.mit.edu	37	3	155876861	155876861	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155876861delC	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_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	156096145	156096145	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156096145delA	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	156162455	156162455	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156162455delC	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Intron|KCNAB1_uc010hvt.1_Intron	NM_172160	NP_751892			potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	156381030	156381030	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156381030delT								SSR3 (108095 upstream) : LOC100287227 (9934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	157487654	157487655	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157487654_157487655delAA								C3orf55 (168635 upstream) : SHOX2 (326146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	157698557	157698557	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157698557delT								C3orf55 (379538 upstream) : SHOX2 (115244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	158283068	158283068	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158283068delT	uc003fbw.1	-											Homo sapiens cDNA FLJ40475 fis, clone TESTI2042946.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	158338168	158338168	+	IGR	DEL	G	-	-	rs12633687	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158338168delG								MLF1 (13916 upstream) : GFM1 (24149 downstream)																																			---	---	---	---
MFSD1	64747	broad.mit.edu	37	3	158523024	158523024	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158523024delA	uc003fcl.1	+						MFSD1_uc003fcm.1_Intron|MFSD1_uc003fcn.1_Intron|MFSD1_uc011bow.1_Intron|MFSD1_uc011box.1_Intron	NM_022736	NP_073573			major facilitator superfamily domain containing						transmembrane transport	integral to membrane					0			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159329324	159329324	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159329324delG	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	159497296	159497296	+	Intron	DEL	A	-	-	rs71994062		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159497296delA	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	159584165	159584165	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159584165delT	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)															---	---	---	---
IFT80	57560	broad.mit.edu	37	3	160093679	160093679	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160093679delA	uc011boy.1	-						IFT80_uc003fda.2_Intron|IFT80_uc003fdb.1_Intron|IFT80_uc003fdd.1_Intron|IFT80_uc003fde.1_Intron	NM_020800	NP_065851			WD repeat domain 56							cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
IFT80	57560	broad.mit.edu	37	3	160108206	160108206	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160108206delA	uc011boy.1	-						IFT80_uc003fda.2_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)															---	---	---	---
NMD3	51068	broad.mit.edu	37	3	160960578	160960578	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160960578delT	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_Intron|NMD3_uc010hwh.2_Intron	NM_015938	NP_057022			NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	160975222	160975223	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160975222_160975223delGT								NMD3 (3903 upstream) : C3orf57 (87358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	160998208	160998208	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160998208delT								NMD3 (26889 upstream) : C3orf57 (64373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161619761	161619761	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161619761delT								OTOL1 (398033 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162936214	162936214	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162936214delT	uc003feg.2	+						uc003feh.2_Intron					Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	162969390	162969390	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162969390delT	uc003feh.2	-											Homo sapiens hypothetical protein LOC647107, mRNA (cDNA clone IMAGE:5103171), partial cds.																														---	---	---	---
SI	6476	broad.mit.edu	37	3	164750559	164750559	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164750559delA	uc003fei.2	-							NM_001041	NP_001032			sucrase-isomaltase						carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)										HNSCC(35;0.089)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165089207	165089207	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165089207delT								SLITRK3 (174738 upstream) : BCHE (401487 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165687935	165687935	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165687935delT								BCHE (132682 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165695036	165695037	+	IGR	DEL	GC	-	-	rs58738986		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165695036_165695037delGC								BCHE (139783 upstream) : None (None downstream)																																			---	---	---	---
SERPINI2	5276	broad.mit.edu	37	3	167170830	167170830	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167170830delA	uc003fer.1	-						SERPINI2_uc003fes.1_Intron|SERPINI2_uc003fet.1_Intron	NM_006217	NP_006208			serpin peptidase inhibitor, clade I (pancpin),						cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(2)|urinary_tract(1)	3																		---	---	---	---
PDCD10	11235	broad.mit.edu	37	3	167402273	167402273	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167402273delA	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				---	---	---	---
SERPINI1	5274	broad.mit.edu	37	3	167507159	167507159	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167507159delA	uc003ffa.3	+	2	441	c.243delA	c.(241-243)CTAfs	p.L81fs	SERPINI1_uc003ffb.3_Frame_Shift_Del_p.L81fs	NM_001122752	NP_001116224	Q99574	NEUS_HUMAN	neuroserpin precursor	81					central nervous system development|peripheral nervous system development|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(1)	1																		---	---	---	---
GOLIM4	27333	broad.mit.edu	37	3	167732372	167732372	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167732372delA	uc003ffe.2	-						GOLIM4_uc011bpe.1_Intron|GOLIM4_uc011bpf.1_Intron|GOLIM4_uc011bpg.1_Intron	NM_014498	NP_055313			golgi integral membrane protein 4						transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5																		---	---	---	---
GOLIM4	27333	broad.mit.edu	37	3	167765996	167765996	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167765996delA	uc003ffe.2	-						GOLIM4_uc011bpe.1_Intron|GOLIM4_uc011bpf.1_Intron|GOLIM4_uc011bpg.1_Intron	NM_014498	NP_055313			golgi integral membrane protein 4						transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5																		---	---	---	---
GOLIM4	27333	broad.mit.edu	37	3	167783967	167783967	+	Intron	DEL	T	-	-	rs76451230		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167783967delT	uc003ffe.2	-						GOLIM4_uc011bpe.1_Intron|GOLIM4_uc011bpf.1_Intron|GOLIM4_uc011bpg.1_Intron	NM_014498	NP_055313			golgi integral membrane protein 4						transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	168796005	168796005	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168796005delA								C3orf50 (247633 upstream) : MECOM (5282 downstream)																																			---	---	---	---
GPR160	26996	broad.mit.edu	37	3	169802469	169802469	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169802469delA	uc003fgi.2	+	4	1299	c.709delA	c.(709-711)AAAfs	p.K237fs	GPR160_uc010hwq.2_Frame_Shift_Del_p.K237fs	NM_014373	NP_055188	Q9UJ42	GP160_HUMAN	G protein-coupled receptor 160	237	Cytoplasmic (Potential).					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)															---	---	---	---
SLC2A2	6514	broad.mit.edu	37	3	170716192	170716192	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170716192delA	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	170950131	170950131	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170950131delA	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	170958022	170958024	+	Intron	DEL	TCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170958022_170958024delTCT	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	171026964	171026964	+	Intron	DEL	A	-	-	rs151336555		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171026964delA	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	171177464	171177465	+	Intron	INS	-	ACAC	ACAC	rs142709083	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171177464_171177465insACAC	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron|TNIK_uc003fhq.2_Intron	NM_015028	NP_055843			TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	172213323	172213323	+	IGR	DEL	A	-	-	rs139867981		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172213323delA								GHSR (47120 upstream) : TNFSF10 (10142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	172282111	172282111	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172282111delT								TNFSF10 (40842 upstream) : NCEH1 (66325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	172323864	172323864	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172323864delA								TNFSF10 (82595 upstream) : NCEH1 (24572 downstream)																																			---	---	---	---
SPATA16	83893	broad.mit.edu	37	3	172654953	172654953	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172654953delA	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)															---	---	---	---
SPATA16	83893	broad.mit.edu	37	3	172733652	172733653	+	Intron	DEL	GT	-	-	rs72039159		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172733652_172733653delGT	uc003fin.3	-							NM_031955	NP_114161			spermatogenesis associated 16						cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding			ovary(2)|skin(1)	3	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)															---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173329793	173329793	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173329793delT	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	173990448	173990459	+	Intron	DEL	GATGGATGGATA	-	-	rs72451726		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173990448_173990459delGATGGATGGATA	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747			neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	175425793	175425793	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175425793delA	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	175586044	175586044	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175586044delT								NAALADL2 (62618 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176673521	176673521	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176673521delC								None (None upstream) : TBL1XR1 (65022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177073127	177073128	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177073127_177073128delAA								TBL1XR1 (158079 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177210432	177210432	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177210432delA								TBL1XR1 (295384 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177315666	177315667	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177315666_177315667delAA								TBL1XR1 (400618 upstream) : KCNMB2 (938557 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177337913	177337914	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177337913_177337914delAA								TBL1XR1 (422865 upstream) : KCNMB2 (916310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177363032	177363033	+	IGR	DEL	AT	-	-	rs66481760		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177363032_177363033delAT								TBL1XR1 (447984 upstream) : KCNMB2 (891191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177429544	177429544	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177429544delT								TBL1XR1 (514496 upstream) : KCNMB2 (824680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177482334	177482335	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177482334_177482335delTG								TBL1XR1 (567286 upstream) : KCNMB2 (771889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177863258	177863258	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177863258delA								TBL1XR1 (948210 upstream) : KCNMB2 (390966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	178587312	178587312	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178587312delA								KCNMB2 (25096 upstream) : ZMAT3 (154215 downstream)																																			---	---	---	---
ZMAT3	64393	broad.mit.edu	37	3	178742629	178742629	+	3'UTR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178742629delC	uc003fjg.2	-	6					ZMAT3_uc010hxa.2_3'UTR|ZMAT3_uc003fji.2_3'UTR	NM_022470	NP_071915			p53 target zinc finger protein isoform 1						apoptosis|protein transport|regulation of growth|response to DNA damage stimulus|transmembrane transport	nucleolus	RNA binding|zinc ion binding			ovary(2)	2	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	178813000	178813001	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178813000_178813001delTC								ZMAT3 (23416 upstream) : PIK3CA (53310 downstream)																																			---	---	---	---
PIK3CA	5290	broad.mit.edu	37	3	178882657	178882658	+	Intron	INS	-	A	A	rs111770110		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178882657_178882658insA	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)			---	---	---	---
PIK3CA	5290	broad.mit.edu	37	3	178917413	178917413	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178917413delA	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)			---	---	---	---
KCNMB3	27094	broad.mit.edu	37	3	178965730	178965730	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178965730delA	uc003fjm.2	-						KCNMB3_uc003fjl.3_Intron|KCNMB3_uc011bqc.1_Intron|KCNMB3_uc003fjn.2_Intron|KCNMB3_uc003fjo.2_Intron|KCNMB3_uc003fjp.1_Intron	NM_014407	NP_055222			calcium-activated potassium channel beta 3						detection of calcium ion|platelet activation|regulation of action potential in neuron	voltage-gated potassium channel complex	calcium-activated potassium channel activity|potassium channel regulator activity				0	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	179036265	179036267	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179036265_179036267delAAA								KCNMB3 (51427 upstream) : ZNF639 (4552 downstream)																																			---	---	---	---
MFN1	55669	broad.mit.edu	37	3	179093166	179093166	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179093166delT	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)															---	---	---	---
GNB4	59345	broad.mit.edu	37	3	179151407	179151408	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179151407_179151408delAA	uc003fjv.3	-							NM_021629	NP_067642			guanine nucleotide-binding protein, beta-4						cellular response to glucagon stimulus|energy reserve metabolic process	plasma membrane	signal transducer activity			skin(2)	2	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)															---	---	---	---
GNB4	59345	broad.mit.edu	37	3	179155351	179155351	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179155351delA	uc003fjv.3	-							NM_021629	NP_067642			guanine nucleotide-binding protein, beta-4						cellular response to glucagon stimulus|energy reserve metabolic process	plasma membrane	signal transducer activity			skin(2)	2	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)															---	---	---	---
NDUFB5	4711	broad.mit.edu	37	3	179334935	179334936	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179334935_179334936insT	uc003fkc.2	+						NDUFB5_uc003fkd.2_Intron|NDUFB5_uc003fke.2_Intron	NM_002492	NP_002483			NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			skin(1)	1	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)		NADH(DB00157)													---	---	---	---
USP13	8975	broad.mit.edu	37	3	179374288	179374289	+	Intron	INS	-	GCTT	GCTT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179374288_179374289insGCTT	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)															---	---	---	---
PEX5L	51555	broad.mit.edu	37	3	179709295	179709295	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179709295delT	uc003fki.1	-						PEX5L_uc003fkj.1_Intron|PEX5L_uc010hxd.1_Intron|PEX5L_uc011bqg.1_Intron|PEX5L_uc011bqh.1_Intron	NM_016559	NP_057643			peroxisomal biogenesis factor 5-like						protein import into peroxisome matrix|regulation of cAMP-mediated signaling	cytosol|peroxisomal membrane	peroxisome matrix targeting signal-1 binding			ovary(3)|large_intestine(1)	4	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	179962346	179962346	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179962346delT								PEX5L (207829 upstream) : TTC14 (357572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180115022	180115022	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180115022delA								PEX5L (360505 upstream) : TTC14 (204896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180249143	180249143	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180249143delA								PEX5L (494626 upstream) : TTC14 (70775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180276753	180276753	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180276753delA								PEX5L (522236 upstream) : TTC14 (43165 downstream)																																			---	---	---	---
SOX2OT	347689	broad.mit.edu	37	3	181382107	181382107	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181382107delT	uc003fkv.2	+						SOX2OT_uc003fkw.3_Intron					Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	181600968	181600969	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181600968_181600969delAC								SOX2OT (141965 upstream) : ATP11B (910322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181733487	181733488	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181733487_181733488delAG								SOX2OT (274484 upstream) : ATP11B (777803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181968339	181968340	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181968339_181968340insA								SOX2OT (509336 upstream) : ATP11B (542951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182054436	182054436	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182054436delA								SOX2OT (595433 upstream) : ATP11B (456855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182262503	182262504	+	IGR	DEL	TG	-	-	rs140900910		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182262503_182262504delTG								SOX2OT (803500 upstream) : ATP11B (248787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182409740	182409742	+	IGR	DEL	CTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182409740_182409742delCTG								SOX2OT (950737 upstream) : ATP11B (101549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182490358	182490359	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182490358_182490359delTT								None (None upstream) : ATP11B (20932 downstream)																																			---	---	---	---
MCCC1	56922	broad.mit.edu	37	3	182763703	182763703	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182763703delT	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)													---	---	---	---
LAMP3	27074	broad.mit.edu	37	3	182872267	182872267	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182872267delA	uc003flh.3	-							NM_014398	NP_055213			lysosomal-associated membrane protein 3						cell proliferation	integral to membrane|lysosomal membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	183277709	183277709	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183277709delT								KLHL6 (4210 upstream) : KLHL24 (75702 downstream)																																			---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183521617	183521617	+	Intron	DEL	T	-	-	rs3214844		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183521617delT	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-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183522777	183522777	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183522777delA	uc003fly.2	+						uc003fma.1_3'UTR	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	183629307	183629308	+	IGR	DEL	TC	-	-	rs35562470		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183629307_183629308delTC								PARL (26614 upstream) : ABCC5 (8418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	183629331	183629332	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183629331_183629332delCT								PARL (26638 upstream) : ABCC5 (8394 downstream)																																			---	---	---	---
HTR3D	200909	broad.mit.edu	37	3	183750908	183750910	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183750908_183750910delTTT	uc011bqv.1	+						HTR3D_uc003fmj.2_Intron|HTR3D_uc011bqu.1_Intron|HTR3D_uc010hxp.2_5'Flank	NM_001163646	NP_001157118			5-hydroxytryptamine receptor 3 subunit D isoform							integral to membrane|plasma membrane	extracellular ligand-gated ion channel activity|receptor activity				0	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	183794264	183794264	+	IGR	DEL	A	-	-	rs67523338		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183794264delA								HTR3C (15805 upstream) : HTR3E (20588 downstream)																																			---	---	---	---
DVL3	1857	broad.mit.edu	37	3	183879215	183879215	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183879215delA	uc003fms.2	+						DVL3_uc011bqw.1_Intron|DVL3_uc003fmt.2_Intron	NM_004423	NP_004414			dishevelled 3						canonical Wnt receptor signaling pathway|intracellular signal transduction|positive regulation of JUN kinase activity|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent	cytoplasm	beta-catenin binding|frizzled binding|protease binding|protein heterodimerization activity|signal transducer activity			ovary(1)|lung(1)|breast(1)	3	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	184367758	184367758	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184367758delA								EPHB3 (67563 upstream) : MAGEF1 (60398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	184422693	184422693	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184422693delT								EPHB3 (122498 upstream) : MAGEF1 (5463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	184470008	184470008	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184470008delA								MAGEF1 (40172 upstream) : VPS8 (59923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	184470805	184470820	+	IGR	DEL	TGGGAGAAGAAGGTGA	-	-	rs71162261	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184470805_184470820delTGGGAGAAGAAGGTGA								MAGEF1 (40969 upstream) : VPS8 (59111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	184477292	184477292	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184477292delA								MAGEF1 (47456 upstream) : VPS8 (52639 downstream)																																			---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184652954	184652954	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184652954delA	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	184737135	184737136	+	Intron	INS	-	AC	AC	rs111857967		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184737135_184737136insAC	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)															---	---	---	---
EHHADH	1962	broad.mit.edu	37	3	184952968	184952968	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184952968delA	uc003fpf.2	-						EHHADH_uc011brs.1_Intron	NM_001966	NP_001957			enoyl-Coenzyme A, hydratase/3-hydroxyacyl							peroxisome	3-hydroxyacyl-CoA dehydrogenase activity|coenzyme binding|dodecenoyl-CoA delta-isomerase activity|enoyl-CoA hydratase activity			ovary(3)	3	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)		NADH(DB00157)													---	---	---	---
SENP2	59343	broad.mit.edu	37	3	185300851	185300851	+	Intron	DEL	A	-	-	rs72296073		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185300851delA	uc011brv.1	+							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)															---	---	---	---
IGF2BP2	10644	broad.mit.edu	37	3	185460284	185460285	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185460284_185460285insA	uc003fpo.2	-						IGF2BP2_uc010hyi.2_Intron|IGF2BP2_uc010hyj.2_Intron|IGF2BP2_uc010hyk.2_Intron|IGF2BP2_uc010hyl.2_Intron|IGF2BP2_uc003fpp.2_Intron|IGF2BP2_uc003fpq.2_Intron	NM_006548	NP_006539			insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)															---	---	---	---
ETV5	2119	broad.mit.edu	37	3	185826275	185826275	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185826275delG	uc003fpz.2	-						ETV5_uc003fpy.2_Frame_Shift_Del_p.P8fs	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	186044188	186044188	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186044188delA	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	186491296	186491297	+	IGR	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186491296_186491297insCA								KNG1 (29555 upstream) : EIF4A2 (10064 downstream)																																			---	---	---	---
ADIPOQ	9370	broad.mit.edu	37	3	186565968	186565969	+	Intron	DEL	AA	-	-	rs72160667		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186565968_186565969delAA	uc003fra.2	+						ADIPOQ_uc010hyy.2_Intron	NM_004797	NP_004788			adiponectin precursor						brown fat cell differentiation|cellular response to drug|cellular response to insulin stimulus|detection of oxidative stress|fatty acid beta-oxidation|generation of precursor metabolites and energy|glucose homeostasis|glucose metabolic process|low-density lipoprotein particle clearance|negative regulation of blood pressure|negative regulation of DNA biosynthetic process|negative regulation of ERK1 and ERK2 cascade|negative regulation of eukaryotic cell surface binding|negative regulation of fat cell differentiation|negative regulation of gluconeogenesis|negative regulation of granulocyte differentiation|negative regulation of heterotypic cell-cell adhesion|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of inflammatory response|negative regulation of intracellular protein transport|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|negative regulation of macrophage differentiation|negative regulation of MAP kinase activity|negative regulation of phagocytosis|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein autophosphorylation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|negative regulation of synaptic transmission|negative regulation of transcription, DNA-dependent|negative regulation of tumor necrosis factor production|negative regulation of tumor necrosis factor-mediated signaling pathway|positive regulation of cAMP-dependent protein kinase activity|positive regulation of cholesterol efflux|positive regulation of fatty acid metabolic process|positive regulation of glucose import|positive regulation of glycogen (starch) synthase activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of metanephric glomerular visceral epithelial cell development|positive regulation of monocyte chemotactic protein-1 production|positive regulation of myeloid cell apoptosis|positive regulation of protein kinase A signaling cascade|positive regulation of renal albumin absorption|protein homooligomerization|protein localization in plasma membrane|response to glucose stimulus|response to tumor necrosis factor	collagen|endoplasmic reticulum|extracellular space	cytokine activity|eukaryotic cell surface binding|hormone activity|protein homodimerization activity			ovary(1)	1	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)														---	---	---	---
ST6GAL1	6480	broad.mit.edu	37	3	186702517	186702552	+	Intron	DEL	TCCTTCCTTCCTTCCCTCCCTCCCTCCCTCCCTCCC	-	-	rs13315159		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186702517_186702552delTCCTTCCTTCCTTCCCTCCCTCCCTCCCTCCCTCCC	uc003frb.2	+						ST6GAL1_uc003frc.2_Intron	NM_173216	NP_775323			ST6 beta-galactosamide						humoral immune response|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			central_nervous_system(1)	1	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)														---	---	---	---
ST6GAL1	6480	broad.mit.edu	37	3	186708609	186708609	+	Intron	DEL	A	-	-	rs111445205		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186708609delA	uc003frb.2	+						ST6GAL1_uc003frc.2_Intron	NM_173216	NP_775323			ST6 beta-galactosamide						humoral immune response|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			central_nervous_system(1)	1	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	186929502	186929502	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186929502delA								RTP1 (10251 upstream) : MASP1 (6436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	187219849	187219850	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187219849_187219850delAA								RTP4 (130482 upstream) : SST (166846 downstream)																																			---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	188679657	188679657	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188679657delA	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)														---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189700671	189700671	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189700671delT	uc011bsk.1	-						LEPREL1_uc003fsg.2_Intron	NM_018192	NP_060662			leprecan-like 1 isoform a						collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	190550004	190550005	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190550004_190550005insA								IL1RAP (174161 upstream) : LOC647309 (20521 downstream)																																			---	---	---	---
UTS2D	257313	broad.mit.edu	37	3	191010792	191010792	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191010792delA	uc003fsu.2	-							NM_198152	NP_937795			urotensin 2 domain containing precursor							extracellular region	hormone activity				0	all_cancers(143;1.77e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000214)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	191139458	191139458	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191139458delT								CCDC50 (23000 upstream) : PYDC2 (39494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191686698	191686698	+	IGR	DEL	A	-	-	rs117663368	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191686698delA								PYDC2 (507455 upstream) : FGF12 (172986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	192954201	192954202	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192954201_192954202insA								C3orf59 (318251 upstream) : HRASLS (4716 downstream)																																			---	---	---	---
ATP13A5	344905	broad.mit.edu	37	3	193052596	193052597	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193052596_193052597insA	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	193130400	193130401	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193130400_193130401delGA	uc003ftd.2	-						ATP13A4_uc010hzi.2_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	193166170	193166170	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193166170delT	uc003ftd.2	-						ATP13A4_uc003fte.1_Intron|ATP13A4_uc011bsr.1_Intron|ATP13A4_uc010hzi.2_Intron	NM_032279	NP_115655			ATPase type 13A4						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)														---	---	---	---
OPA1	4976	broad.mit.edu	37	3	193331351	193331352	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193331351_193331352insT	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	193333585	193333585	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193333585delT	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	193491509	193491509	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193491509delT								OPA1 (75910 upstream) : LOC100128023 (219375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	193545160	193545161	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193545160_193545161insT								OPA1 (129561 upstream) : LOC100128023 (165723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	193681638	193681638	+	IGR	DEL	T	-	-	rs34475889		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193681638delT								OPA1 (266039 upstream) : LOC100128023 (29246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	193845708	193845709	+	IGR	INS	-	G	G	rs138130278	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193845708_193845709insG								LOC100128023 (133681 upstream) : HES1 (8225 downstream)																																			---	---	---	---
ATP13A3	79572	broad.mit.edu	37	3	194167075	194167076	+	Intron	INS	-	T	T	rs144259444	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194167075_194167076insT	uc003fty.3	-						ATP13A3_uc003ftz.1_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	194457942	194457943	+	IGR	INS	-	TCT	TCT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194457942_194457943insTCT								FAM43A (48178 upstream) : C3orf21 (331072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	194712076	194712081	+	IGR	DEL	CTCCTA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194712076_194712081delCTCCTA								FAM43A (302312 upstream) : C3orf21 (76934 downstream)																																			---	---	---	---
C3orf21	152002	broad.mit.edu	37	3	194982930	194982930	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194982930delA	uc003fum.3	-							NM_152531	NP_689744			hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	195288005	195288006	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195288005_195288006insA								PPP1R2 (17781 upstream) : APOD (7567 downstream)																																			---	---	---	---
SDHAP2	727956	broad.mit.edu	37	3	195392917	195392917	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195392917delT	uc003fuw.2	+						SDHAP2_uc003fut.3_Intron|SDHAP2_uc003fuu.3_Intron|SDHAP2_uc011btb.1_Intron|SDHAP2_uc011btc.1_Intron|SDHAP2_uc003fuv.2_Intron					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0																		---	---	---	---
MUC4	4585	broad.mit.edu	37	3	195480194	195480194	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195480194delC	uc011bto.1	-						MUC4_uc010hzq.2_5'UTR|MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron	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	195660331	195660334	+	IGR	DEL	CTTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195660331_195660334delCTTC								TNK2 (21515 upstream) : SDHAP1 (26458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	195878159	195878160	+	Intron	DEL	AA	-	-	rs113968075		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195878159_195878160delAA	uc011bts.1	+						uc011btt.1_Intron					Homo sapiens cDNA FLJ25996 fis, clone DMC06615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	196177274	196177276	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196177274_196177276delTTT								UBXN7 (17929 upstream) : RNF168 (21353 downstream)																																			---	---	---	---
RNF168	165918	broad.mit.edu	37	3	196215352	196215353	+	Intron	INS	-	A	A	rs66889619		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196215352_196215353insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	196395233	196395234	+	IGR	INS	-	AAATGA	AAATGA	rs143273785	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196395233_196395234insAAATGA								LRRC33 (6361 upstream) : C3orf34 (37915 downstream)																																			---	---	---	---
PIGX	54965	broad.mit.edu	37	3	196448634	196448634	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196448634delT	uc010iaj.2	+						PIGX_uc003fwx.3_Intron|PIGX_uc011btx.1_Intron	NM_017861	NP_060331			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane					0	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;1.08e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00322)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	196581570	196581571	+	IGR	DEL	TT	-	-	rs75988318		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196581570_196581571delTT								PAK2 (22054 upstream) : SENP5 (13156 downstream)																																			---	---	---	---
SENP5	205564	broad.mit.edu	37	3	196638680	196638681	+	Intron	INS	-	A	A	rs79698804		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196638680_196638681insA	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)														---	---	---	---
SENP5	205564	broad.mit.edu	37	3	196655007	196655007	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196655007delA	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)														---	---	---	---
MFI2	4241	broad.mit.edu	37	3	196746721	196746721	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196746721delA	uc003fxk.3	-						MFI2_uc003fxl.3_Intron|MFI2_uc011bua.1_Intron	NM_005929	NP_005920			melanoma-associated antigen p97 isoform 1						cellular iron ion homeostasis|iron ion transport	anchored to membrane|extracellular region|integral to plasma membrane	ferric iron binding|protein binding				0	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-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;0.00536)														---	---	---	---
LRCH3	84859	broad.mit.edu	37	3	197608027	197608029	+	Intron	DEL	GAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197608027_197608029delGAG	uc011bul.1	+						LRCH3_uc011bum.1_Intron|LRCH3_uc011bun.1_Intron|LRCH3_uc003fyk.2_Intron	NM_032773	NP_116162			leucine-rich repeats and calponin homology (CH)							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)														---	---	---	---
LMLN	89782	broad.mit.edu	37	3	197723027	197723027	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197723027delT	uc011buo.1	+						LMLN_uc003fyt.2_Intron|LMLN_uc010iar.2_Intron|LMLN_uc010ias.2_Intron|LMLN_uc003fyu.2_Intron	NM_033029	NP_149018			leishmanolysin-like isoform 2						cell adhesion|cell division|mitosis|proteolysis	cytoplasm|membrane	metalloendopeptidase activity|zinc ion binding			skin(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)														---	---	---	---
ZNF595	152687	broad.mit.edu	37	4	67784	67784	+	Intron	DEL	T	-	-	rs146895580		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67784delT	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_RNA|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330			zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)														---	---	---	---
ZNF718	255403	broad.mit.edu	37	4	100644	100644	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100644delT	uc003fzt.3	+						ZNF595_uc003fzu.1_Intron	NM_001039127	NP_001034216			zinc finger protein 718						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0681)|Epithelial(2;0.0838)|all cancers(2;0.135)|LUSC - Lung squamous cell carcinoma(95;0.18)														---	---	---	---
ZNF876P	642280	broad.mit.edu	37	4	224273	224273	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:224273delT	uc010iba.2	+							NR_027481				Homo sapiens cDNA clone IMAGE:4828836.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	409706	409707	+	IGR	DEL	AA	-	-	rs34544548		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:409706_409707delAA								ZNF141 (31947 upstream) : ABCA11P (9517 downstream)																																			---	---	---	---
ZNF721	170960	broad.mit.edu	37	4	490416	490416	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:490416delA	uc003gag.2	-						PIGG_uc003gaj.3_5'Flank|PIGG_uc003gak.3_5'Flank|PIGG_uc011bux.1_5'Flank|PIGG_uc010ibf.2_5'Flank|PIGG_uc003gal.3_5'Flank|ZNF721_uc010ibe.2_Intron|ZNF721_uc003gah.1_Intron|PIGG_uc003gai.2_5'Flank|PIGG_uc011buw.1_5'Flank|PIGG_uc003gam.2_5'Flank|PIGG_uc003gan.2_5'Flank	NM_133474	NP_597731			zinc finger protein 721							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	778080	778098	+	IGR	DEL	GGCCTGAACCACCGCACCT	-	-	rs6148267		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:778080_778098delGGCCTGAACCACCGCACCT								PCGF3 (13655 upstream) : CPLX1 (648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	824480	824481	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:824480_824481insT								CPLX1 (4535 upstream) : GAK (18585 downstream)																																			---	---	---	---
C4orf42	92070	broad.mit.edu	37	4	1276178	1276179	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1276178_1276179insA	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	1349097	1349097	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1349097delG	uc003gde.3	+							NM_020894	NP_065945			hypothetical protein LOC57654												0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)															---	---	---	---
LETM1	3954	broad.mit.edu	37	4	1852034	1852034	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1852034delA	uc003gdv.2	-						LETM1_uc011bvg.1_Intron	NM_012318	NP_036450			leucine zipper-EF-hand containing transmembrane						cristae formation	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			central_nervous_system(1)	1			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	1984148	1984150	+	IGR	DEL	TTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1984148_1984150delTTC								WHSC1 (215 upstream) : WHSC2 (294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	2052129	2052129	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2052129delT								C4orf48 (6432 upstream) : NAT8L (9458 downstream)																																			---	---	---	---
POLN	353497	broad.mit.edu	37	4	2214656	2214657	+	Intron	DEL	TT	-	-	rs75183121		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2214656_2214657delTT	uc003ger.2	-						POLN_uc011bvi.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					---	---	---	---
Unknown	0	broad.mit.edu	37	4	2550506	2550506	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2550506delA								RNF4 (32925 upstream) : FAM193A (47322 downstream)																																			---	---	---	---
FAM193A	8603	broad.mit.edu	37	4	2728279	2728279	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2728279delC	uc010icl.2	+						FAM193A_uc010ick.2_Intron|FAM193A_uc003gfd.2_Intron|FAM193A_uc011bvm.1_Intron|FAM193A_uc011bvn.1_Intron|FAM193A_uc011bvo.1_Intron|FAM193A_uc010icm.2_Intron	NM_003704	NP_003695			hypothetical protein LOC8603											ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	2779450	2779451	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2779450_2779451delTT								TNIP2 (21347 upstream) : SH3BP2 (15299 downstream)																																			---	---	---	---
GRK4	2868	broad.mit.edu	37	4	2978126	2978126	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2978126delT	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)														---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3360055	3360055	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3360055delT	uc003ggw.2	+						RGS12_uc003ggu.2_Intron|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_Intron|RGS12_uc003ggv.2_Intron|RGS12_uc003ggy.1_Intron	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)														---	---	---	---
HGFAC	3083	broad.mit.edu	37	4	3450973	3450973	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3450973delG	uc003ghc.2	+	14	1798	c.1795delG	c.(1795-1797)GGGfs	p.G599fs	HGFAC_uc010icw.2_Frame_Shift_Del_p.G606fs	NM_001528	NP_001519	Q04756	HGFA_HUMAN	HGF activator preproprotein	599	Peptidase S1.				proteolysis	extracellular space	protein binding|serine-type endopeptidase activity			central_nervous_system(2)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3589447	3589448	+	Intron	INS	-	GA	GA	rs144006715		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3589447_3589448insGA	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3624110	3624111	+	IGR	INS	-	A	A	rs150135720		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3624110_3624111insA								LRPAP1 (89886 upstream) : ADRA2C (143964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3634279	3634280	+	IGR	DEL	AG	-	-	rs116268291		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3634279_3634280delAG								LRPAP1 (100055 upstream) : ADRA2C (133795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3746598	3746598	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3746598delA								LRPAP1 (212374 upstream) : ADRA2C (21477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3817025	3817029	+	IGR	DEL	TATAG	-	-	rs79806569		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3817025_3817029delTATAG								ADRA2C (46774 upstream) : LOC348926 (126641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3923166	3923167	+	IGR	INS	-	ACAT	ACAT	rs140924089	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3923166_3923167insACAT								ADRA2C (152915 upstream) : LOC348926 (20503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	4576705	4576706	+	Intron	DEL	AC	-	-	rs35226933		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4576705_4576706delAC	uc003gid.2	+											Homo sapiens, clone IMAGE:5204729, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	4774736	4774736	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4774736delT	uc003gie.1	+											Homo sapiens cDNA FLJ31519 fis, clone NT2RI2000116.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	4826370	4826371	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4826370_4826371delAC								STX18 (282595 upstream) : MSX1 (35021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	5037809	5037809	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5037809delA								CYTL1 (16612 upstream) : STK32B (15718 downstream)																																			---	---	---	---
STK32B	55351	broad.mit.edu	37	4	5352799	5352800	+	Intron	INS	-	AAC	AAC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5352799_5352800insAAC	uc003gih.1	+						STK32B_uc010ida.1_Intron	NM_018401	NP_060871			serine/threonine kinase 32B								ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
EVC2	132884	broad.mit.edu	37	4	5710988	5710990	+	5'Flank	DEL	AGG	-	-	rs67550450		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5710988_5710990delAGG	uc003gij.2	-						EVC2_uc011bwb.1_5'UTR|EVC2_uc003gik.2_5'UTR|EVC_uc003gil.1_5'Flank|EVC_uc003gim.1_5'Flank	NM_147127	NP_667338			limbin							integral to membrane				large_intestine(3)|ovary(2)	5																		---	---	---	---
JAKMIP1	152789	broad.mit.edu	37	4	6091949	6091949	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6091949delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	6662353	6662364	+	IGR	DEL	AGGAGGAGGAGA	-	-	rs115852982		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6662353_6662364delAGGAGGAGGAGA								MRFAP1 (17904 upstream) : LOC93622 (13454 downstream)																																			---	---	---	---
KIAA0232	9778	broad.mit.edu	37	4	6797975	6797976	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6797975_6797976delTT	uc003gjr.3	+						KIAA0232_uc003gjq.3_Intron	NM_014743	NP_055558			hypothetical protein LOC9778								ATP binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	7076857	7076857	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7076857delT								GRPEL1 (7057 upstream) : FLJ36777 (22294 downstream)																																			---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7780664	7780664	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7780664delT	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7811544	7811544	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7811544delA	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
ABLIM2	84448	broad.mit.edu	37	4	7975229	7975230	+	Intron	DEL	AA	-	-	rs35927675		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7975229_7975230delAA	uc003gko.2	-						ABLIM2_uc003gkk.2_Intron|ABLIM2_uc003gkl.2_Intron|ABLIM2_uc003gkj.3_Intron|ABLIM2_uc003gkm.3_Intron|ABLIM2_uc003gkp.2_Intron|ABLIM2_uc003gkq.2_Intron|ABLIM2_uc003gkr.2_Intron|ABLIM2_uc003gki.2_Intron	NM_001130084	NP_001123556			actin binding LIM protein family, member 2						axon guidance|cytoskeleton organization	actin cytoskeleton|cytoplasm|intermediate filament cytoskeleton|nucleus	actin binding|zinc ion binding			pancreas(3)	3																		---	---	---	---
SH3TC1	54436	broad.mit.edu	37	4	8219843	8219844	+	Intron	DEL	AT	-	-	rs1281137	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8219843_8219844delAT	uc003gkv.3	+						SH3TC1_uc003gkw.3_Intron|SH3TC1_uc003gkx.3_Intron	NM_018986	NP_061859			SH3 domain and tetratricopeptide repeats 1								binding			large_intestine(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	8313876	8313876	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8313876delA								HTRA3 (5046 upstream) : ACOX3 (54134 downstream)																																			---	---	---	---
ACOX3	8310	broad.mit.edu	37	4	8433315	8433315	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8433315delA	uc003glc.3	-						ACOX3_uc003gld.3_Intron	NM_003501	NP_003492			acyl-Coenzyme A oxidase 3 isoform a						bile acid metabolic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|pristanoyl-CoA oxidase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	8819264	8819264	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8819264delC								CPZ (197778 upstream) : HMX1 (49509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	8879286	8879287	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8879286_8879287insG								HMX1 (5743 upstream) : LOC650293 (72190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	8886277	8886277	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8886277delT								HMX1 (12734 upstream) : LOC650293 (65200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	9100772	9100773	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9100772_9100773insA								LOC650293 (148646 upstream) : USP17 (259336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	9553874	9553874	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9553874delA								DEFB131 (101635 upstream) : MIR548I2 (3915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	9751510	9751510	+	IGR	DEL	A	-	-	rs111706217		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9751510delA								MIR548I2 (193573 upstream) : DRD5 (31748 downstream)																																			---	---	---	---
WDR1	9948	broad.mit.edu	37	4	10090633	10090634	+	Intron	DEL	CC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10090633_10090634delCC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	10700857	10700858	+	IGR	INS	-	AC	AC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10700857_10700858insAC								CLNK (14471 upstream) : MIR572 (669593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11244805	11244806	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11244805_11244806insT								CLNK (558419 upstream) : MIR572 (125645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11392765	11392767	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11392765_11392767delTTT								MIR572 (22220 upstream) : HS3ST1 (7222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11724494	11724494	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11724494delT								HS3ST1 (293957 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11856811	11856811	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11856811delT								HS3ST1 (426274 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11982717	11982718	+	IGR	DEL	TT	-	-	rs35552066		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11982717_11982718delTT								HS3ST1 (552180 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12075905	12075905	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12075905delT								HS3ST1 (645368 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12304241	12304242	+	IGR	DEL	AC	-	-	rs71878185		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12304241_12304242delAC								HS3ST1 (873704 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	13278990	13278990	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13278990delA								None (None upstream) : HSP90AB2P (56047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	13342946	13342947	+	IGR	INS	-	TTG	TTG	rs140310771	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13342946_13342947insTTG								HSP90AB2P (3022 upstream) : RAB28 (26400 downstream)																																			---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13582681	13582681	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13582681delA	uc003gmz.1	-							NM_148894	NP_683692			biorientation of chromosomes in cell division								DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
CC2D2A	57545	broad.mit.edu	37	4	15511903	15511904	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15511903_15511904insT	uc010idv.2	+						CC2D2A_uc003gnx.2_Intron|CC2D2A_uc003gnu.2_Intron|CC2D2A_uc003gnv.2_Intron	NM_001080522	NP_001073991			coiled-coil and C2 domain containing 2A isoform						cell projection organization	cilium|microtubule basal body				pancreas(2)|ovary(1)	3																		---	---	---	---
FBXL5	26234	broad.mit.edu	37	4	15642604	15642604	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15642604delA	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	15863482	15863483	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15863482_15863483insG								CD38 (12776 upstream) : FGFBP1 (73712 downstream)																																			---	---	---	---
PROM1	8842	broad.mit.edu	37	4	15981927	15981930	+	Intron	DEL	AAAA	-	-	rs71675065		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15981927_15981930delAAAA	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	16027342	16027343	+	Intron	INS	-	CA	CA	rs139033375	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16027342_16027343insCA	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																		---	---	---	---
TAPT1	202018	broad.mit.edu	37	4	16166467	16166467	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16166467delA	uc010ied.1	-						TAPT1_uc011bxd.1_Intron|TAPT1_uc011bxe.1_Intron	NM_153365	NP_699196			transmembrane anterior posterior transformation							integral to membrane	growth hormone-releasing hormone receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	16495976	16495976	+	IGR	DEL	A	-	-	rs73798787		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16495976delA								FLJ39653 (236166 upstream) : LDB2 (7191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	17442430	17442430	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17442430delA								LDB2 (542006 upstream) : QDPR (45590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18330181	18330181	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18330181delT								LCORL (306796 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	19234908	19234908	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19234908delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	19809220	19809221	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19809220_19809221delTT								None (None upstream) : SLIT2 (446014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	20066183	20066184	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20066183_20066184insT								None (None upstream) : SLIT2 (189051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	20244168	20244169	+	IGR	DEL	GT	-	-	rs34968915		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20244168_20244169delGT								None (None upstream) : SLIT2 (11066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	22227190	22227190	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22227190delA								KCNIP4 (276816 upstream) : GPR125 (161809 downstream)																																			---	---	---	---
GPR125	166647	broad.mit.edu	37	4	22446406	22446406	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22446406delA	uc003gqm.1	-						GPR125_uc010ieo.1_Intron|GPR125_uc003gqn.1_5'Flank|GPR125_uc003gqo.2_Intron	NM_145290	NP_660333			G protein-coupled receptor 125 precursor						neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)																---	---	---	---
GBA3	57733	broad.mit.edu	37	4	22750449	22750449	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	23068601	23068602	+	IGR	INS	-	TG	TG	rs145335795	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23068601_23068602insTG								GBA3 (247410 upstream) : PPARGC1A (725043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23159500	23159502	+	IGR	DEL	AAA	-	-	rs77636837		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23159500_23159502delAAA								GBA3 (338309 upstream) : PPARGC1A (634143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23567351	23567352	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23567351_23567352delAA								GBA3 (746160 upstream) : PPARGC1A (226293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23600426	23600426	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23600426delT								GBA3 (779235 upstream) : PPARGC1A (193219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24287051	24287051	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24287051delA								PPARGC1A (395351 upstream) : MIR573 (234764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24439451	24439452	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24439451_24439452insT								PPARGC1A (547751 upstream) : MIR573 (82363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24477048	24477048	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24477048delT								PPARGC1A (585348 upstream) : MIR573 (44767 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	25587065	25587067	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25587065_25587067delTTT								ANAPC4 (166946 upstream) : SLC34A2 (70368 downstream)																																			---	---	---	---
SLC34A2	10568	broad.mit.edu	37	4	25665878	25665878	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25665878delT	uc003grr.2	+	4	386	c.305delT	c.(304-306)ATTfs	p.I102fs	SLC34A2_uc003grs.2_Frame_Shift_Del_p.I101fs|SLC34A2_uc010iev.2_Frame_Shift_Del_p.I101fs	NM_006424	NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (sodium phosphate),	102	Helical; Name=M1; (Potential).				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)																---	---	---	---
SEL1L3	23231	broad.mit.edu	37	4	25781994	25781995	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25781994_25781995insC	uc003gru.3	-						SEL1L3_uc003grv.2_Intron	NM_015187	NP_056002			sel-1 suppressor of lin-12-like 3							integral to membrane	binding				0																		---	---	---	---
CCKAR	886	broad.mit.edu	37	4	26494532	26494532	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26494532delT	uc003gse.1	-							NM_000730	NP_000721			cholecystokinin A receptor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|elevation of cytosolic calcium ion concentration|response to nutrient	integral to plasma membrane	cholecystokinin receptor activity			lung(3)|pancreas(1)	4		Breast(46;0.0503)			Ceruletide(DB00403)													---	---	---	---
STIM2	57620	broad.mit.edu	37	4	27004738	27004738	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27004738delA	uc003gsh.3	+						STIM2_uc003gsg.3_Intron|STIM2_uc010iex.2_Intron|STIM2_uc010iey.2_Intron	NM_020860	NP_065911			stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	27162863	27162863	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27162863delT								STIM2 (137055 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	27192659	27192660	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27192659_27192660delTT								STIM2 (166851 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	27998720	27998720	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27998720delT								STIM2 (972912 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28579307	28579307	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28579307delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28701950	28701950	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28701950delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28819968	28819969	+	5'Flank	DEL	AT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28819968_28819969delAT	hsa-mir-4275|MI0015883	+																																									---	---	---	---
Unknown	0	broad.mit.edu	37	4	29512628	29512635	+	IGR	DEL	AAAAAAAA	-	-	rs35110959		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29512628_29512635delAAAAAAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29848248	29848248	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29848248delA								None (None upstream) : PCDH7 (873789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	30635284	30635284	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30635284delA								None (None upstream) : PCDH7 (86753 downstream)																																			---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	30767736	30767737	+	Intron	DEL	AA	-	-	rs33952570		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30767736_30767737delAA	uc011bxx.1	+						PCDH7_uc011bxw.1_Intron	NM_002589	NP_002580			protocadherin 7 isoform a precursor						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4																		---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	31006574	31006575	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31006574_31006575delAC	uc011bxx.1	+						PCDH7_uc011bxw.1_Intron	NM_002589	NP_002580			protocadherin 7 isoform a precursor						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4																		---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	31018018	31018019	+	Intron	INS	-	T	T	rs80034774		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31018018_31018019insT	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	31622827	31622828	+	IGR	INS	-	CTCACA	CTCACA	rs150977796	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31622827_31622828insCTCACA								PCDH7 (474406 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	31753994	31753994	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31753994delA								PCDH7 (605573 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	31765414	31765415	+	IGR	INS	-	CA	CA	rs140367279	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31765414_31765415insCA								PCDH7 (616993 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32000666	32000667	+	IGR	DEL	AC	-	-	rs72211534		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32000666_32000667delAC								PCDH7 (852245 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32320023	32320023	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32320023delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33135019	33135019	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33135019delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33544768	33544769	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33544768_33544769insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33787540	33787540	+	IGR	DEL	A	-	-	rs35137181		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33787540delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33860189	33860189	+	IGR	DEL	G	-	-	rs111479250		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33860189delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	34020320	34020320	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34020320delT	uc003gsn.2	-											Homo sapiens, clone IMAGE:5172449, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	34644526	34644526	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34644526delA								None (None upstream) : None (None downstream)																																			---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36095249	36095249	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36095249delA	uc003gsq.1	-							NM_015230	NP_056045			ArfGAP with RhoGAP domain, ankyrin repeat and PH						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36230062	36230062	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36230062delT	uc003gsq.1	-						ARAP2_uc003gsr.1_Intron	NM_015230	NP_056045			ArfGAP with RhoGAP domain, ankyrin repeat and PH						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
KIAA1239	57495	broad.mit.edu	37	4	37339422	37339422	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37339422delT	uc011bxz.1	+							NM_001144990	NP_001138462			hypothetical protein LOC57495												0																		---	---	---	---
C4orf19	55286	broad.mit.edu	37	4	37487865	37487865	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37487865delT	uc003gsw.3	+							NM_001104629	NP_001098099			hypothetical protein LOC55286												0																		---	---	---	---
C4orf19	55286	broad.mit.edu	37	4	37532624	37532624	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37532624delA	uc003gsw.3	+							NM_001104629	NP_001098099			hypothetical protein LOC55286												0																		---	---	---	---
RELL1	768211	broad.mit.edu	37	4	37597549	37597549	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37597549delA	uc003gsz.2	-							NM_001085399	NP_001078868			receptor expressed in lymphoid tissues like 1							cytoplasm|integral to membrane|microtubule cytoskeleton|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	38729770	38729770	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38729770delT								KLF3 (26642 upstream) : TLR10 (44493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	38763234	38763234	+	IGR	DEL	A	-	-	rs34421855		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38763234delA								KLF3 (60106 upstream) : TLR10 (11029 downstream)																																			---	---	---	---
TLR6	10333	broad.mit.edu	37	4	38857487	38857488	+	Intron	INS	-	AAAT	AAAT	rs144221405	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38857487_38857488insAAAT	uc010ifg.1	-							NM_006068	NP_006059			toll-like receptor 6 precursor						activation of NF-kappaB-inducing kinase activity|cellular response to diacyl bacterial lipopeptide|defense response to bacterium|detection of diacyl bacterial lipopeptide|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-6 biosynthetic process|positive regulation of JUN kinase activity|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	integral to plasma membrane|phagocytic vesicle membrane	lipopeptide binding|transmembrane receptor activity			ovary(2)	2																		---	---	---	---
TMEM156	80008	broad.mit.edu	37	4	38990181	38990182	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38990181_38990182delTC	uc003gto.2	-						TMEM156_uc010ifj.2_Intron	NM_024943	NP_079219			transmembrane protein 156							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	39161043	39161044	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39161043_39161044delGA								KLHL5 (37215 upstream) : WDR19 (22980 downstream)																																			---	---	---	---
WDR19	57728	broad.mit.edu	37	4	39226487	39226487	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39226487delT	uc003gtv.2	+						WDR19_uc003gtu.1_Intron|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																		---	---	---	---
RFC1	5981	broad.mit.edu	37	4	39313233	39313233	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39313233delA	uc003gty.1	-						RFC1_uc003gtx.1_Intron	NM_002913	NP_002904			replication factor C large subunit						DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|telomere maintenance via telomerase|transcription, DNA-dependent|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|enzyme activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
LIAS	11019	broad.mit.edu	37	4	39478849	39478850	+	3'UTR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39478849_39478850delAA	uc003guf.2	+	11					LIAS_uc003gug.2_3'UTR|LIAS_uc003guh.2_3'UTR	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	39505928	39505928	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39505928delA	uc003guk.1	-						UGDH_uc011byp.1_Intron|UGDH_uc003gul.1_Intron	NM_003359	NP_003350			UDP-glucose dehydrogenase						glycosaminoglycan biosynthetic process|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	electron carrier activity|NAD binding|UDP-glucose 6-dehydrogenase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	39788816	39788818	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39788816_39788818delTTT								UBE2K (4408 upstream) : PDS5A (35666 downstream)																																			---	---	---	---
PDS5A	23244	broad.mit.edu	37	4	39929854	39929854	+	Intron	DEL	A	-	-	rs149442914		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39929854delA	uc003guv.3	-						PDS5A_uc010ifo.2_Intron|PDS5A_uc003guw.3_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																		---	---	---	---
N4BP2	55728	broad.mit.edu	37	4	40144243	40144243	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40144243delT	uc003guy.3	+						N4BP2_uc010ifq.2_Intron|N4BP2_uc010ifr.2_Intron	NM_018177	NP_060647			Nedd4 binding protein 2							cytoplasm	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding			lung(3)|breast(2)|kidney(2)|ovary(1)	8																		---	---	---	---
RHOH	399	broad.mit.edu	37	4	40234012	40234012	+	Intron	DEL	T	-	-	rs35342029		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40234012delT	uc003guz.2	+							NM_004310	NP_004301			ras homolog gene family, member H precursor						negative regulation of I-kappaB kinase/NF-kappaB cascade|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|T cell differentiation	cytosol|mitochondrion|plasma membrane	GTP binding|GTPase inhibitor activity|kinase inhibitor activity|Rho GTPase binding			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	40397845	40397845	+	IGR	DEL	A	-	-	rs77154620		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40397845delA								CHRNA9 (40872 upstream) : RBM47 (27427 downstream)																																			---	---	---	---
RBM47	54502	broad.mit.edu	37	4	40441160	40441160	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40441160delA	uc003gvc.2	-						RBM47_uc003gvd.2_Intron|RBM47_uc003gve.2_Intron|RBM47_uc011bys.1_Intron|RBM47_uc003gvg.1_Intron	NM_001098634	NP_001092104			RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3																		---	---	---	---
RBM47	54502	broad.mit.edu	37	4	40494071	40494071	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40494071delA	uc003gvc.2	-						RBM47_uc003gvd.2_Intron|RBM47_uc003gve.2_Intron|RBM47_uc011bys.1_Intron|RBM47_uc003gvg.1_Intron	NM_001098634	NP_001092104			RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	40704872	40704872	+	IGR	DEL	C	-	-	rs10000266	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40704872delC								RBM47 (72232 upstream) : NSUN7 (47042 downstream)																																			---	---	---	---
APBB2	323	broad.mit.edu	37	4	40888506	40888506	+	Intron	DEL	A	-	-	rs75478168		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40888506delA	uc003gvl.2	-						APBB2_uc010ifu.2_Intron|APBB2_uc003gvm.2_Intron|APBB2_uc003gvn.2_Intron	NM_173075	NP_775098			amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
APBB2	323	broad.mit.edu	37	4	41057690	41057690	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41057690delA	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																		---	---	---	---
APBB2	323	broad.mit.edu	37	4	41103976	41103978	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41103976_41103978delAAA	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																		---	---	---	---
APBB2	323	broad.mit.edu	37	4	41115004	41115004	+	Intron	DEL	A	-	-	rs74602286		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41115004delA	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	41476999	41476999	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41476999delA	uc003gvu.3	+						LIMCH1_uc003gvt.1_Intron|LIMCH1_uc003gvv.3_Intron|LIMCH1_uc003gvw.3_Intron|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Intron|LIMCH1_uc003gvy.3_Intron	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																		---	---	---	---
LIMCH1	22998	broad.mit.edu	37	4	41615211	41615211	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41615211delT	uc003gvu.3	+						LIMCH1_uc003gvt.1_Intron|LIMCH1_uc003gvv.3_Intron|LIMCH1_uc003gvw.3_Intron|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Intron|LIMCH1_uc003gvy.3_Intron|LIMCH1_uc003gwa.3_Intron|LIMCH1_uc003gvz.3_Intron|LIMCH1_uc011byu.1_Intron|LIMCH1_uc003gwc.3_Intron|LIMCH1_uc003gwd.3_Intron|LIMCH1_uc011byv.1_5'Flank|LIMCH1_uc003gwb.1_Intron	NM_014988	NP_055803			LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42037517	42037519	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42037517_42037519delTTT	uc003gwl.2	+						SLC30A9_uc011byx.1_Intron	NM_006345	NP_006336			solute carrier family 30 (zinc transporter),						nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42080153	42080153	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42080153delT	uc003gwl.2	+						SLC30A9_uc011byx.1_Intron	NM_006345	NP_006336			solute carrier family 30 (zinc transporter),						nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	42233258	42233258	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42233258delT								BEND4 (78363 upstream) : SHISA3 (166598 downstream)																																			---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42480384	42480384	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42480384delA	uc003gwr.2	-						ATP8A1_uc003gwq.2_Intron|ATP8A1_uc003gws.2_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	42814991	42814991	+	IGR	DEL	T	-	-	rs79947622		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42814991delT								ATP8A1 (155869 upstream) : GRXCR1 (80293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	42865392	42865392	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42865392delT								ATP8A1 (206270 upstream) : GRXCR1 (29892 downstream)																																			---	---	---	---
KCTD8	386617	broad.mit.edu	37	4	44177044	44177044	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44177044delT	uc003gwu.2	-	2	1469	c.1185delA	c.(1183-1185)AAAfs	p.K395fs		NM_198353	NP_938167	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerisation domain	395						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)			---	---	---	---
YIPF7	285525	broad.mit.edu	37	4	44651969	44651969	+	Intron	DEL	A	-	-	rs35447406		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44651969delA	uc010ifx.1	-						YIPF7_uc010ify.1_Intron	NM_182592	NP_872398			Yip1 domain family, member 7							endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	45557591	45557591	+	IGR	DEL	T	-	-	rs34590965		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45557591delT								GNPDA2 (828979 upstream) : GABRG1 (480198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	46137414	46137414	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46137414delT								GABRG1 (11332 upstream) : GABRA2 (114167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	46644846	46644846	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46644846delT								GABRA2 (252425 upstream) : COX7B2 (92003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	46727886	46727886	+	IGR	DEL	C	-	-	rs62303512		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46727886delC								GABRA2 (335465 upstream) : COX7B2 (8963 downstream)																																			---	---	---	---
COMMD8	54951	broad.mit.edu	37	4	47455026	47455027	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47455026_47455027insC	uc003gxi.2	-							NM_017845	NP_060315			COMM domain containing 8								protein binding				0																		---	---	---	---
CORIN	10699	broad.mit.edu	37	4	47788686	47788686	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47788686delA	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	47899965	47899965	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47899965delA	uc010igh.2	-						NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_Intron|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540			nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
SLAIN2	57606	broad.mit.edu	37	4	48364441	48364441	+	Intron	DEL	T	-	-	rs76098263		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48364441delT	uc003gya.3	+							NM_020846	NP_065897			SLAIN motif family, member 2							centrosome					0																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48625212	48625213	+	Intron	DEL	AC	-	-	rs776579	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48625212_48625213delAC	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gyl.1_Intron|FRYL_uc003gym.1_Intron	NM_015030	NP_055845			furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	48873997	48873997	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48873997delT								OCIAD1 (10166 upstream) : OCIAD2 (13410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49099749	49099753	+	IGR	DEL	TCCGG	-	-	rs60947727		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49099749_49099753delTCCGG								CWH43 (35656 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49178374	49178374	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49178374delT								CWH43 (114281 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49267384	49267384	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49267384delG								CWH43 (203291 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49609816	49609817	+	IGR	INS	-	T	T	rs77046170		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49609816_49609817insT								CWH43 (545723 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49649283	49649284	+	IGR	INS	-	A	A	rs138495585		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49649283_49649284insA								CWH43 (585190 upstream) : None (None downstream)																																			---	---	---	---
SPATA18	132671	broad.mit.edu	37	4	52926826	52926826	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	53111157	53111157	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53111157delT								SPATA18 (147700 upstream) : USP46 (345972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53174225	53174225	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53174225delT								SPATA18 (210768 upstream) : USP46 (282904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53206619	53206619	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53206619delT								SPATA18 (243162 upstream) : USP46 (250510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53244074	53244074	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53244074delC								SPATA18 (280617 upstream) : USP46 (213055 downstream)																																			---	---	---	---
USP46	64854	broad.mit.edu	37	4	53474785	53474785	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53474785delA	uc003gzn.2	-						USP46_uc003gzm.3_Intron|USP46_uc011bzr.1_Intron|USP46_uc011bzs.1_Intron	NM_022832	NP_073743			ubiquitin specific peptidase 46 isoform 1						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)															---	---	---	---
USP46	64854	broad.mit.edu	37	4	53496419	53496419	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53496419delA	uc003gzn.2	-						USP46_uc003gzm.3_Intron|USP46_uc011bzr.1_Intron|USP46_uc011bzs.1_Intron	NM_022832	NP_073743			ubiquitin specific peptidase 46 isoform 1						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	54256109	54256109	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54256109delT	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)			---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54833852	54833855	+	Intron	DEL	TTTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54833852_54833855delTTTG	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	54871506	54871509	+	Intron	DEL	TTTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54871506_54871509delTTTG	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	55073247	55073247	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55073247delT	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	55160807	55160808	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55160807_55160808insG	uc003han.3	+						PDGFRA_uc003haa.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)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	55230981	55230981	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55230981delA								PDGFRA (66570 upstream) : KIT (293114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	55409125	55409125	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55409125delA								PDGFRA (244714 upstream) : KIT (114970 downstream)																																			---	---	---	---
KIT	3815	broad.mit.edu	37	4	55569860	55569860	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55569860delT	uc010igr.2	+						KIT_uc010igs.2_Intron	NM_000222	NP_000213			v-kit Hardy-Zuckerman 4 feline sarcoma viral						male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity			soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1)	5118	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)		1	Mis|O		GIST|AML|TGCT|mastocytosis|mucosal melanoma	GIST|epithelioma	Piebald trait		Mast_Cell_disease_Familial_Clustering_of|Piebaldism|Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Gastrointestinal_Stromal_Tumors				---	---	---	---
Unknown	0	broad.mit.edu	37	4	55756073	55756073	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55756073delA								KIT (149194 upstream) : KDR (188354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	55774229	55774230	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55774229_55774230insG								KIT (167350 upstream) : KDR (170197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	56096913	56096913	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56096913delG								KDR (105151 upstream) : SRD5A3 (115496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	56644866	56644866	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56644866delT								NMU (142401 upstream) : LOC644145 (41371 downstream)																																			---	---	---	---
KIAA1211	57482	broad.mit.edu	37	4	57149511	57149511	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57149511delT	uc003hbk.2	+						KIAA1211_uc010iha.2_Intron	NM_020722	NP_065773			hypothetical protein LOC57482											ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
AASDH	132949	broad.mit.edu	37	4	57236111	57236111	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57236111delA	uc003hbn.2	-						AASDH_uc010ihb.2_Intron|AASDH_uc011caa.1_Intron|AASDH_uc003hbo.2_Intron|AASDH_uc011cab.1_Intron|AASDH_uc010ihc.2_Intron|AASDH_uc003hbp.2_Intron	NM_181806	NP_861522			aminoadipate-semialdehyde dehydrogenase						fatty acid metabolic process		acid-thiol ligase activity|acyl carrier activity|ATP binding|cofactor binding			ovary(4)	4	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)																---	---	---	---
PPAT	5471	broad.mit.edu	37	4	57267248	57267248	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57267248delA	uc003hbr.2	-							NM_002703	NP_002694			phosphoribosyl pyrophosphate amidotransferase						glutamine metabolic process|nucleoside metabolic process|purine base biosynthetic process|purine ribonucleoside monophosphate biosynthetic process	cytosol	4 iron, 4 sulfur cluster binding|amidophosphoribosyltransferase activity|metal ion binding				0	Glioma(25;0.08)|all_neural(26;0.101)				L-Glutamine(DB00130)|Thioguanine(DB00352)													---	---	---	---
PPAT	5471	broad.mit.edu	37	4	57299748	57299748	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57299748delA	uc003hbr.2	-						PAICS_uc003hbs.1_5'Flank|PAICS_uc011cac.1_5'Flank|PAICS_uc003hbt.1_5'Flank|PAICS_uc003hbu.1_5'Flank|PAICS_uc010ihd.1_5'Flank	NM_002703	NP_002694			phosphoribosyl pyrophosphate amidotransferase						glutamine metabolic process|nucleoside metabolic process|purine base biosynthetic process|purine ribonucleoside monophosphate biosynthetic process	cytosol	4 iron, 4 sulfur cluster binding|amidophosphoribosyltransferase activity|metal ion binding				0	Glioma(25;0.08)|all_neural(26;0.101)				L-Glutamine(DB00130)|Thioguanine(DB00352)													---	---	---	---
SRP72	6731	broad.mit.edu	37	4	57352462	57352462	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57352462delT	uc003hbv.2	+						SRP72_uc010ihe.2_Intron|SRP72_uc003hbw.1_Intron	NM_006947	NP_008878			signal recognition particle 72kDa						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|nucleolus|plasma membrane|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding			ovary(1)	1	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	57500223	57500223	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57500223delA								ARL9 (110165 upstream) : HOPX (13931 downstream)																																			---	---	---	---
HOPX	84525	broad.mit.edu	37	4	57544923	57544923	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57544923delT	uc003hcc.2	-						HOPX_uc003hca.2_Intron|HOPX_uc003hcb.2_Intron|HOPX_uc003hcd.2_Intron|HOPX_uc003hce.2_Intron	NM_001145460	NP_001138932			HOP homeobox isoform c						negative regulation of cell differentiation|trophectodermal cell differentiation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
SPINK2	6691	broad.mit.edu	37	4	57677781	57677781	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57677781delA	uc003hcg.1	-							NM_021114	NP_066937			serine protease inhibitor, Kazal type 2							extracellular region	serine-type endopeptidase inhibitor activity				0	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	58356048	58356048	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58356048delA								IGFBP7 (379509 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58408223	58408223	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58408223delA								IGFBP7 (431684 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58540368	58540368	+	IGR	DEL	T	-	-	rs35229320		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58540368delT								IGFBP7 (563829 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58704623	58704623	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58704623delT								IGFBP7 (728084 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	59801938	59801940	+	IGR	DEL	AAA	-	-	rs34490794		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59801938_59801940delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60783087	60783087	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60783087delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61162699	61162699	+	IGR	DEL	T	-	-	rs34247246		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61162699delT								None (None upstream) : LPHN3 (904275 downstream)																																			---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62206142	62206142	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62206142delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	63006189	63006190	+	IGR	INS	-	AG	AG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63006189_63006190insAG								LPHN3 (68022 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63664721	63664722	+	IGR	INS	-	AGTC	AGTC	rs113503707		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63664721_63664722insAGTC								LPHN3 (726554 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63914626	63914627	+	IGR	DEL	TC	-	-	rs145521370		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63914626_63914627delTC								LPHN3 (976459 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64027932	64027932	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64027932delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64580107	64580107	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64580107delA								None (None upstream) : TECRL (564078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64849033	64849033	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64849033delT								None (None upstream) : TECRL (295152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	65641531	65641531	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65641531delA								TECRL (366353 upstream) : EPHA5 (543751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	69252422	69252423	+	IGR	DEL	TT	-	-	rs35711300		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69252422_69252423delTT								YTHDC1 (36598 upstream) : UGT2B15 (259893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	69262501	69262501	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69262501delT								YTHDC1 (46677 upstream) : UGT2B15 (249815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	69444216	69444216	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69444216delA								YTHDC1 (228392 upstream) : UGT2B15 (68100 downstream)																																			---	---	---	---
UGT2B28	54490	broad.mit.edu	37	4	70160633	70160633	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70160633delA	uc003hej.2	+	6					UGT2B28_uc010ihr.2_3'UTR	NM_053039	NP_444267			UDP glucuronosyltransferase 2 family,						xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1					Flunitrazepam(DB01544)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	70239332	70239333	+	IGR	DEL	AA	-	-	rs112145669		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70239332_70239333delAA								UGT2B28 (78565 upstream) : UGT2B4 (106551 downstream)																																			---	---	---	---
SULT1B1	27284	broad.mit.edu	37	4	70615191	70615192	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70615191_70615192insA	uc003hen.2	-							NM_014465	NP_055280			sulfotransferase family, cytosolic, 1B, member						3'-phosphoadenosine 5'-phosphosulfate metabolic process|cellular biogenic amine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|thyroid hormone metabolic process|xenobiotic metabolic process	cytosol					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	70816622	70816622	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70816622delA								CSN1S1 (4334 upstream) : CSN2 (4353 downstream)																																			---	---	---	---
AMBN	258	broad.mit.edu	37	4	71469349	71469350	+	Intron	DEL	AC	-	-	rs112130724		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71469349_71469350delAC	uc003hfl.2	+							NM_016519	NP_057603			ameloblastin precursor						bone mineralization|cell adhesion|cell proliferation|odontogenesis of dentine-containing tooth	proteinaceous extracellular matrix	growth factor activity|structural constituent of tooth enamel			ovary(3)|skin(1)	4			Lung(101;0.235)															---	---	---	---
GRSF1	2926	broad.mit.edu	37	4	71702259	71702262	+	Intron	DEL	GTTT	-	-	rs72046994		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71702259_71702262delGTTT	uc010iia.1	-						GRSF1_uc011caz.1_Intron|GRSF1_uc003hfs.2_Intron	NM_002092	NP_002083			G-rich RNA sequence binding factor 1 isoform 1						mRNA polyadenylation		mRNA binding|nucleotide binding				0		all_hematologic(202;0.21)	Lung(101;0.235)															---	---	---	---
DCK	1633	broad.mit.edu	37	4	71889231	71889231	+	Intron	DEL	T	-	-	rs3833976		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71889231delT	uc003hfx.2	+						DCK_uc011cbb.1_Intron	NM_000788	NP_000779			deoxycytidine kinase						purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)													---	---	---	---
SLC4A4	8671	broad.mit.edu	37	4	72352882	72352882	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72352882delA	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron|SLC4A4_uc003hgc.3_Intron|SLC4A4_uc010iid.2_Intron	NM_001098484	NP_001091954			solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)															---	---	---	---
ADAMTS3	9508	broad.mit.edu	37	4	73386721	73386722	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73386721_73386722delTT	uc003hgk.1	-							NM_014243	NP_055058			ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	73797863	73797863	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73797863delT								ADAMTS3 (363347 upstream) : COX18 (122553 downstream)																																			---	---	---	---
COX18	285521	broad.mit.edu	37	4	73930892	73930893	+	Intron	INS	-	G	G	rs79402424		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73930892_73930893insG	uc003hgm.1	-						COX18_uc003hgn.1_Intron|COX18_uc011cbc.1_Intron|COX18_uc010iih.1_Intron	NM_173827	NP_776188			mitochondrial COX18 precursor						protein insertion into mitochondrial membrane|respiratory chain complex IV assembly	integral to mitochondrial inner membrane	protein transporter activity				0	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	74592493	74592493	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74592493delA								RASSF6 (106153 upstream) : IL8 (13782 downstream)																																			---	---	---	---
IL8	3576	broad.mit.edu	37	4	74687915	74687916	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74687915_74687916delAA	uc011cbh.1	+							NM_000584	NP_000575			interleukin 8 precursor						angiogenesis|calcium-mediated signaling|cell cycle arrest|cellular response to lipopolysaccharide|embryonic digestive tract development|G-protein coupled receptor protein signaling pathway|immune response|induction of positive chemotaxis|inflammatory response|negative regulation of cell proliferation|neutrophil activation|neutrophil chemotaxis|positive regulation of neutrophil chemotaxis|regulation of cell adhesion|regulation of retroviral genome replication	extracellular space|intracellular	chemokine activity|interleukin-8 receptor binding			ovary(2)	2	Breast(15;0.00102)		all cancers(17;0.00169)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)	LUSC - Lung squamous cell carcinoma(721;0.008)	Ketoprofen(DB01009)|Salbutamol(DB01001)|Simvastatin(DB00641)|Zileuton(DB00744)													---	---	---	---
EREG	2069	broad.mit.edu	37	4	75228375	75228376	+	5'Flank	INS	-	T	T	rs143651424	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75228375_75228376insT	uc003hie.1	+						EREG_uc003hid.2_5'Flank	NM_001432	NP_001423			epiregulin preproprotein						angiogenesis|cell-cell signaling|cytokine-mediated signaling pathway|epidermal growth factor receptor signaling pathway|female meiosis|keratinocyte differentiation|keratinocyte proliferation|luteinizing hormone signaling pathway|mRNA transcription|negative regulation of epithelial cell proliferation|negative regulation of smooth muscle cell differentiation|negative regulation of transcription, DNA-dependent|oocyte maturation|organ morphogenesis|ovarian cumulus expansion|ovulation|positive regulation of cell division|positive regulation of cytokine production|positive regulation of DNA replication|positive regulation of epidermal growth factor receptor activity|positive regulation of fibroblast proliferation|positive regulation of innate immune response|positive regulation of interleukin-6 biosynthetic process|positive regulation of mitosis|positive regulation of phosphorylation|positive regulation of smooth muscle cell proliferation|primary follicle stage|wound healing	extracellular space|integral to plasma membrane	epidermal growth factor receptor binding|growth factor activity			breast(1)|skin(1)	2			Lung(101;0.196)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	75750921	75750921	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75750921delT								BTC (31039 upstream) : PARM1 (107377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	76010133	76010136	+	IGR	DEL	AGGG	-	-	rs9991977		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76010133_76010136delAGGG								PARM1 (34810 upstream) : RCHY1 (394219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	76168026	76168026	+	IGR	DEL	A	-	-	rs75771353		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76168026delA								PARM1 (192703 upstream) : RCHY1 (236329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	76399788	76399788	+	IGR	DEL	A	-	-	rs72016439		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76399788delA								PARM1 (424465 upstream) : RCHY1 (4567 downstream)																																			---	---	---	---
RCHY1	25898	broad.mit.edu	37	4	76431851	76431853	+	Intron	DEL	AAA	-	-	rs5859467		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76431851_76431853delAAA	uc003hik.2	-						RCHY1_uc003hij.2_Intron|RCHY1_uc003hil.2_Intron|RCHY1_uc010iip.2_Intron|RCHY1_uc010iiq.2_Intron|RCHY1_uc010iir.2_Intron	NM_015436	NP_056251			ring finger and CHY zinc finger domain						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein autoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nuclear speck|ubiquitin ligase complex	electron carrier activity|p53 binding|protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)															---	---	---	---
USO1	8615	broad.mit.edu	37	4	76668170	76668171	+	Intron	DEL	TT	-	-	rs71818647		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76668170_76668171delTT	uc003hiu.2	+							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)															---	---	---	---
SDAD1	55153	broad.mit.edu	37	4	76892547	76892547	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76892547delT	uc003hje.3	-	9	895	c.776delA	c.(775-777)AACfs	p.N259fs	SDAD1_uc003hjf.3_Frame_Shift_Del_p.N162fs|SDAD1_uc011cbr.1_Frame_Shift_Del_p.N222fs	NM_018115	NP_060585	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	259	Potential.				protein transport|ribosomal large subunit biogenesis	nucleolus	protein binding			ovary(1)	1			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
ART3	419	broad.mit.edu	37	4	77018528	77018528	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77018528delA	uc003hjo.2	+						ART3_uc003hjk.2_Intron|ART3_uc010ija.1_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)															---	---	---	---
SCARB2	950	broad.mit.edu	37	4	77094999	77094999	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77094999delT	uc003hju.1	-						SCARB2_uc011cbu.1_Intron	NM_005506	NP_005497			scavenger receptor class B, member 2						cell adhesion|protein targeting to lysosome	integral to plasma membrane|lysosomal lumen|lysosomal membrane|membrane fraction	enzyme binding|receptor activity				0			Lung(101;0.196)															---	---	---	---
SEPT11	55752	broad.mit.edu	37	4	77933163	77933163	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77933163delT	uc003hkj.2	+						SEPT11_uc010ijh.1_Intron|SEPT11_uc011cca.1_Intron|SEPT11_uc003hkk.1_5'Flank	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	78604437	78604437	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78604437delA								CXCL13 (71451 upstream) : CNOT6L (30105 downstream)																																			---	---	---	---
CNOT6L	246175	broad.mit.edu	37	4	78695895	78695895	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78695895delA	uc011ccd.1	-						CNOT6L_uc003hks.2_Intron|CNOT6L_uc011cce.1_Intron	NM_144571	NP_653172			CCR4-NOT transcription complex, subunit 6-like						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	exonuclease activity|protein binding			large_intestine(1)	1																		---	---	---	---
MRPL1	65008	broad.mit.edu	37	4	78841921	78841921	+	Intron	DEL	T	-	-	rs112819752		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78841921delT	uc003hku.2	+						MRPL1_uc010iji.1_Intron	NM_020236	NP_064621			mitochondrial ribosomal protein L1 precursor								RNA binding				0																		---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79054667	79054667	+	Intron	DEL	A	-	-	rs113756389		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79054667delA	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	79343327	79343327	+	Intron	DEL	T	-	-	rs72048849		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79343327delT	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																		---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79366578	79366579	+	Intron	INS	-	TT	TT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79366578_79366579insTT	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																		---	---	---	---
ANXA3	306	broad.mit.edu	37	4	79477007	79477007	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79477007delA	uc003hld.2	+						ANXA3_uc003hle.2_Intron|ANXA3_uc010ijk.2_Intron	NM_005139	NP_005130			annexin A3						defense response to bacterium|neutrophil degranulation|phagocytosis|positive regulation of angiogenesis|positive regulation of endothelial cell migration|positive regulation of sequence-specific DNA binding transcription factor activity	phagocytic vesicle membrane|plasma membrane|specific granule	calcium ion binding|calcium-dependent phospholipid binding|phospholipase A2 inhibitor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	79546111	79546112	+	IGR	INS	-	AG	AG	rs151016289	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79546111_79546112insAG								ANXA3 (14509 upstream) : BMP2K (151420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	79658501	79658501	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79658501delA								ANXA3 (126899 upstream) : BMP2K (39031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	79678936	79678936	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79678936delA								ANXA3 (147334 upstream) : BMP2K (18596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	80334364	80334365	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80334364_80334365delTG								GK2 (4992 upstream) : GDEP (414260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	80593730	80593730	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80593730delA								GK2 (264358 upstream) : GDEP (154895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	80665604	80665604	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80665604delT								GK2 (336232 upstream) : GDEP (83021 downstream)																																			---	---	---	---
ANTXR2	118429	broad.mit.edu	37	4	80905931	80905932	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80905931_80905932delAA	uc003hlz.3	-						ANTXR2_uc003hly.3_Intron|ANTXR2_uc003hlx.1_Intron|ANTXR2_uc010ijn.2_Intron	NM_001145794	NP_001139266			anthrax toxin receptor 2 isoform 2							endoplasmic reticulum membrane|extracellular region|integral to membrane|plasma membrane	metal ion binding|protein binding|receptor activity			ovary(1)	1														Juvenile_Hyaline_Fibromatosis				---	---	---	---
C4orf22	255119	broad.mit.edu	37	4	81572859	81572862	+	Intron	DEL	TGTG	-	-	rs34777741		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81572859_81572862delTGTG	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983			hypothetical protein LOC255119											skin(2)	2																		---	---	---	---
PRKG2	5593	broad.mit.edu	37	4	82011512	82011512	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82011512delA	uc003hmh.2	-						PRKG2_uc011ccf.1_Intron|PRKG2_uc011ccg.1_Intron|PRKG2_uc011cch.1_Intron	NM_006259	NP_006250			protein kinase, cGMP-dependent, type II						platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	82268753	82268753	+	IGR	DEL	A	-	-	rs6813968		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82268753delA								PRKG2 (132535 upstream) : RASGEF1B (79466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	83141617	83141619	+	IGR	DEL	AAA	-	-	rs11315700		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83141617_83141619delAAA								RASGEF1B (748556 upstream) : HNRNPD (132848 downstream)																																			---	---	---	---
SCD5	79966	broad.mit.edu	37	4	83659017	83659017	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83659017delA	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)																---	---	---	---
SCD5	79966	broad.mit.edu	37	4	83694475	83694476	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83694475_83694476delTC	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)																---	---	---	---
LIN54	132660	broad.mit.edu	37	4	83854533	83854534	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83854533_83854534delAA	uc003hnx.3	-						LIN54_uc003hnz.3_Intron|LIN54_uc003hny.3_Intron|LIN54_uc010ijt.2_Intron|LIN54_uc010iju.2_Intron|LIN54_uc010ijv.2_Intron	NM_194282	NP_919258			lin-54 homolog isoform a						cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Hepatocellular(203;0.114)																---	---	---	---
COPS4	51138	broad.mit.edu	37	4	83966627	83966627	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83966627delA	uc003hoa.2	+						COPS4_uc003hob.2_Intron|COPS4_uc010ijw.2_Intron|COPS4_uc010ijx.2_Intron	NM_016129	NP_057213			COP9 signalosome subunit 4						cullin deneddylation	cytoplasm|signalosome	protein binding			kidney(1)	1		Hepatocellular(203;0.114)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	84091346	84091346	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84091346delA								PLAC8 (55435 upstream) : COQ2 (91343 downstream)																																			---	---	---	---
HPSE	10855	broad.mit.edu	37	4	84241719	84241720	+	Intron	DEL	AA	-	-	rs75657185		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84241719_84241720delAA	uc003hoj.3	-						HPSE_uc010ika.2_Intron|HPSE_uc011ccq.1_Intron|HPSE_uc011ccr.1_Intron|HPSE_uc011ccs.1_Intron|HPSE_uc011cct.1_Intron|HPSE_uc003hok.3_Intron	NM_001098540	NP_001092010			heparanase precursor						carbohydrate metabolic process|cell adhesion|proteoglycan metabolic process	extracellular region|lysosomal membrane|nucleus	beta-glucuronidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Heparin(DB01109)													---	---	---	---
HELQ	113510	broad.mit.edu	37	4	84339020	84339020	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84339020delT	uc003hom.2	-						HELQ_uc010ikb.2_Intron|HELQ_uc003hol.3_Intron|HELQ_uc010ikc.2_Intron	NM_133636	NP_598375			DNA helicase HEL308								ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|breast(1)|skin(1)	3													Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
HELQ	113510	broad.mit.edu	37	4	84356729	84356730	+	Intron	DEL	AA	-	-	rs10711036		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84356729_84356730delAA	uc003hom.2	-						HELQ_uc010ikb.2_Intron|HELQ_uc003hol.3_Intron|HELQ_uc010ikc.2_Intron	NM_133636	NP_598375			DNA helicase HEL308								ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|breast(1)|skin(1)	3													Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
Unknown	0	broad.mit.edu	37	4	84539192	84539192	+	IGR	DEL	A	-	-	rs11288454		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84539192delA								AGPAT9 (12167 upstream) : NKX6-1 (875244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	84610956	84610956	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84610956delT								AGPAT9 (83931 upstream) : NKX6-1 (803480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	84748099	84748099	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84748099delT	uc010ikd.1	-											Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	84788567	84788567	+	Intron	DEL	T	-	-	rs58411231		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84788567delT	uc010ikd.1	-											Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	85149208	85149208	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85149208delA	uc010ikd.1	-						uc003hoz.1_Intron					Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	85413599	85413599	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85413599delG								AGPAT9 (886574 upstream) : NKX6-1 (837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	85575255	85575255	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85575255delA								CDS1 (2763 upstream) : WDFY3 (15442 downstream)																																			---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85688266	85688266	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85688266delT	uc003hpd.2	-							NM_014991	NP_055806			WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85694189	85694190	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85694189_85694190delTT	uc003hpd.2	-							NM_014991	NP_055806			WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85696326	85696327	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85696326_85696327insA	uc003hpd.2	-							NM_014991	NP_055806			WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	86242923	86242925	+	IGR	DEL	AAA	-	-	rs66540163		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86242923_86242925delAAA								C4orf12 (314755 upstream) : ARHGAP24 (153359 downstream)																																			---	---	---	---
ARHGAP24	83478	broad.mit.edu	37	4	86707139	86707139	+	Intron	DEL	T	-	-	rs34673338		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86707139delT	uc003hpk.2	+						ARHGAP24_uc003hpj.2_Intron|ARHGAP24_uc003hpl.2_Intron	NM_001025616	NP_001020787			Rho GTPase activating protein 24 isoform 1						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)														---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	87302392	87302392	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87302392delC	uc003hpu.2	-						MAPK10_uc003hpt.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	87705769	87705769	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87705769delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	89009680	89009680	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89009680delA								PKD2 (10752 upstream) : ABCG2 (1737 downstream)																																			---	---	---	---
HERC5	51191	broad.mit.edu	37	4	89392495	89392495	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89392495delT	uc003hrt.2	+						HERC5_uc011cdm.1_Intron	NM_016323	NP_057407			hect domain and RLD 5						innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)														---	---	---	---
HERC5	51191	broad.mit.edu	37	4	89409834	89409834	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89409834delT	uc003hrt.2	+						HERC5_uc011cdm.1_Intron	NM_016323	NP_057407			hect domain and RLD 5						innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)														---	---	---	---
FAM13A	10144	broad.mit.edu	37	4	89653782	89653783	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89653782_89653783delAA	uc003hse.1	-						FAM13A_uc011cdp.1_Intron|FAM13A_uc003hsa.1_Intron|FAM13A_uc003hsb.1_Intron|FAM13A_uc003hsd.1_Intron|FAM13A_uc003hsc.1_Intron|FAM13A_uc011cdq.1_Intron|FAM13A_uc003hsf.1_Intron|FAM13A_uc003hsg.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																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91663243	91663244	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91663243_91663244delAG	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron|FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91846976	91846976	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91846976delT	uc003hsv.3	+						FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	93096483	93096483	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93096483delA								FAM190A (573114 upstream) : GRID2 (129067 downstream)																																			---	---	---	---
GRID2	2895	broad.mit.edu	37	4	93808703	93808704	+	Intron	INS	-	C	C	rs139177066	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93808703_93808704insC	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	93850337	93850337	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93850337delT	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	94349185	94349186	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94349185_94349186insA	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	94869443	94869443	+	IGR	DEL	A	-	-	rs35469069		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94869443delA								ATOH1 (118301 upstream) : SMARCAD1 (259316 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	94972248	94972248	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94972248delA								ATOH1 (221106 upstream) : SMARCAD1 (156511 downstream)																																			---	---	---	---
PDLIM5	10611	broad.mit.edu	37	4	95500622	95500622	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95500622delA	uc003hti.2	+						PDLIM5_uc003htf.2_Intron|PDLIM5_uc003htg.2_Intron|PDLIM5_uc011cdx.1_Intron|PDLIM5_uc003hth.2_Intron|PDLIM5_uc003htj.2_Intron|PDLIM5_uc003htk.2_Intron|PDLIM5_uc011cdy.1_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)														---	---	---	---
PDLIM5	10611	broad.mit.edu	37	4	95578859	95578859	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
BMPR1B	658	broad.mit.edu	37	4	95933191	95933191	+	Intron	DEL	A	-	-	rs76517516		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95933191delA	uc003htm.3	+							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)														---	---	---	---
BMPR1B	658	broad.mit.edu	37	4	95991325	95991325	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95991325delA	uc003htm.3	+							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	96147974	96147975	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96147974_96147975insT	uc003htp.1	-						UNC5C_uc010ilc.1_Intron|UNC5C_uc003htq.2_Intron	NM_003728	NP_003719			unc5C precursor						apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)														---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96178607	96178607	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96178607delA	uc003htp.1	-						UNC5C_uc010ilc.1_Intron|UNC5C_uc003htq.2_Intron	NM_003728	NP_003719			unc5C precursor						apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)														---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96199633	96199633	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96199633delT	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	96622922	96622922	+	IGR	DEL	C	-	-	rs9994276	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96622922delC								UNC5C (152760 upstream) : PDHA2 (138317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97899433	97899433	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97899433delA								None (None upstream) : C4orf37 (580601 downstream)																																			---	---	---	---
C4orf37	285555	broad.mit.edu	37	4	99065179	99065180	+	5'Flank	DEL	AA	-	-	rs36208505		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99065179_99065180delAA	uc003htt.1	-							NM_174952	NP_777612			hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	99707067	99707072	+	IGR	DEL	TTTTTT	-	-	rs71588967		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99707067_99707072delTTTTTT								TSPAN5 (127340 upstream) : EIF4E (92535 downstream)																																			---	---	---	---
EIF4E	1977	broad.mit.edu	37	4	99833405	99833405	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99833405delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	99896601	99896601	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99896601delT								EIF4E (44815 upstream) : METAP1 (20187 downstream)																																			---	---	---	---
METAP1	23173	broad.mit.edu	37	4	99919685	99919685	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99919685delA	uc003huf.3	+							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)														---	---	---	---
ADH6	130	broad.mit.edu	37	4	100128480	100128480	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100128480delA	uc003hup.3	-						uc003hum.1_Intron|ADH6_uc003huo.2_Intron|ADH6_uc011cef.1_Intron|ADH6_uc010ile.2_Intron	NM_000672	NP_000663			class V alcohol dehydrogenase isoform 2						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	100196380	100196381	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100196380_100196381delTC	uc003hum.1	+											Homo sapiens full length insert cDNA clone ZD94A03.																														---	---	---	---
ADH1A	124	broad.mit.edu	37	4	100200890	100200890	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100200890delA	uc003hur.1	-						uc003hum.1_Intron|ADH1A_uc011ceg.1_Intron	NM_000667	NP_000658			class I alcohol dehydrogenase, alpha subunit						ethanol oxidation|transcription, DNA-dependent|xenobiotic metabolic process	cytosol	alcohol dehydrogenase activity, zinc-dependent|protein binding|zinc ion binding			large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(123;9.56e-08)	Fomepizole(DB01213)|NADH(DB00157)													---	---	---	---
RG9MTD2	93587	broad.mit.edu	37	4	100470093	100470094	+	3'UTR	DEL	TT	-	-	rs35333223		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100470093_100470094delTT	uc003huy.2	-	8					RG9MTD2_uc003huz.3_3'UTR|RG9MTD2_uc003hva.3_3'UTR	NM_152292	NP_689505			RNA (guanine-9-) methyltransferase domain								methyltransferase activity			ovary(2)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;1.7e-08)														---	---	---	---
MTTP	4547	broad.mit.edu	37	4	100527027	100527028	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100527027_100527028delTG	uc003hvc.3	+						MTTP_uc011cej.1_Intron	NM_000253	NP_000244			microsomal triglyceride transfer protein large						lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	100672780	100672781	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100672780_100672781delTT								MTTP (127627 upstream) : DAPP1 (65200 downstream)																																			---	---	---	---
H2AFZ	3015	broad.mit.edu	37	4	100870671	100870672	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100870671_100870672insC	uc003hvo.1	-						DNAJB14_uc003hvl.2_5'Flank|DNAJB14_uc010ili.2_5'Flank|DNAJB14_uc003hvm.2_5'Flank|H2AFZ_uc003hvn.1_Frame_Shift_Ins_p.E77fs|LOC256880_uc003hvp.1_5'Flank	NM_002106	NP_002097			H2A histone family, member Z						nucleosome assembly	nucleosome|nucleus	DNA binding				0				OV - Ovarian serous cystadenocarcinoma(123;2.32e-08)												OREG0016271	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EMCN	51705	broad.mit.edu	37	4	101344248	101344249	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101344248_101344249insA	uc003hvr.2	-						EMCN_uc011cel.1_Intron|EMCN_uc011cem.1_Intron	NM_016242	NP_057326			endomucin isoform 1							extracellular region|integral to membrane|plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	101674893	101674893	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101674893delA								EMCN (235643 upstream) : PPP3CA (269694 downstream)																																			---	---	---	---
PPP3CA	5530	broad.mit.edu	37	4	102004650	102004650	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102004650delA	uc011cen.1	-						PPP3CA_uc003hvu.2_Intron|PPP3CA_uc010ilj.2_Intron|PPP3CA_uc003hvt.2_Intron|PPP3CA_uc003hvs.2_Intron|PPP3CA_uc010ilk.2_Intron	NM_000944	NP_000935			protein phosphatase 3, catalytic subunit, alpha						protein dephosphorylation	calcineurin complex|cytosol|nucleus	calcium ion binding|calmodulin binding			ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102729817	102729818	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102729817_102729818delAA	uc003hvy.3	+						BANK1_uc003hvx.3_Intron|BANK1_uc010ill.2_Intron	NM_017935	NP_060405			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102839362	102839362	+	Intron	DEL	A	-	-	rs3733198	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102839362delA	uc003hvy.3	+						BANK1_uc003hvx.3_Intron|BANK1_uc010ill.2_Intron|BANK1_uc003hvz.3_Intron	NM_017935	NP_060405			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102942660	102942661	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102942660_102942661insT	uc003hvy.3	+						BANK1_uc003hvx.3_Intron|BANK1_uc010ill.2_Intron|BANK1_uc003hvz.3_Intron	NM_017935	NP_060405			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102965187	102965187	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	103407746	103407746	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103407746delA								SLC39A8 (141091 upstream) : NFKB1 (14740 downstream)																																			---	---	---	---
MANBA	4126	broad.mit.edu	37	4	103653071	103653071	+	Intron	DEL	T	-	-	rs11445346		TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
UBE2D3	7323	broad.mit.edu	37	4	103730907	103730907	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103730907delA	uc003hwk.2	-						UBE2D3_uc003hwi.2_Intron|UBE2D3_uc003hwj.2_Intron|UBE2D3_uc003hwl.2_Intron|UBE2D3_uc011cet.1_Intron|UBE2D3_uc011ceu.1_Intron|UBE2D3_uc003hwo.2_Intron|UBE2D3_uc003hwp.2_Intron|UBE2D3_uc003hwq.2_Intron|UBE2D3_uc003hwr.2_Intron	NM_181887	NP_871616			ubiquitin-conjugating enzyme E2D 3 isoform 1						apoptosis|BMP signaling pathway|DNA repair|negative regulation of type I interferon production|proteasomal ubiquitin-dependent protein catabolic process|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein monoubiquitination|transforming growth factor beta receptor signaling pathway	endosome membrane|plasma membrane	ATP binding|protein binding|ubiquitin-protein ligase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.13e-08)														---	---	---	---
CENPE	1062	broad.mit.edu	37	4	104116398	104116398	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104116398delA	uc003hxb.1	-						CENPE_uc003hxc.1_Intron	NM_001813	NP_001804			centromere protein E						blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	104918668	104918668	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104918668delT								TACR3 (277695 upstream) : CXXC4 (474677 downstream)																																			---	---	---	---
CXXC4	80319	broad.mit.edu	37	4	105401778	105401779	+	Intron	DEL	AA	-	-	rs34786106		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105401778_105401779delAA	uc003hxg.2	-						CXXC4_uc010ilo.2_Intron	NM_025212	NP_079488			CXXC finger 4						negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway|zygotic specification of dorsal/ventral axis		DNA binding|PDZ domain binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;3.05e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	105416718	105416718	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105416718delA	uc003hxh.1	+						CXXC4_uc010ilo.2_5'Flank					Homo sapiens cDNA FLJ37242 fis, clone BRAMY2004335.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	105706044	105706044	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105706044delT								CXXC4 (289986 upstream) : TET2 (361899 downstream)																																			---	---	---	---
ARHGEF38	54848	broad.mit.edu	37	4	106551895	106551895	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	106762481	106762482	+	Intron	DEL	AA	-	-	rs78459491		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106762481_106762482delAA	uc003hxz.3	+						GSTCD_uc003hxy.3_Intron|GSTCD_uc011cfb.1_Intron	NM_001031720	NP_001026890			glutathione S-transferase, C-terminal domain							cytoplasm	rRNA methyltransferase activity			breast(1)|central_nervous_system(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)														---	---	---	---
TBCK	93627	broad.mit.edu	37	4	107115421	107115421	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107115421delA	uc010ilv.2	-						TBCK_uc003hyb.2_Intron|TBCK_uc003hye.2_Intron|TBCK_uc003hyc.2_Intron|TBCK_uc003hyd.2_Intron|TBCK_uc003hyf.2_Intron	NM_001163435	NP_001156907			TBC domain-containing protein kinase-like							intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5																		---	---	---	---
TBCK	93627	broad.mit.edu	37	4	107156505	107156505	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107156505delT	uc010ilv.2	-	15	1735	c.1370delA	c.(1369-1371)AACfs	p.N457fs	TBCK_uc003hyb.2_Frame_Shift_Del_p.N200fs|TBCK_uc003hye.2_Frame_Shift_Del_p.N418fs|TBCK_uc003hyc.2_Frame_Shift_Del_p.N394fs|TBCK_uc003hyd.2_Frame_Shift_Del_p.N285fs|TBCK_uc003hyf.2_Frame_Shift_Del_p.N457fs	NM_001163435	NP_001156907	Q8TEA7	TBCK_HUMAN	TBC domain-containing protein kinase-like	457						intracellular	Rab GTPase activator activity	p.N457fs*15(1)		large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	107342446	107342446	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107342446delT								AIMP1 (72067 upstream) : DKK2 (500514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	108407752	108407752	+	IGR	DEL	A	-	-	rs35222964		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108407752delA								DKK2 (202906 upstream) : PAPSS1 (127071 downstream)																																			---	---	---	---
SGMS2	166929	broad.mit.edu	37	4	108779826	108779828	+	Intron	DEL	TGC	-	-	rs146689045		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108779826_108779828delTGC	uc003hyl.3	+							NM_001136258	NP_001129730			sphingomyelin synthase 2						sphingomyelin biosynthetic process	integral to Golgi membrane|integral to plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			lung(1)	1				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)	Choline(DB00122)													---	---	---	---
SGMS2	166929	broad.mit.edu	37	4	108807358	108807358	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108807358delT	uc003hyl.3	+						uc003hym.1_Intron	NM_001136258	NP_001129730			sphingomyelin synthase 2						sphingomyelin biosynthetic process	integral to Golgi membrane|integral to plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			lung(1)	1				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)	Choline(DB00122)													---	---	---	---
LEF1	51176	broad.mit.edu	37	4	109045531	109045531	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109045531delT	uc003hyt.1	-						LEF1_uc011cfj.1_Intron|LEF1_uc011cfk.1_Intron|LEF1_uc003hyu.1_Intron|LEF1_uc003hyv.1_Intron|LEF1_uc010imb.1_Intron	NM_016269	NP_057353			lymphoid enhancer-binding factor 1 isoform 1						canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	109172525	109172525	+	IGR	DEL	A	-	-	rs77713018		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109172525delA								LEF1 (82947 upstream) : LOC285456 (286821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	109316828	109316828	+	IGR	DEL	A	-	-	rs79720193		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109316828delA								LEF1 (227250 upstream) : LOC285456 (142518 downstream)																																			---	---	---	---
RPL34	6164	broad.mit.edu	37	4	109546421	109546421	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109546421delT	uc003hyz.2	+						RPL34_uc003hza.2_Intron	NM_000995	NP_000986			ribosomal protein L34						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000286)														---	---	---	---
AGXT2L1	64850	broad.mit.edu	37	4	109670331	109670331	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109670331delA	uc003hzc.2	-						AGXT2L1_uc010imc.2_Intron|AGXT2L1_uc011cfm.1_Intron|AGXT2L1_uc011cfn.1_Intron|AGXT2L1_uc011cfo.1_Intron	NM_031279	NP_112569			alanine-glyoxylate aminotransferase 2-like 1						cellular amino acid metabolic process	mitochondrion	alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000281)														---	---	---	---
AGXT2L1	64850	broad.mit.edu	37	4	109674221	109674221	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109674221delA	uc003hzc.2	-						AGXT2L1_uc010imc.2_Intron|AGXT2L1_uc011cfm.1_Intron|AGXT2L1_uc011cfn.1_Intron|AGXT2L1_uc011cfo.1_Intron	NM_031279	NP_112569			alanine-glyoxylate aminotransferase 2-like 1						cellular amino acid metabolic process	mitochondrion	alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000281)														---	---	---	---
COL25A1	84570	broad.mit.edu	37	4	109814790	109814790	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109814790delA	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzd.2_Intron|COL25A1_uc003hzf.2_Intron	NM_198721	NP_942014			collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)														---	---	---	---
COL25A1	84570	broad.mit.edu	37	4	110094412	110094412	+	Intron	DEL	A	-	-	rs77313371	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110094412delA	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzh.1_Intron	NM_198721	NP_942014			collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)														---	---	---	---
CFI	3426	broad.mit.edu	37	4	110680248	110680249	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110680248_110680249insA	uc003hzr.3	-						CFI_uc003hzq.2_Intron|CFI_uc011cft.1_Intron|CFI_uc003hzs.3_Intron	NM_000204	NP_000195			complement factor I preproprotein						complement activation, classical pathway|innate immune response|proteolysis	extracellular space|membrane	scavenger receptor activity|serine-type endopeptidase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)														---	---	---	---
GAR1	54433	broad.mit.edu	37	4	110738627	110738627	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110738627delA	uc003hzt.2	+						GAR1_uc003hzu.2_Intron|GAR1_uc010imh.1_Intron|GAR1_uc010imi.2_Intron	NM_018983	NP_061856			nucleolar protein family A, member 1						rRNA processing|snRNA pseudouridine synthesis	box H/ACA snoRNP complex|Cajal body	cation channel activity|pseudouridine synthase activity|snoRNA binding				0																		---	---	---	---
EGF	1950	broad.mit.edu	37	4	110909149	110909151	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110909149_110909151delAAA	uc003hzy.3	+						EGF_uc011cfu.1_Intron|EGF_uc011cfv.1_Intron|EGF_uc010imk.2_Intron	NM_001963	NP_001954			epidermal growth factor precursor						angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)													---	---	---	---
EGF	1950	broad.mit.edu	37	4	110923814	110923814	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110923814delT	uc003hzy.3	+						EGF_uc011cfu.1_Intron|EGF_uc011cfv.1_Intron|EGF_uc010imk.2_Intron	NM_001963	NP_001954			epidermal growth factor precursor						angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)													---	---	---	---
EGF	1950	broad.mit.edu	37	4	110925365	110925368	+	Intron	DEL	CATA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110925365_110925368delCATA	uc003hzy.3	+						EGF_uc011cfu.1_Intron|EGF_uc011cfv.1_Intron|EGF_uc010imk.2_Intron	NM_001963	NP_001954			epidermal growth factor precursor						angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)													---	---	---	---
ENPEP	2028	broad.mit.edu	37	4	111477750	111477751	+	Intron	INS	-	T	T	rs144238520	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111477750_111477751insT	uc003iab.3	+							NM_001977	NP_001968			glutamyl aminopeptidase						cell migration|cell proliferation|cell-cell signaling|proteolysis	integral to plasma membrane	aminopeptidase activity|metalloexopeptidase activity|zinc ion binding			skin(3)|ovary(1)|breast(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)	L-Glutamic Acid(DB00142)													---	---	---	---
PITX2	5308	broad.mit.edu	37	4	111549105	111549105	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111549105delA	uc003iad.2	-						PITX2_uc003iae.2_Intron|PITX2_uc010iml.2_Intron|PITX2_uc003iaf.2_Intron	NM_153426	NP_700475			paired-like homeodomain transcription factor 2						determination of left/right symmetry|organ morphogenesis	transcription factor complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription factor binding				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	111958888	111958889	+	IGR	INS	-	TG	TG	rs142877121	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111958888_111958889insTG								MIR297 (177085 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112711736	112711737	+	IGR	INS	-	GTGT	GTGT	rs149992961	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112711736_112711737insGTGT								MIR297 (929933 upstream) : C4orf32 (354816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112838486	112838486	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112838486delA								None (None upstream) : C4orf32 (228067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112968409	112968409	+	IGR	DEL	A	-	-	rs111534501		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112968409delA								None (None upstream) : C4orf32 (98144 downstream)																																			---	---	---	---
C4orf32	132720	broad.mit.edu	37	4	113092292	113092292	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113092292delA	uc003iah.2	+							NM_152400	NP_689613			chromosome 4 open reading frame 32							integral to membrane					0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.00198)														---	---	---	---
AP1AR	55435	broad.mit.edu	37	4	113186056	113186056	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113186056delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	113590683	113590684	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113590683_113590684insT								LARP7 (11942 upstream) : ANK2 (148555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	113640071	113640092	+	IGR	DEL	GCATGAGCCACCGCACCCGGTC	-	-	rs72053136		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113640071_113640092delGCATGAGCCACCGCACCCGGTC								LARP7 (61330 upstream) : ANK2 (99147 downstream)																																			---	---	---	---
CAMK2D	817	broad.mit.edu	37	4	114473292	114473292	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114473292delA	uc003ibi.2	-						CAMK2D_uc003ibj.2_Intron|CAMK2D_uc003ibk.2_Intron|CAMK2D_uc003ibo.3_Intron|CAMK2D_uc003ibm.2_Intron|CAMK2D_uc003ibn.2_Intron|CAMK2D_uc003ibl.2_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	114795149	114795149	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114795149delA	uc003ibp.1	+											Homo sapiens cDNA FLJ34906 fis, clone NT2RI2002120.																														---	---	---	---
ARSJ	79642	broad.mit.edu	37	4	114883052	114883061	+	Intron	DEL	TCTGTGTGTG	-	-	rs76913992		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114883052_114883061delTCTGTGTGTG	uc003ibq.1	-						ARSJ_uc010imu.1_Intron|ARSJ_uc010imv.1_Intron	NM_024590	NP_078866			arylsulfatase J precursor							extracellular region	arylsulfatase activity|metal ion binding			ovary(1)	1		Ovarian(17;0.0035)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00194)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	116556532	116556532	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116556532delT								NDST4 (521500 upstream) : MIR1973 (664349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	116684458	116684459	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116684458_116684459delCA								NDST4 (649426 upstream) : MIR1973 (536422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117916367	117916367	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117916367delA								MIR1973 (695443 upstream) : TRAM1L1 (88349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118386478	118386478	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118386478delT								TRAM1L1 (379742 upstream) : NDST3 (568295 downstream)																																			---	---	---	---
NDST3	9348	broad.mit.edu	37	4	119096742	119096743	+	Intron	INS	-	G	G	rs146407601	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119096742_119096743insG	uc003ibx.2	+						NDST3_uc011cgf.1_Intron	NM_004784	NP_004775			N-deacetylase/N-sulfotransferase (heparan							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1																		---	---	---	---
PRSS12	8492	broad.mit.edu	37	4	119239769	119239769	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119239769delT	uc003ica.1	-							NM_003619	NP_003610			neurotrypsin precursor							membrane	scavenger receptor activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	119428156	119428156	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119428156delT								PRSS12 (154234 upstream) : CEP170L (9339 downstream)																																			---	---	---	---
SEC24D	9871	broad.mit.edu	37	4	119646772	119646772	+	Intron	DEL	T	-	-	rs34866027		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119646772delT	uc003ici.3	-						SEC24D_uc003ich.3_Intron|SEC24D_uc003icj.3_Intron	NM_014822	NP_055637			Sec24-related protein D						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0																		---	---	---	---
SEC24D	9871	broad.mit.edu	37	4	119659245	119659245	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119659245delA	uc003ici.3	-						SEC24D_uc003ich.3_Intron|SEC24D_uc003icj.3_Intron|SEC24D_uc003icl.2_Intron	NM_014822	NP_055637			Sec24-related protein D						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0																		---	---	---	---
SEC24D	9871	broad.mit.edu	37	4	119739918	119739919	+	Intron	DEL	AA	-	-	rs113682586		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119739918_119739919delAA	uc003ici.3	-						SEC24D_uc003icj.3_Intron|SEC24D_uc003icl.2_Intron|SEC24D_uc010imz.1_Intron|SEC24D_uc011cgg.1_Intron	NM_014822	NP_055637			Sec24-related protein D						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	120774052	120774052	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120774052delA								PDE5A (224071 upstream) : MAD2L1 (206527 downstream)																																			---	---	---	---
PRDM5	11107	broad.mit.edu	37	4	121671843	121671848	+	Intron	DEL	ACACAC	-	-	rs62325576		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121671843_121671848delACACAC	uc003idn.2	-						PRDM5_uc003ido.2_Intron|PRDM5_uc010ine.2_Intron	NM_018699	NP_061169			PR domain containing 5						histone deacetylation|histone H3-K9 methylation|mitotic cell cycle|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	repressing transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	121879122	121879122	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121879122delT								PRDM5 (35109 upstream) : C4orf31 (77660 downstream)																																			---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123090635	123090635	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123090635delT	uc003ieh.2	+							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	123168298	123168298	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123168298delT	uc003ieh.2	+						KIAA1109_uc003iek.2_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
SPATA5	166378	broad.mit.edu	37	4	123968730	123968730	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123968730delT	uc003iez.3	+							NM_145207	NP_660208			spermatogenesis associated 5						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0																		---	---	---	---
SPATA5	166378	broad.mit.edu	37	4	124038872	124038872	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124038872delA	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	124515771	124515772	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124515771_124515772insA								SPRY1 (190864 upstream) : LOC285419 (55650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125055108	125055108	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125055108delT								LOC285419 (203590 upstream) : ANKRD50 (530360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125391768	125391771	+	IGR	DEL	TCTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125391768_125391771delTCTT								LOC285419 (540250 upstream) : ANKRD50 (193697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125723989	125723989	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125723989delA								ANKRD50 (90102 upstream) : FAT4 (513578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125873504	125873504	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125873504delT								ANKRD50 (239617 upstream) : FAT4 (364063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126084791	126084792	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126084791_126084792delAC								ANKRD50 (450904 upstream) : FAT4 (152775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126882452	126882452	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126882452delA								MIR2054 (453990 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	127391296	127391296	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127391296delA								MIR2054 (962834 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	128259017	128259018	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128259017_128259018delAA								None (None upstream) : INTU (295102 downstream)																																			---	---	---	---
INTU	27152	broad.mit.edu	37	4	128605947	128605947	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128605947delT	uc003ifk.1	+						INTU_uc011cgq.1_Intron	NM_015693	NP_056508			PDZ domain containing 6											ovary(1)	1																		---	---	---	---
LARP1B	55132	broad.mit.edu	37	4	128999754	128999755	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128999754_128999755delAA	uc003iga.2	+						LARP1B_uc003ifw.1_Intron|LARP1B_uc003ifx.2_Intron|LARP1B_uc003ify.2_Intron|LARP1B_uc003ifz.1_Intron	NM_018078	NP_060548			La ribonucleoprotein domain family member 2								RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	129420377	129420377	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129420377delT	uc003igh.1	+											Homo sapiens cDNA FLJ36097 fis, clone TESTI2020956.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	129480521	129480521	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129480521delT								PGRMC2 (271573 upstream) : PHF17 (250258 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	129525426	129525426	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129525426delA								PGRMC2 (316478 upstream) : PHF17 (205353 downstream)																																			---	---	---	---
PHF17	79960	broad.mit.edu	37	4	129760813	129760813	+	Intron	DEL	T	-	-	rs67592201		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129760813delT	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	129800281	129800281	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129800281delA								PHF17 (3903 upstream) : SCLT1 (4871 downstream)																																			---	---	---	---
SCLT1	132320	broad.mit.edu	37	4	129864050	129864050	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129864050delA	uc003igp.2	-						SCLT1_uc003ign.2_Intron|SCLT1_uc003igo.2_Intron|SCLT1_uc003igq.2_Intron|SCLT1_uc010iob.1_Intron	NM_144643	NP_653244			sodium channel associated protein 1							centrosome				ovary(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	130624014	130624014	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130624014delC								C4orf33 (590172 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	131326665	131326665	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131326665delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	132112323	132112323	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132112323delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	132664184	132664185	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132664184_132664185delTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133469918	133469919	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133469918_133469919delTG								None (None upstream) : PCDH10 (600551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133607382	133607382	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133607382delA								None (None upstream) : PCDH10 (463088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134616328	134616328	+	IGR	DEL	A	-	-	rs78843077	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134616328delA								PCDH10 (503597 upstream) : PABPC4L (501163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135068882	135068883	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135068882_135068883delGT								PCDH10 (956151 upstream) : PABPC4L (48608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135091493	135091494	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135091493_135091494insT								PCDH10 (978762 upstream) : PABPC4L (25997 downstream)																																			---	---	---	---
PABPC4L	132430	broad.mit.edu	37	4	135123784	135123784	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135123784delT	uc010ioe.2	-							NM_001114734	NP_001108206			poly(A) binding protein, cytoplasmic 4-like												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	135443724	135443724	+	IGR	DEL	A	-	-	rs74814805		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135443724delA								PABPC4L (320821 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138063366	138063366	+	IGR	DEL	A	-	-	rs11353344		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138063366delA								None (None upstream) : PCDH18 (376710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139592649	139592649	+	IGR	DEL	T	-	-	rs11334325		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139592649delT								SLC7A11 (429146 upstream) : CCRN4L (344294 downstream)																																			---	---	---	---
ELF2	1998	broad.mit.edu	37	4	140051394	140051394	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140051394delA	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	140095753	140095754	+	Intron	INS	-	A	A	rs146623081	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140095753_140095754insA	uc003ihq.2	-											Homo sapiens ets family transcription factor ELF2A (ELF2) mRNA, complete cds, alternatively spliced.						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)																	---	---	---	---
SETD7	80854	broad.mit.edu	37	4	140470714	140470714	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140470714delT	uc003ihw.2	-						SETD7_uc003ihx.2_Intron	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	140528730	140528731	+	IGR	DEL	TT	-	-	rs34665500		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140528730_140528731delTT								SETD7 (51153 upstream) : MGST2 (58191 downstream)																																			---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140649383	140649383	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140649383delA	uc003ihz.1	-						MGST2_uc010ioi.1_Intron|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)																	---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140750129	140750130	+	Intron	INS	-	AGGA	AGGA	rs35172258		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140750129_140750130insAGGA	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)																	---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140782631	140782632	+	Intron	INS	-	TG	TG	rs142661058	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140782631_140782632insTG	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)																	---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140899765	140899766	+	Intron	INS	-	AAAAA	AAAAA	rs144597788	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140899765_140899766insAAAAA	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)																	---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140937205	140937205	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140937205delA	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	142347543	142347546	+	IGR	DEL	TCTG	-	-	rs150413371		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142347543_142347546delTCTG								ZNF330 (191695 upstream) : IL15 (210208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	142885924	142885925	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142885924_142885925insT								IL15 (231313 upstream) : INPP4B (63259 downstream)																																			---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143003118	143003118	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143003118delA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143295173	143295173	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143295173delA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011cho.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	144548643	144548643	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144548643delT								LOC441046 (59330 upstream) : GYPE (243377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	144748426	144748426	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144748426delT								LOC441046 (259113 upstream) : GYPE (43594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	145132704	145132711	+	IGR	DEL	TTGTTTTT	-	-	rs138604023	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145132704_145132711delTTGTTTTT								GYPA (70800 upstream) : HHIP (434462 downstream)																																			---	---	---	---
HHIP	64399	broad.mit.edu	37	4	145656549	145656549	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145656549delT	uc003ijs.1	+							NM_022475	NP_071920			hedgehog-interacting protein precursor							cytoplasm|extracellular region	catalytic activity|protein binding|zinc ion binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	145661924	145661924	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145661924delA								HHIP (2043 upstream) : ANAPC10 (254390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	145863533	145863534	+	IGR	INS	-	AT	AT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145863533_145863534insAT								HHIP (203652 upstream) : ANAPC10 (52780 downstream)																																			---	---	---	---
ABCE1	6059	broad.mit.edu	37	4	146031237	146031241	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146031237_146031241delTTTTT	uc003ijx.2	+						ABCE1_uc003ijy.2_Intron|ABCE1_uc010iot.2_Intron	NM_001040876	NP_001035809			ATP-binding cassette, sub-family E, member 1						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	146054017	146054019	+	IGR	DEL	TAA	-	-	rs36227674		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146054017_146054019delTAA								ABCE1 (3342 upstream) : OTUD4 (784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	146204320	146204320	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146204320delA								OTUD4 (103488 upstream) : SMAD1 (198631 downstream)																																			---	---	---	---
MMAA	166785	broad.mit.edu	37	4	146561669	146561669	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146561669delT	uc003ikh.3	+						MMAA_uc003ikg.2_Intron|MMAA_uc003iki.1_Intron|MMAA_uc010iow.2_Intron	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	146597189	146597189	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146597189delA								MMAA (16003 upstream) : C4orf51 (4167 downstream)																																			---	---	---	---
C4orf51	646603	broad.mit.edu	37	4	146605920	146605920	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146605920delA	uc003ikk.2	+							NM_001080531	NP_001074000			chromosome 4 open reading frame 51												0																		---	---	---	---
ZNF827	152485	broad.mit.edu	37	4	146851554	146851554	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146851554delT	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)																	---	---	---	---
TTC29	83894	broad.mit.edu	37	4	147714365	147714365	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147714365delA	uc003ikw.3	-						TTC29_uc010ipc.2_Intron|TTC29_uc003ikx.3_Intron|TTC29_uc010ipd.1_Intron	NM_031956	NP_114162			tetratricopeptide repeat domain 29								binding				0	all_hematologic(180;0.151)																	---	---	---	---
TTC29	83894	broad.mit.edu	37	4	147868505	147868506	+	5'Flank	INS	-	T	T	rs150304175	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147868505_147868506insT	uc003ikw.3	-						TTC29_uc010ipc.2_5'Flank|TTC29_uc003ikx.3_5'Flank|TTC29_uc010ipd.1_5'Flank	NM_031956	NP_114162			tetratricopeptide repeat domain 29								binding				0	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	148066672	148066672	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148066672delT								TTC29 (199638 upstream) : MIR548G (199109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	148558080	148558081	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148558080_148558081insA								TMEM184C (1410 upstream) : PRMT10 (1455 downstream)																																			---	---	---	---
ARHGAP10	79658	broad.mit.edu	37	4	148659171	148659172	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148659171_148659172delTT	uc003ilf.2	+						ARHGAP10_uc003ile.1_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	148757987	148757987	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148757987delT	uc003ilf.2	+						ARHGAP10_uc003ile.1_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	148886159	148886160	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148886159_148886160insT	uc003ilf.2	+						ARHGAP10_uc003ilg.2_Intron|ARHGAP10_uc003ilh.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	148982618	148982618	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148982618delA	uc003ilf.2	+						ARHGAP10_uc003ilg.2_Intron|ARHGAP10_uc003ilh.2_Intron|ARHGAP10_uc003ili.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	149112206	149112206	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149112206delT	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	149531609	149531611	+	IGR	DEL	TTT	-	-	rs113725846		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149531609_149531611delTTT								NR3C2 (167966 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	149818024	149818024	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149818024delT								NR3C2 (454381 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150046613	150046613	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150046613delT								NR3C2 (682970 upstream) : DCLK2 (953467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150057774	150057775	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150057774_150057775delAA								NR3C2 (694131 upstream) : DCLK2 (942305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150103406	150103406	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150103406delA								NR3C2 (739763 upstream) : DCLK2 (896674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150112091	150112092	+	IGR	INS	-	CA	CA	rs151285051	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150112091_150112092insCA								NR3C2 (748448 upstream) : DCLK2 (887988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150333218	150333219	+	IGR	INS	-	TGTG	TGTG	rs141787303	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150333218_150333219insTGTG								NR3C2 (969575 upstream) : DCLK2 (666861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150681175	150681176	+	Intron	INS	-	AAGGA	AAGGA	rs142645861	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150681175_150681176insAAGGA	uc003ill.2	-											Homo sapiens cDNA clone IMAGE:5295442.																														---	---	---	---
DCLK2	166614	broad.mit.edu	37	4	151160754	151160754	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151160754delA	uc003ilm.3	+						DCLK2_uc003iln.3_Intron|DCLK2_uc003ilo.3_Intron|DCLK2_uc003ilp.3_Intron	NM_001040260	NP_001035350			doublecortin-like kinase 2 isoform a						intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)																	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151642666	151642667	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151642666_151642667delTT	uc010ipj.2	-						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)																	---	---	---	---
RPS3A	6189	broad.mit.edu	37	4	152024906	152024907	+	Intron	INS	-	TA	TA	rs150306635	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152024906_152024907insTA	uc003ilz.2	+						RPS3A_uc011cie.1_3'UTR|SNORD73A_uc003ima.1_5'Flank	NM_001006	NP_000997			ribosomal protein S3a						cell differentiation|endocrine pancreas development|induction of apoptosis|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_hematologic(180;0.093)																	---	---	---	---
SH3D19	152503	broad.mit.edu	37	4	152090445	152090445	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152090445delA	uc010ipl.1	-						SH3D19_uc003imb.2_5'Flank|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	152718650	152718651	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152718650_152718651delTT								PET112L (36504 upstream) : FBXW7 (523760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	152809899	152809900	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152809899_152809900insA								PET112L (127753 upstream) : FBXW7 (432511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	152876504	152876504	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152876504delA	uc003imn.2	+						uc003imo.2_5'Flank					Homo sapiens cDNA clone IMAGE:5266192.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	153052163	153052163	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153052163delT								PET112L (370017 upstream) : FBXW7 (190248 downstream)														p.?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	4	153210960	153210960	+	IGR	DEL	T	-	-	rs77271717		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153210960delT								PET112L (528814 upstream) : FBXW7 (31451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	153217052	153217052	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153217052delT								PET112L (534906 upstream) : FBXW7 (25359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	153523392	153523393	+	IGR	DEL	GT	-	-	rs72103828		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153523392_153523393delGT								FBXW7 (67049 upstream) : TMEM154 (23878 downstream)																																			---	---	---	---
TMEM154	201799	broad.mit.edu	37	4	153549745	153549745	+	Intron	DEL	C	-	-	rs72117571		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153549745delC	uc003imw.1	-							NM_152680	NP_689893			transmembrane protein 154 precursor							integral to membrane					0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	153985588	153985588	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153985588delA								FHDC1 (84740 upstream) : TRIM2 (88682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	154050857	154050858	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154050857_154050858insC								FHDC1 (150009 upstream) : TRIM2 (23412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	154589166	154589167	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154589166_154589167delGA								KIAA0922 (31306 upstream) : TLR2 (16274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	154729949	154729952	+	IGR	DEL	TCCT	-	-	rs33966514		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154729949_154729952delTCCT								SFRP2 (19721 upstream) : DCHS2 (425575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	154730065	154730080	+	IGR	DEL	TCCCTCCTTCCCTCCT	-	-	rs35815886	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154730065_154730080delTCCCTCCTTCCCTCCT								SFRP2 (19837 upstream) : DCHS2 (425447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	155148632	155148633	+	IGR	DEL	TG	-	-	rs61224692	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155148632_155148633delTG								SFRP2 (438404 upstream) : DCHS2 (6894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	155886569	155886569	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155886569delA								RBM46 (136605 upstream) : NPY2R (243212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	155892288	155892289	+	IGR	DEL	TG	-	-	rs57498442		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155892288_155892289delTG								RBM46 (142324 upstream) : NPY2R (237492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	155923472	155923473	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155923472_155923473insC								RBM46 (173508 upstream) : NPY2R (206308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	156121398	156121398	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156121398delA								RBM46 (371434 upstream) : NPY2R (8383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	156429546	156429547	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156429546_156429547insT								MAP9 (131424 upstream) : GUCY1A3 (158315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	156546824	156546824	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156546824delA								MAP9 (248702 upstream) : GUCY1A3 (41038 downstream)																																			---	---	---	---
GUCY1A3	2982	broad.mit.edu	37	4	156609393	156609396	+	Intron	DEL	AAAA	-	-	rs111517203		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156609393_156609396delAAAA	uc003iov.2	+						GUCY1A3_uc003iou.2_Intron|GUCY1A3_uc010iqc.2_Intron|GUCY1A3_uc003iow.2_Intron|GUCY1A3_uc010iqd.2_Intron|GUCY1A3_uc003iox.2_Intron|GUCY1A3_uc003ioz.2_Intron|GUCY1A3_uc003ioy.2_Intron|GUCY1A3_uc010iqe.2_Intron|GUCY1A3_uc003ipa.2_Intron|GUCY1A3_uc003ipb.2_Intron	NM_000856	NP_000847			guanylate cyclase 1, soluble, alpha 3 isoform A						blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble	GTP binding|guanylate cyclase activity|heme binding|receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	157161706	157161707	+	IGR	INS	-	T	T	rs111940091	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157161706_157161707insT								CTSO (286658 upstream) : PDGFC (521057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	157359518	157359519	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157359518_157359519insT								CTSO (484470 upstream) : PDGFC (323245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	158453328	158453328	+	IGR	DEL	A	-	-	rs11361945		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158453328delA								GRIA2 (166104 upstream) : LOC340017 (40314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	158576064	158576065	+	IGR	INS	-	CT	CT	rs144362199	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158576064_158576065insCT								LOC340017 (78769 upstream) : FAM198B (469668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	158600510	158600510	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158600510delA								LOC340017 (103215 upstream) : FAM198B (445223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	159320776	159320777	+	IGR	DEL	AA	-	-	rs111768545		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159320776_159320777delAA								TMEM144 (144338 upstream) : RXFP1 (122270 downstream)																																			---	---	---	---
C4orf45	152940	broad.mit.edu	37	4	159925158	159925158	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	159953372	159953372	+	Intron	DEL	A	-	-	rs79804808		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159953372delA	uc003iqf.1	-						C4orf45_uc010iqt.1_Intron	NM_152543	NP_689756			hypothetical protein LOC152940												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	160157004	160157004	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160157004delT								C4orf45 (132899 upstream) : RAPGEF2 (31994 downstream)																																			---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160216873	160216874	+	Intron	DEL	GT	-	-	rs71589223	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160216873_160216874delGT	uc003iqg.3	+							NM_014247	NP_055062			Rap guanine nucleotide exchange factor 2						cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)														---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160251797	160251797	+	Intron	DEL	A	-	-	rs78225051		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160251797delA	uc003iqg.3	+							NM_014247	NP_055062			Rap guanine nucleotide exchange factor 2						cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	160428017	160428017	+	IGR	DEL	T	-	-	rs71798752		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160428017delT								RAPGEF2 (146718 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	161550980	161550980	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161550980delA								None (None upstream) : FSTL5 (754071 downstream)																																			---	---	---	---
FSTL5	56884	broad.mit.edu	37	4	162771127	162771127	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162771127delA	uc003iqh.2	-						FSTL5_uc003iqi.2_Intron|FSTL5_uc010iqv.2_Intron	NM_020116	NP_064501			follistatin-like 5 isoform a							extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)														---	---	---	---
FSTL5	56884	broad.mit.edu	37	4	162901299	162901301	+	Intron	DEL	GAT	-	-	rs35605957		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162901299_162901301delGAT	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	163319312	163319313	+	IGR	DEL	TA	-	-	rs138511928		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163319312_163319313delTA								FSTL5 (234126 upstream) : NAF1 (728547 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	163460398	163460398	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163460398delT								FSTL5 (375212 upstream) : NAF1 (587462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	163473137	163473138	+	IGR	INS	-	T	T	rs141768102	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163473137_163473138insT								FSTL5 (387951 upstream) : NAF1 (574722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	164024278	164024279	+	IGR	INS	-	C	C	rs149103493	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164024278_164024279insC								FSTL5 (939092 upstream) : NAF1 (23581 downstream)																																			---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	165105233	165105233	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165105233delA	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	165111546	165111546	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165111546delA	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	165715544	165715546	+	Intron	DEL	AAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165715544_165715546delAAG	uc003iqu.1	+											Homo sapiens cDNA FLJ37936 fis, clone CTONG2005468.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	165830880	165830880	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165830880delT								MARCH1 (525678 upstream) : TRIM61 (44720 downstream)																																			---	---	---	---
TRIM61	391712	broad.mit.edu	37	4	165901690	165901690	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165901690delA	uc003iqw.2	-							NM_001012414	NP_001012414			tripartite motif-containing 61							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	166156151	166156151	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166156151delA	uc003irb.2	+						KLHL2_uc011cjm.1_Intron|KLHL2_uc003irc.2_Intron	NM_007246	NP_009177			kelch-like 2, Mayven isoform 1						intracellular protein transport	actin cytoskeleton|cytoplasm	actin binding|transporter activity				0	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)														---	---	---	---
CPE	1363	broad.mit.edu	37	4	166377709	166377710	+	Intron	DEL	TC	-	-	rs33985842		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166377709_166377710delTC	uc003irg.3	+							NM_001873	NP_001864			carboxypeptidase E preproprotein						cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process	extracellular region|nucleus|plasma membrane	metallocarboxypeptidase activity|protein binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
CPE	1363	broad.mit.edu	37	4	166403589	166403589	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166403589delT	uc003irg.3	+							NM_001873	NP_001864			carboxypeptidase E preproprotein						cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process	extracellular region|nucleus|plasma membrane	metallocarboxypeptidase activity|protein binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	166619791	166619791	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166619791delT								CPE (200310 upstream) : TLL1 (174619 downstream)																																			---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166806752	166806753	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166806752_166806753delAA	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	166910329	166910329	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166910329delA	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	167062229	167062230	+	IGR	INS	-	TG	TG	rs144191160	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167062229_167062230insTG								TLL1 (37236 upstream) : SPOCK3 (592306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	167349490	167349490	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167349490delA								TLL1 (324497 upstream) : SPOCK3 (305046 downstream)																																			---	---	---	---
SPOCK3	50859	broad.mit.edu	37	4	168126155	168126155	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168126155delT	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)														---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169239602	169239603	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169239602_169239603insG	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)												OREG0016394	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DDX60L	91351	broad.mit.edu	37	4	169343491	169343491	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169343491delA	uc003irq.3	-						DDX60L_uc003irr.1_Intron|DDX60L_uc003irs.1_Intron	NM_001012967	NP_001012985			DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)														---	---	---	---
CBR4	84869	broad.mit.edu	37	4	169922982	169922982	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169922982delT	uc003iry.2	-						CBR4_uc011cjy.1_Intron|CBR4_uc003irz.1_3'UTR	NM_032783	NP_116172			carbonic reductase 4						fatty acid biosynthetic process|protein homotetramerization	mitochondrial matrix	NADPH binding|NADPH dehydrogenase (quinone) activity|protein binding|quinone binding				0		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	169947485	169947488	+	IGR	DEL	AGAG	-	-	rs143394467		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169947485_169947488delAGAG								CBR4 (16063 upstream) : SH3RF1 (67919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	169953263	169953264	+	IGR	DEL	AA	-	-	rs77106537		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169953263_169953264delAA								CBR4 (21841 upstream) : SH3RF1 (62143 downstream)																																			---	---	---	---
SH3RF1	57630	broad.mit.edu	37	4	170021500	170021500	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170021500delT	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)														---	---	---	---
SH3RF1	57630	broad.mit.edu	37	4	170186259	170186259	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170186259delT	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)														---	---	---	---
NEK1	4750	broad.mit.edu	37	4	170387388	170387388	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170387388delA	uc003isb.1	-						NEK1_uc003isc.1_Intron|NEK1_uc003isd.1_Intron|NEK1_uc003ise.1_Intron|NEK1_uc003isf.1_Intron	NM_012224	NP_036356			NIMA-related kinase 1						cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)														---	---	---	---
CLCN3	1182	broad.mit.edu	37	4	170556960	170556961	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170556960_170556961insT	uc003isi.2	+						CLCN3_uc003ish.2_Intron|CLCN3_uc011cjz.1_Intron|CLCN3_uc011cka.1_Intron	NM_001829	NP_001820			chloride channel 3 isoform b						endosomal lumen acidification	cell surface|early endosome membrane|Golgi membrane|integral to membrane|late endosome membrane|transport vesicle membrane	antiporter activity|ATP binding|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity			breast(2)|ovary(1)	3		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	170960560	170960561	+	IGR	DEL	TG	-	-	rs143585271	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170960560_170960561delTG								MFAP3L (13131 upstream) : AADAT (20813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	172052518	172052518	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172052518delT								None (None upstream) : GALNTL6 (682057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	172246208	172246208	+	IGR	DEL	A	-	-	rs116129649	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172246208delA								None (None upstream) : GALNTL6 (488367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	172317960	172317960	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172317960delA								None (None upstream) : GALNTL6 (416615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	172478076	172478077	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172478076_172478077delGT								None (None upstream) : GALNTL6 (256498 downstream)																																			---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173408430	173408431	+	Intron	INS	-	TTCTTTCC	TTCTTTCC	rs11281424		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173408430_173408431insTTCTTTCC	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	173721781	173721781	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173721781delT	uc003isv.2	+							NM_001034845	NP_001030017			N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	174021530	174021530	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174021530delA								GALNTL6 (59974 upstream) : GALNT7 (68374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	174306621	174306622	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174306621_174306622delAA								SAP30 (7939 upstream) : SCRG1 (2678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	174441883	174441883	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174441883delA								SCRG1 (114355 upstream) : HAND2 (5769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	174727139	174727139	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174727139delT								MORF4 (189345 upstream) : FBXO8 (430673 downstream)																																			---	---	---	---
KIAA1712	80817	broad.mit.edu	37	4	175231156	175231158	+	In_Frame_Del	DEL	TCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175231156_175231158delTCT	uc003itr.2	+	8	1248_1250	c.834_836delTCT	c.(832-837)AATCTT>AAT	p.L280del	KIAA1712_uc010iro.2_In_Frame_Del_p.L280del|KIAA1712_uc003its.2_RNA	NM_001040157	NP_001035247	Q9C0F1	CEP44_HUMAN	HBV PreS1-transactivated protein 3 isoform a	280						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)														---	---	---	---
GLRA3	8001	broad.mit.edu	37	4	175744394	175744395	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175744394_175744395insA	uc003ity.1	-						GLRA3_uc003itz.1_Intron	NM_006529	NP_006520			glycine receptor, alpha 3 isoform a						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity			ovary(3)	3		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)													---	---	---	---
SPATA4	132851	broad.mit.edu	37	4	177109228	177109229	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177109228_177109229insA	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	177837491	177837492	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177837491_177837492insT								VEGFC (123596 upstream) : NEIL3 (393499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	177851289	177851289	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177851289delA								VEGFC (137394 upstream) : NEIL3 (379702 downstream)																																			---	---	---	---
LOC285501	285501	broad.mit.edu	37	4	178751158	178751158	+	Intron	DEL	C	-	-	rs71599333		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178751158delC	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	179309048	179309048	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179309048delT								LOC285501 (397145 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180071170	180071173	+	IGR	DEL	TGTT	-	-	rs6552342		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180071170_180071173delTGTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180248087	180248087	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180248087delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181276458	181276458	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181276458delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181378937	181378938	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181378937_181378938delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	182933033	182933034	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182933033_182933034insC	uc003iva.1	-											Homo sapiens cDNA FLJ31634 fis, clone NT2RI2003419.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	183002986	183002987	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183002986_183002987insA	uc003iva.1	-											Homo sapiens cDNA FLJ31634 fis, clone NT2RI2003419.																														---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183593042	183593043	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183593042_183593043delTT	uc003ivd.1	+							NM_001080477	NP_001073946			odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	183802410	183802410	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183802410delG								ODZ3 (78233 upstream) : DCTD (8835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	183808032	183808032	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183808032delA								ODZ3 (83855 upstream) : DCTD (3213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	183934459	183934482	+	IGR	DEL	TCTTCCTCTTCCTCCTCTTCTTCC	-	-	rs139034545		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183934459_183934482delTCTTCCTCTTCCTCCTCTTCTTCC								DCTD (95829 upstream) : FAM92A3 (24336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	183982295	183982297	+	IGR	DEL	TTT	-	-	rs112010545		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183982295_183982297delTTT								FAM92A3 (21024 upstream) : C4orf38 (35877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184306045	184306047	+	IGR	DEL	AGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184306045_184306047delAGA								WWC2 (64118 upstream) : CDKN2AIP (59742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184328983	184328984	+	IGR	INS	-	CTTT	CTTT	rs144708260	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184328983_184328984insCTTT								WWC2 (87056 upstream) : CDKN2AIP (36805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	185158584	185158585	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185158584_185158585insA								ENPP6 (19470 upstream) : IRF2 (150293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	185470585	185470585	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185470585delT								IRF2 (74859 upstream) : CASP3 (78267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	185797294	185797295	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185797294_185797295delAA								ACSL1 (50079 upstream) : HELT (142700 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	185901001	185901002	+	IGR	INS	-	AG	AG	rs143763056	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185901001_185901002insAG								ACSL1 (153786 upstream) : HELT (38993 downstream)																																			---	---	---	---
SNX25	83891	broad.mit.edu	37	4	186162754	186162754	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186162754delT	uc003ixh.2	+							NM_031953	NP_114159			sorting nexin 25						cell communication|protein transport	endosome membrane	phosphatidylinositol binding|signal transducer activity			ovary(2)|breast(2)|pancreas(1)	5		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)														---	---	---	---
SNX25	83891	broad.mit.edu	37	4	186222535	186222535	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186222535delT	uc003ixh.2	+						SNX25_uc010ish.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)														---	---	---	---
UFSP2	55325	broad.mit.edu	37	4	186323261	186323261	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186323261delT	uc003ixo.2	-						UFSP2_uc003ixn.2_Intron|UFSP2_uc003ixq.2_Intron|UFSP2_uc003ixp.2_Intron	NM_018359	NP_060829			UFM1-specific peptidase 2							endoplasmic reticulum|nucleus	small conjugating protein-specific protease activity				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;3.4e-25)|Epithelial(43;2.23e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;8.1e-05)|GBM - Glioblastoma multiforme(59;0.000148)|STAD - Stomach adenocarcinoma(60;0.000782)|LUSC - Lung squamous cell carcinoma(40;0.00939)|COAD - Colon adenocarcinoma(29;0.0108)|READ - Rectum adenocarcinoma(43;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	187298624	187298627	+	Intron	DEL	ACAC	-	-	rs71934504		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187298624_187298627delACAC	uc003izb.1	-											Homo sapiens coagulation factor XI (plasma thromboplastin antecedent), mRNA (cDNA clone IMAGE:4831055).																														---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187516470	187516471	+	Intron	INS	-	GA	GA	rs34794741		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187516470_187516471insGA	uc003izf.2	-						FAT1_uc010isn.2_Intron|FAT1_uc003ize.2_Intron	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	187543488	187543488	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187543488delG	uc003izf.2	-							NM_005245	NP_005236			FAT tumor suppressor 1 precursor						actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12															HNSCC(5;0.00058)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	187692790	187692790	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187692790delA								FAT1 (44940 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	187824192	187824192	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187824192delT								FAT1 (176342 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	188802300	188802301	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188802300_188802301insT								None (None upstream) : ZFP42 (114624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189093473	189093473	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189093473delG								TRIML1 (24824 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189336136	189336136	+	Intron	DEL	A	-	-	rs141882123		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189336136delA	uc003izo.1	+											Homo sapiens cDNA FLJ38649 fis, clone HHDPC2007302.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	189827360	189827372	+	IGR	DEL	TTAGGCCAGTTGC	-	-	rs112427171		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189827360_189827372delTTAGGCCAGTTGC								TRIML1 (758711 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190555264	190555291	+	IGR	DEL	CCTCCAGATTTAGGAGATGTCAAGGGAG	-	-	rs28647764	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190555264_190555291delCCTCCAGATTTAGGAGATGTCAAGGGAG								None (None upstream) : FRG1 (306683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190565126	190565126	+	IGR	DEL	A	-	-	rs71876512		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190565126delA								None (None upstream) : FRG1 (296848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190617583	190617584	+	IGR	INS	-	AAGTAT	AAGTAT	rs138661908		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190617583_190617584insAAGTAT								None (None upstream) : FRG1 (244390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190825682	190825683	+	Intron	INS	-	T	T	rs138468383		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190825682_190825683insT	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	190891116	190891117	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190891116_190891117delAA								FRG1 (6758 upstream) : TUBB4Q (12562 downstream)																																			---	---	---	---
AHRR	57491	broad.mit.edu	37	5	417847	417847	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:417847delA	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)															---	---	---	---
CEP72	55722	broad.mit.edu	37	5	613493	613494	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:613493_613494delTT	uc003jbf.2	+						CEP72_uc011clz.1_Intron	NM_018140	NP_060610			centrosomal protein 72 kDa						G2/M transition of mitotic cell cycle|gamma-tubulin complex localization|spindle organization	centrosome|cytosol				ovary(1)	1			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)															---	---	---	---
CEP72	55722	broad.mit.edu	37	5	616928	616931	+	Intron	DEL	TGTA	-	-	rs72403184		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:616928_616931delTGTA	uc003jbf.2	+						CEP72_uc011clz.1_Intron	NM_018140	NP_060610			centrosomal protein 72 kDa						G2/M transition of mitotic cell cycle|gamma-tubulin complex localization|spindle organization	centrosome|cytosol				ovary(1)	1			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	733371	733372	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:733371_733372insC								TPPP (39861 upstream) : ZDHHC11 (62348 downstream)																																			---	---	---	---
ZDHHC11	79844	broad.mit.edu	37	5	847521	847522	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:847521_847522insA	uc011cma.1	-						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)															---	---	---	---
SLC12A7	10723	broad.mit.edu	37	5	1100148	1100150	+	Intron	DEL	AGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1100148_1100150delAGA	uc003jbu.2	-							NM_006598	NP_006589			solute carrier family 12 (potassium/chloride						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	1191741	1191741	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1191741delT								SLC12A7 (79569 upstream) : SLC6A19 (9969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	1191890	1191891	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1191890_1191891insA								SLC12A7 (79718 upstream) : SLC6A19 (9819 downstream)																																			---	---	---	---
CLPTM1L	81037	broad.mit.edu	37	5	1333412	1333412	+	Intron	DEL	A	-	-	rs68084960		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1333412delA	uc003jch.2	-						CLPTM1L_uc003jcg.2_Intron	NM_030782	NP_110409			CLPTM1-like						apoptosis	integral to membrane				breast(1)|central_nervous_system(1)	2	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)														---	---	---	---
SDHAP3	728609	broad.mit.edu	37	5	1593156	1593156	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1593156delA	uc010itg.1	-						SDHAP3_uc011cme.1_Intron					Homo sapiens cDNA clone IMAGE:40127561.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	1827770	1827771	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1827770_1827771insC								NDUFS6 (11607 upstream) : IRX4 (49770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2250400	2250401	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2250400_2250401insA								IRX4 (367520 upstream) : IRX2 (495880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2994042	2994042	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2994042delG								C5orf38 (238530 upstream) : IRX1 (602126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3081074	3081075	+	IGR	DEL	TC	-	-	rs139453891	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3081074_3081075delTC								C5orf38 (325562 upstream) : IRX1 (515093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3117374	3117374	+	IGR	DEL	C	-	-	rs147452492	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3117374delC								C5orf38 (361862 upstream) : IRX1 (478794 downstream)																																			---	---	---	---
IRX1	79192	broad.mit.edu	37	5	3599265	3599266	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3599265_3599266delTC	uc003jde.2	+							NM_024337	NP_077313			iroquois homeobox protein 1							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	3755223	3755224	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3755223_3755224delTT								IRX1 (153707 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4420508	4420509	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4420508_4420509insTG								IRX1 (818992 upstream) : LOC340094 (613963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4739765	4739766	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4739765_4739766delTC								None (None upstream) : LOC340094 (294706 downstream)																																			---	---	---	---
ADAMTS16	170690	broad.mit.edu	37	5	5149459	5149460	+	Intron	INS	-	CT	CT	rs141179360	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5149459_5149460insCT	uc003jdl.2	+						ADAMTS16_uc003jdk.1_Intron|ADAMTS16_uc003jdj.1_Intron	NM_139056	NP_620687			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	6877981	6877982	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6877981_6877982delAA								PAPD7 (120820 upstream) : ADCY2 (518361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8419228	8419233	+	Intron	DEL	GGGTGT	-	-	rs147727584		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8419228_8419233delGGGTGT	uc003jeh.1	-											Homo sapiens cDNA clone IMAGE:5297486.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	8541452	8541453	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8541452_8541453delTT								MTRR (640219 upstream) : SEMA5A (493685 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8966237	8966237	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8966237delA								None (None upstream) : SEMA5A (68901 downstream)																																			---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9162495	9162496	+	Intron	DEL	TG	-	-	rs3034740		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9162495_9162496delTG	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9265611	9265611	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9265611delC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	9919379	9919379	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9919379delA								LOC285692 (15443 upstream) : FAM173B (307059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	9983370	9983371	+	IGR	INS	-	AC	AC	rs140824065	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9983370_9983371insAC								LOC285692 (79434 upstream) : FAM173B (243067 downstream)																																			---	---	---	---
MARCH6	10299	broad.mit.edu	37	5	10398699	10398700	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10398699_10398700delTT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876			membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
MARCH6	10299	broad.mit.edu	37	5	10415851	10415851	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10415851delT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876			membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	10521154	10521154	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10521154delT								ROPN1L (56017 upstream) : DAP (158189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	10527892	10527892	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10527892delT								ROPN1L (62755 upstream) : DAP (151451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	10605646	10605647	+	IGR	INS	-	TT	TT	rs35551777		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10605646_10605647insTT								ROPN1L (140509 upstream) : DAP (73696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	10879570	10879571	+	IGR	DEL	TT	-	-	rs150095281	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10879570_10879571delTT								DAP (118183 upstream) : CTNND2 (92381 downstream)																																			---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11071686	11071687	+	Intron	DEL	AA	-	-	rs34608744		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11071686_11071687delAA	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	11485458	11485459	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11485458_11485459delTG	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11558449	11558450	+	Intron	INS	-	AC	AC	rs137933433	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11558449_11558450insAC	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11656531	11656532	+	Intron	DEL	AA	-	-	rs111429693		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11656531_11656532delAA	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	13187293	13187294	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13187293_13187294insT								None (None upstream) : DNAH5 (503143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13205147	13205149	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13205147_13205149delAAA								None (None upstream) : DNAH5 (485288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13379201	13379202	+	IGR	DEL	AT	-	-	rs142557494		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13379201_13379202delAT								None (None upstream) : DNAH5 (311235 downstream)																																			---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13830525	13830525	+	Intron	DEL	A	-	-	rs112224533		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13830525delA	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				---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13891061	13891061	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13891061delA	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				---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14308828	14308829	+	Intron	INS	-	TCCA	TCCA	rs138136266		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14308828_14308829insTCCA	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron|TRIO_uc003jfh.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14406144	14406144	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14406144delG	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc003jfh.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
FAM105A	54491	broad.mit.edu	37	5	14607340	14607340	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14607340delA	uc003jfj.2	+							NM_019018	NP_061891			hypothetical protein LOC54491											ovary(1)	1	Lung NSC(4;0.00592)																	---	---	---	---
ANKH	56172	broad.mit.edu	37	5	14806431	14806432	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14806431_14806432delAA	uc003jfm.3	-							NM_054027	NP_473368			progressive ankylosis protein						locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	15417768	15417768	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15417768delA								ANKH (545881 upstream) : FBXL7 (82537 downstream)																																			---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15694148	15694149	+	Intron	INS	-	C	C	rs144640907	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15694148_15694149insC	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
MARCH11	441061	broad.mit.edu	37	5	16119475	16119476	+	Intron	DEL	AA	-	-	rs61583487	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16119475_16119476delAA	uc003jfo.2	-							NM_001102562	NP_001096032			membrane-associated ring finger (C3HC4) 11							cytoplasmic vesicle membrane|integral to membrane	ligase activity|zinc ion binding				0																		---	---	---	---
MARCH11	441061	broad.mit.edu	37	5	16133184	16133184	+	Intron	DEL	T	-	-	rs11361544		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16133184delT	uc003jfo.2	-							NM_001102562	NP_001096032			membrane-associated ring finger (C3HC4) 11							cytoplasmic vesicle membrane|integral to membrane	ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	16389148	16389148	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16389148delA								MARCH11 (209251 upstream) : ZNF622 (62481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	16419313	16419314	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16419313_16419314delGA								MARCH11 (239416 upstream) : ZNF622 (32315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	16446849	16446849	+	IGR	DEL	A	-	-	rs80053380		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16446849delA								MARCH11 (266952 upstream) : ZNF622 (4780 downstream)																																			---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16668191	16668191	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16668191delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	17057398	17057398	+	IGR	DEL	T	-	-	rs72734400	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17057398delT								MYO10 (121013 upstream) : LOC285696 (72739 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17128418	17128419	+	IGR	DEL	TT	-	-	rs11323997		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17128418_17128419delTT								MYO10 (192033 upstream) : LOC285696 (1718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17295004	17295006	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17295004_17295006delAAA								BASP1 (18069 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17492748	17492750	+	IGR	DEL	TTT	-	-	rs76301324		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17492748_17492750delTTT								BASP1 (215813 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17670209	17670209	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17670209delA								BASP1 (393274 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17804488	17804488	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17804488delT								BASP1 (527553 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17876315	17876315	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17876315delT	uc003jgb.2	+											Homo sapiens cDNA clone IMAGE:5201079.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	18076948	18076948	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18076948delA								BASP1 (800013 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18138766	18138766	+	IGR	DEL	G	-	-	rs78470183		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18138766delG								BASP1 (861831 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18392183	18392184	+	IGR	INS	-	T	T	rs146732357	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18392183_18392184insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18602531	18602532	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18602531_18602532delTT								None (None upstream) : CDH18 (870625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18968596	18968597	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18968596_18968597insTG								None (None upstream) : CDH18 (504560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19086326	19086327	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19086326_19086327insTG								None (None upstream) : CDH18 (386830 downstream)																																			---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19814467	19814467	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19814467delA	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	20036538	20036538	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20036538delA								CDH18 (48231 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20587228	20587228	+	IGR	DEL	A	-	-	rs11335001		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20587228delA								CDH18 (598921 upstream) : GUSBP1 (754714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	21275945	21275945	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21275945delT								None (None upstream) : GUSBP1 (65997 downstream)																																			---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21404544	21404545	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21404544_21404545insA	uc011cnn.1	+											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	21516506	21516507	+	Intron	INS	-	AATA	AATA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21516506_21516507insAATA	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																		---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21845108	21845109	+	Intron	INS	-	TAGA	TAGA	rs143176975	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21845108_21845109insTAGA	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	22300466	22300467	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22300466_22300467insT	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22742291	22742291	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22742291delA	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	23160349	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23160349delT								CDH12 (306618 upstream) : PRDM9 (347375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23326291	23326291	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23326291delA								CDH12 (472560 upstream) : PRDM9 (181433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23767438	23767438	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23767438delA								PRDM9 (238734 upstream) : CDH10 (719772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24052334	24052335	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24052334_24052335delGA	uc003jgq.1	+											Homo sapiens cDNA FLJ34836 fis, clone NT2NE2010400.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	24396825	24396826	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24396825_24396826delTC								PRDM9 (868121 upstream) : CDH10 (90384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24888479	24888479	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24888479delA								CDH10 (243568 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	26632610	26632611	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26632610_26632611insT								None (None upstream) : CDH9 (248098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27637432	27637434	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27637432_27637434delTTT								CDH9 (598743 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27774659	27774659	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27774659delG								CDH9 (735970 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28688865	28688867	+	IGR	DEL	CTT	-	-	rs34740402		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28688865_28688867delCTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29236946	29236946	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29236946delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29463598	29463598	+	IGR	DEL	T	-	-	rs79503634	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29463598delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29669662	29669663	+	IGR	INS	-	AA	AA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29669662_29669663insAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30824948	30824949	+	IGR	INS	-	TA	TA	rs72531129		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30824948_30824949insTA								None (None upstream) : CDH6 (368847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	31083765	31083768	+	IGR	DEL	AGAA	-	-	rs10606771		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31083765_31083768delAGAA								None (None upstream) : CDH6 (110028 downstream)																																			---	---	---	---
CDH6	1004	broad.mit.edu	37	5	31294199	31294199	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31294199delA	uc003jhe.1	+	3	685	c.359delA	c.(358-360)GAAfs	p.E120fs	CDH6_uc003jhd.1_Frame_Shift_Del_p.E120fs	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein	120	Extracellular (Potential).|Cadherin 1.				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	31396018	31396019	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31396018_31396019delTT								CDH6 (70781 upstream) : RNASEN (4583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	31399314	31399315	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31399314_31399315delAA								CDH6 (74077 upstream) : RNASEN (1287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	31585824	31585825	+	IGR	DEL	GT	-	-	rs113799912		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31585824_31585825delGT								C5orf22 (30660 upstream) : PDZD2 (53692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	31589835	31589836	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31589835_31589836insT								C5orf22 (34671 upstream) : PDZD2 (49681 downstream)																																			---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31837839	31837840	+	Intron	INS	-	A	A	rs12188517	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31837839_31837840insA	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	31844168	31844169	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31844168_31844169insG	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	32073714	32073714	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32073714delG	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	32112011	32112012	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32112011_32112012insA								PDZD2 (974 upstream) : GOLPH3 (12812 downstream)																																			---	---	---	---
ZFR	51663	broad.mit.edu	37	5	32397564	32397564	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	32498617	32498617	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32498617delA								ZFR (53773 upstream) : SUB1 (86988 downstream)																																			---	---	---	---
SUB1	10923	broad.mit.edu	37	5	32593526	32593526	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32593526delT	uc003jhs.2	+						SUB1_uc003jht.2_Intron	NM_006713	NP_006704			activated RNA polymerase II transcription						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleolus|transcription factor complex	protein binding|single-stranded DNA binding|transcription coactivator activity				0																		---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32739289	32739289	+	Intron	DEL	G	-	-	rs58981865		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32739289delG	uc003jhv.2	+						NPR3_uc010iuo.2_Intron|NPR3_uc011cnz.1_Intron|NPR3_uc003jhu.2_Intron	NM_000908	NP_000899			natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)													---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32770135	32770135	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32770135delA	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	32801717	32801718	+	IGR	INS	-	T	T	rs143276761	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32801717_32801718insT								C5orf23 (9898 upstream) : TARS (639084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32828596	32828597	+	IGR	INS	-	TG	TG	rs138001353	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32828596_32828597insTG								C5orf23 (36777 upstream) : TARS (612205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32849941	32849942	+	IGR	INS	-	AC	AC	rs147381124	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32849941_32849942insAC								C5orf23 (58122 upstream) : TARS (590860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32978084	32978085	+	IGR	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32978084_32978085insCA								C5orf23 (186265 upstream) : TARS (462717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	33183336	33183337	+	IGR	INS	-	G	G	rs149853300	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33183336_33183337insG								C5orf23 (391517 upstream) : TARS (257465 downstream)																																			---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33611154	33611154	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33611154delA	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	33735133	33735134	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33735133_33735134insT	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	33838116	33838116	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33838116delT	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)			---	---	---	---
RXFP3	51289	broad.mit.edu	37	5	33938339	33938339	+	3'UTR	DEL	G	-	-	rs3832336		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33938339delG	uc003jic.1	+	1						NM_016568	NP_057652			relaxin/insulin-like family peptide receptor 3							integral to plasma membrane	N-formyl peptide receptor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	34017120	34017120	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34017120delT								AMACR (8914 upstream) : C1QTNF3 (844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34551778	34551778	+	IGR	DEL	T	-	-	rs11290922		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34551778delT								C1QTNF3 (508461 upstream) : RAI14 (104655 downstream)																																			---	---	---	---
RAI14	26064	broad.mit.edu	37	5	34791608	34791608	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34791608delA	uc003jir.2	+						RAI14_uc010iur.2_Intron|RAI14_uc011coj.1_Intron|RAI14_uc010ius.1_Intron|RAI14_uc003jis.2_Intron|RAI14_uc003jit.2_Intron|RAI14_uc011cok.1_Intron	NM_015577	NP_056392			retinoic acid induced 14 isoform a							cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)																	---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35775361	35775361	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35775361delA	uc003jjo.2	+						SPEF2_uc003jjp.1_Intron|SPEF2_uc003jjr.2_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)															---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35801615	35801615	+	Intron	DEL	A	-	-	rs113114692		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35801615delA	uc003jjo.2	+						SPEF2_uc003jjp.1_Intron|SPEF2_uc003jjr.2_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)															---	---	---	---
UGT3A1	133688	broad.mit.edu	37	5	35954653	35954654	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35954653_35954654delCA	uc003jjv.1	-						UGT3A1_uc003jjw.1_Intron	NM_152404	NP_689617			UDP glycosyltransferase 3 family, polypeptide A1							integral to membrane	glucuronosyltransferase activity			ovary(2)|central_nervous_system(1)	3	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	36032707	36032707	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36032707delT								UGT3A1 (31580 upstream) : UGT3A2 (2417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	36095941	36095942	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36095941_36095942insT								UGT3A2 (28957 upstream) : LMBRD2 (7472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	36191495	36191498	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36191495_36191498delTTTT								SKP2 (7350 upstream) : C5orf33 (1197 downstream)																																			---	---	---	---
C5orf33	133686	broad.mit.edu	37	5	36200229	36200230	+	Intron	INS	-	A	A	rs35054254		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36200229_36200230insA	uc003jkf.3	-						C5orf33_uc003jke.3_Intron|C5orf33_uc010iux.2_Intron|C5orf33_uc003jkg.3_Intron|C5orf33_uc011cov.1_Intron	NM_001085411	NP_001078880			hypothetical protein LOC133686 isoform 1								NAD+ kinase activity				0	all_lung(31;5.63e-05)		Epithelial(62;0.0254)|all cancers(62;0.0805)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	36434358	36434358	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36434358delT								RANBP3L (132347 upstream) : SLC1A3 (172099 downstream)																																			---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	37022321	37022321	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37022321delT	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron	NM_133433	NP_597677			delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)															---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	37044327	37044327	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37044327delT	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron	NM_133433	NP_597677			delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37221410	37221410	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37221410delA	uc011cpa.1	-							NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	38181920	38181922	+	IGR	DEL	AAA	-	-	rs72478770		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38181920_38181922delAAA								GDNF (342138 upstream) : EGFLAM (76611 downstream)																																			---	---	---	---
DAB2	1601	broad.mit.edu	37	5	39424859	39424859	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39424859delA	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	39506199	39506199	+	IGR	DEL	G	-	-	rs35053786		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39506199delG								DAB2 (80864 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	39556287	39556287	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39556287delA								DAB2 (130952 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	39964365	39964365	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39964365delA								DAB2 (539030 upstream) : PTGER4 (715667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40274634	40274635	+	IGR	DEL	AA	-	-	rs74934098		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40274634_40274635delAA								DAB2 (849299 upstream) : PTGER4 (405397 downstream)																																			---	---	---	---
PLCXD3	345557	broad.mit.edu	37	5	41322336	41322336	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41322336delA	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																		---	---	---	---
PLCXD3	345557	broad.mit.edu	37	5	41354526	41354526	+	Intron	DEL	T	-	-	rs79645165		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41354526delT	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	41840640	41840641	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41840640_41840641insG	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	41861520	41861520	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41861520delA	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)													---	---	---	---
GHR	2690	broad.mit.edu	37	5	42518984	42518984	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42518984delA	uc003jmt.2	+							NM_000163	NP_000154			growth hormone receptor precursor						2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|JAK-STAT cascade|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(4)|kidney(1)|skin(1)	6		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)													---	---	---	---
ZNF131	7690	broad.mit.edu	37	5	43166768	43166768	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43166768delT	uc011cpw.1	+						ZNF131_uc003jnj.3_Intron|ZNF131_uc003jnk.2_Intron|ZNF131_uc003jnn.3_Intron|ZNF131_uc003jnl.1_Intron|ZNF131_uc010ivm.1_Intron	NM_003432	NP_003423			zinc finger protein 131							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
NNT	23530	broad.mit.edu	37	5	43666736	43666737	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43666736_43666737delTT	uc003joe.2	+						NNT_uc003jof.2_Intron	NM_012343	NP_036475			nicotinamide nucleotide transhydrogenase						tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	43833765	43833765	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43833765delT								NNT (128098 upstream) : FGF10 (471332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	44431009	44431009	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44431009delA								FGF10 (42225 upstream) : MRPS30 (378018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	44552155	44552156	+	IGR	INS	-	A	A	rs142966080	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44552155_44552156insA								FGF10 (163371 upstream) : MRPS30 (256871 downstream)																																			---	---	---	---
MRPS30	10884	broad.mit.edu	37	5	44813123	44813123	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44813123delA	uc003joh.2	+							NM_016640	NP_057724			mitochondrial ribosomal protein S30						apoptosis|translation	mitochondrion|ribosome	structural constituent of ribosome				0	Lung NSC(6;8.08e-07)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	44828507	44828507	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44828507delT								MRPS30 (12893 upstream) : HCN1 (430846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	44845928	44845929	+	IGR	INS	-	CA	CA	rs142050913	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44845928_44845929insCA								MRPS30 (30314 upstream) : HCN1 (413424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	49491792	49491792	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49491792delA								None (None upstream) : EMB (200241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	49868648	49868650	+	IGR	DEL	AAA	-	-	rs112244310		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49868648_49868650delAAA								EMB (131414 upstream) : PARP8 (93083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	52731125	52731125	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52731125delA								MOCS2 (325527 upstream) : FST (45470 downstream)																																			---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53387612	53387614	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53387612_53387614delAAA	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	53770009	53770010	+	IGR	INS	-	TCTG	TCTG	rs141861757	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53770009_53770010insTCTG								HSPB3 (17802 upstream) : SNX18 (43579 downstream)																																			---	---	---	---
IL6ST	3572	broad.mit.edu	37	5	55256464	55256464	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55256464delT	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	56402175	56402175	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56402175delA								MIER3 (134674 upstream) : GPBP1 (67600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56962637	56962638	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56962637_56962638insT								ACTBL2 (184001 upstream) : PLK2 (787174 downstream)																																			---	---	---	---
PLK2	10769	broad.mit.edu	37	5	57754160	57754160	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57754160delA	uc003jrn.2	-						PLK2_uc011cql.1_Frame_Shift_Del_p.Y133fs	NM_006622	NP_006613			polo-like kinase 2						positive regulation of I-kappaB kinase/NF-kappaB cascade		ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(2)|lung(1)|skin(1)	4		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)														---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59062977	59062977	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59062977delT	uc003jsa.2	-						PDE4D_uc003jry.2_Intron|PDE4D_uc003jrz.2_Intron|PDE4D_uc003jsb.2_Intron|PDE4D_uc003jsc.2_Intron	NM_001104631	NP_001098101			phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59575511	59575512	+	Intron	INS	-	T	T	rs71606628		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59575511_59575512insT	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)													---	---	---	---
NDUFAF2	91942	broad.mit.edu	37	5	60362964	60362964	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60362964delT	uc003jsp.3	+						NDUFAF2_uc003jso.3_Intron	NM_174889	NP_777549			NADH dehydrogenase (ubiquinone) 1 alpha							membrane|mitochondrion	electron carrier activity|NADH dehydrogenase (ubiquinone) activity				0		Lung NSC(810;3.36e-05)|Prostate(74;0.0225)|Ovarian(174;0.17)|Breast(144;0.237)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	61310360	61310361	+	IGR	INS	-	A	A	rs77148312		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61310360_61310361insA								FLJ37543 (307998 upstream) : KIF2A (291628 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61469476	61469477	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61469476_61469477delAC								FLJ37543 (467114 upstream) : KIF2A (132512 downstream)																																			---	---	---	---
IPO11	51194	broad.mit.edu	37	5	61739925	61739925	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61739925delT	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	61832270	61832273	+	Intron	DEL	ATTT	-	-	rs111535340		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61832270_61832273delATTT	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)														---	---	---	---
CWC27	10283	broad.mit.edu	37	5	64157081	64157081	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64157081delT	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	64778365	64778365	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64778365delA	uc003jtp.2	-						ADAMTS6_uc003jtq.2_5'Flank	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)														---	---	---	---
CENPK	64105	broad.mit.edu	37	5	64848599	64848599	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64848599delA	uc003jts.2	-						CENPK_uc003jtt.2_Intron|CENPK_uc003jtu.2_Intron	NM_022145	NP_071428			SoxLZ/Sox6 leucine zipper binding protein						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00466)														---	---	---	---
SGTB	54557	broad.mit.edu	37	5	64976249	64976250	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64976249_64976250insA	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)														---	---	---	---
SFRS12	140890	broad.mit.edu	37	5	65458491	65458491	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	65769295	65769297	+	IGR	DEL	AAA	-	-	rs72275887		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65769295_65769297delAAA								SFRS12 (292583 upstream) : MAST4 (122879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	66516795	66516795	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66516795delT								CD180 (24178 upstream) : PIK3R1 (994809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	66961568	66961568	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66961568delT								CD180 (468951 upstream) : PIK3R1 (550036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67436517	67436518	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67436517_67436518insA								CD180 (943900 upstream) : PIK3R1 (75086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67831548	67831549	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67831548_67831549delAA								PIK3R1 (233901 upstream) : SLC30A5 (558269 downstream)																																			---	---	---	---
SLC30A5	64924	broad.mit.edu	37	5	68405267	68405270	+	Intron	DEL	TGTA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68405267_68405270delTGTA	uc003jvh.2	+						SLC30A5_uc003jvi.2_Intron	NM_022902	NP_075053			solute carrier family 30 (zinc transporter),						cellular zinc ion homeostasis|cobalt ion transport|regulation of proton transport|response to zinc ion	apical plasma membrane|Golgi apparatus|integral to plasma membrane|membrane fraction|secretory granule membrane	zinc ion binding|zinc ion transmembrane transporter activity			central_nervous_system(1)	1		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)														---	---	---	---
CCNB1	891	broad.mit.edu	37	5	68470536	68470536	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68470536delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	69870538	69870538	+	Intron	DEL	T	-	-	rs114037286	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69870538delT	uc011crh.1	+						LOC100170939_uc010ixu.2_Intron|LOC100170939_uc003jys.2_Intron|uc011cro.1_Intron|uc003jzj.2_Intron|uc010iyc.2_Intron|uc003jzu.2_Intron					Homo sapiens cDNA FLJ36702 fis, clone UTERU2009206.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	70492710	70492710	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70492710delA	uc010iyn.2	-						uc011crv.1_Intron					Homo sapiens cDNA FLJ78390 complete cds.																														---	---	---	---
BDP1	55814	broad.mit.edu	37	5	70841098	70841098	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70841098delA	uc003kbp.1	+						BDP1_uc003kbo.2_3'UTR|BDP1_uc003kbq.1_Intron|BDP1_uc003kbr.1_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)														---	---	---	---
BDP1	55814	broad.mit.edu	37	5	70846204	70846205	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70846204_70846205delAA	uc003kbp.1	+						BDP1_uc003kbq.1_Intron|BDP1_uc003kbr.1_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)														---	---	---	---
MCCC2	64087	broad.mit.edu	37	5	70939896	70939899	+	Intron	DEL	GTGC	-	-	rs71859051		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70939896_70939899delGTGC	uc003kbs.3	+						MCCC2_uc003kbt.3_Intron	NM_022132	NP_071415			methylcrotonoyl-Coenzyme A carboxylase 2 (beta)						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	70973131	70973132	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70973131_70973132delCA								MCCC2 (18603 upstream) : CARTPT (41862 downstream)																																			---	---	---	---
MRPS27	23107	broad.mit.edu	37	5	71534683	71534683	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71534683delT	uc003kbz.3	-						MRPS27_uc003kca.3_Intron|MRPS27_uc011cse.1_Intron|MRPS27_uc010iza.2_Intron|MRPS27_uc010iyz.1_5'Flank	NM_015084	NP_055899			mitochondrial ribosomal protein S27							mitochondrion|ribosome					0		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-53)														---	---	---	---
FCHO2	115548	broad.mit.edu	37	5	72370376	72370376	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72370376delT	uc003kcl.2	+						FCHO2_uc011csl.1_Intron|FCHO2_uc010izb.2_Intron|FCHO2_uc011csn.1_Intron	NM_138782	NP_620137			FCH domain only 2 isoform a											ovary(1)	1		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	72590836	72590836	+	IGR	DEL	T	-	-	rs73762044	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72590836delT								TMEM174 (119868 upstream) : FOXD1 (151251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72706356	72706356	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72706356delT								TMEM174 (235388 upstream) : FOXD1 (35731 downstream)																																			---	---	---	---
RGNEF	64283	broad.mit.edu	37	5	73142411	73142412	+	Intron	INS	-	T	T	rs142259999	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73142411_73142412insT	uc011csq.1	+						RGNEF_uc003kcx.2_Intron|RGNEF_uc003kcy.1_Intron|RGNEF_uc010izf.2_Intron|RGNEF_uc011csr.1_Intron	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)														---	---	---	---
RGNEF	64283	broad.mit.edu	37	5	73154250	73154251	+	Intron	INS	-	CTCA	CTCA	rs140928003	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73154250_73154251insCTCA	uc011csq.1	+						RGNEF_uc003kcx.2_Intron|RGNEF_uc010izf.2_Intron|RGNEF_uc011csr.1_Intron	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	73445072	73445072	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73445072delT								RGNEF (207659 upstream) : ENC1 (478163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73462209	73462211	+	IGR	DEL	TGT	-	-	rs34823215		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73462209_73462211delTGT								RGNEF (224796 upstream) : ENC1 (461024 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73716850	73716850	+	IGR	DEL	A	-	-	rs113651546		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73716850delA								RGNEF (479437 upstream) : ENC1 (206385 downstream)																																			---	---	---	---
FAM169A	26049	broad.mit.edu	37	5	74153913	74153914	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74153913_74153914insA	uc003kdm.2	-						FAM169A_uc010izm.2_Intron|FAM169A_uc003kdl.2_Intron	NM_015566	NP_056381			hypothetical protein LOC26049												0																		---	---	---	---
FAM169A	26049	broad.mit.edu	37	5	74192536	74192536	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74192536delA	uc010izm.2	-							NM_015566	NP_056381			hypothetical protein LOC26049												0																		---	---	---	---
COL4A3BP	10087	broad.mit.edu	37	5	74721075	74721076	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74721075_74721076insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	75365643	75365644	+	IGR	DEL	TC	-	-	rs62362229		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75365643_75365644delTC								POC5 (352330 upstream) : SV2C (13661 downstream)																																			---	---	---	---
CRHBP	1393	broad.mit.edu	37	5	76258448	76258450	+	Intron	DEL	AAA	-	-	rs113614086		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76258448_76258450delAAA	uc003ker.2	+							NM_001882	NP_001873			corticotropin releasing hormone binding protein						female pregnancy|learning or memory|signal transduction	soluble fraction					0		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)														---	---	---	---
AGGF1	55109	broad.mit.edu	37	5	76352404	76352404	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76352404delA	uc003ket.2	+							NM_018046	NP_060516			angiogenic factor VG5Q						angiogenesis|cell adhesion|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|RNA processing|vasculogenesis	extracellular region|perinuclear region of cytoplasm	eukaryotic cell surface binding|nucleic acid binding|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)														---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76512992	76512993	+	Intron	INS	-	T	T	rs145643633	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76512992_76512993insT	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	76673835	76673836	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76673835_76673836delAC	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	76697492	76697492	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76697492delT	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	76821368	76821368	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76821368delA								WDR41 (33036 upstream) : OTP (103170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	76842129	76842129	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76842129delA								WDR41 (53797 upstream) : OTP (82409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	76853307	76853307	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76853307delA								WDR41 (64975 upstream) : OTP (71231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	76896705	76896705	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76896705delA								WDR41 (108373 upstream) : OTP (27833 downstream)																																			---	---	---	---
AP3B1	8546	broad.mit.edu	37	5	77370758	77370758	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77370758delA	uc003kfj.2	-							NM_003664	NP_003655			adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)										Hermansky-Pudlak_syndrome				---	---	---	---
AP3B1	8546	broad.mit.edu	37	5	77382669	77382669	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77382669delT	uc003kfj.2	-							NM_003664	NP_003655			adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)										Hermansky-Pudlak_syndrome				---	---	---	---
AP3B1	8546	broad.mit.edu	37	5	77564229	77564229	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77564229delA	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				---	---	---	---
Unknown	0	broad.mit.edu	37	5	77609535	77609537	+	IGR	DEL	AAA	-	-	rs78984756		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77609535_77609537delAAA								AP3B1 (19007 upstream) : SCAMP1 (46802 downstream)																																			---	---	---	---
LHFPL2	10184	broad.mit.edu	37	5	77795972	77795972	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77795972delA	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	77911166	77911166	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77911166delA	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)														---	---	---	---
BHMT	635	broad.mit.edu	37	5	78421780	78421780	+	Intron	DEL	G	-	-	rs694290	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78421780delG	uc003kfu.3	+						BHMT_uc011cti.1_Intron	NM_001713	NP_001704			betaine-homocysteine methyltransferase						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)													---	---	---	---
JMY	133746	broad.mit.edu	37	5	78608215	78608215	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78608215delT	uc003kfx.3	+						JMY_uc003kfw.1_Intron	NM_152405	NP_689618			junction-mediating and regulatory protein						'de novo' actin filament nucleation|actin polymerization-dependent cell motility|Arp2/3 complex-mediated actin nucleation|cell cycle arrest|DNA repair|induction of apoptosis|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	cell leading edge|cytoplasm|cytoskeleton|nucleus	actin binding|transcription coactivator activity				0		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)														---	---	---	---
HOMER1	9456	broad.mit.edu	37	5	78739362	78739363	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78739362_78739363insT	uc003kfy.2	-						HOMER1_uc010jab.2_Intron|HOMER1_uc010jac.2_Intron|HOMER1_uc010jad.2_Intron	NM_004272	NP_004263			homer 1						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic density|postsynaptic membrane					0		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	78857768	78857768	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78857768delT								HOMER1 (48068 upstream) : PAPD4 (50475 downstream)																																			---	---	---	---
PAPD4	167153	broad.mit.edu	37	5	78931385	78931385	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78931385delT	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)														---	---	---	---
CMYA5	202333	broad.mit.edu	37	5	79030050	79030050	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79030050delA	uc003kgc.2	+	2	5534	c.5462delA	c.(5461-5463)CAAfs	p.Q1821fs		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1821						perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)														---	---	---	---
CMYA5	202333	broad.mit.edu	37	5	79067945	79067946	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79067945_79067946delAA	uc003kgc.2	+							NM_153610	NP_705838			cardiomyopathy associated 5							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	79236240	79236240	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79236240delA								CMYA5 (140192 upstream) : MTX3 (36301 downstream)																																			---	---	---	---
MTX3	345778	broad.mit.edu	37	5	79282756	79282756	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79282756delA	uc010jag.2	-						MTX3_uc010jah.2_Intron|MTX3_uc003kge.3_Intron|MTX3_uc003kgf.1_RNA	NM_001010891	NP_001010891			metaxin 3						protein targeting to mitochondrion	mitochondrial outer membrane					0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	79685424	79685424	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79685424delG								LOC441089 (37639 upstream) : ZFYVE16 (18414 downstream)																																			---	---	---	---
MSH3	4437	broad.mit.edu	37	5	80088494	80088494	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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					---	---	---	---
ACOT12	134526	broad.mit.edu	37	5	80631972	80631972	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80631972delT	uc003khl.3	-						RNU5E_uc011cto.1_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	80694883	80694884	+	Intron	INS	-	C	C	rs57901206		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80694883_80694884insC	uc011cto.1	+							NR_002754				Homo sapiens RNA, U5E small nuclear (RNU5E), non-coding RNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	81614226	81614226	+	IGR	DEL	A	-	-	rs71756795		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81614226delA								ATP6AP1L (80 upstream) : TMEM167A (734441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	81679585	81679585	+	RNA	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81679585delT	uc010jat.1	+	1		c.822delT								Homo sapiens cDNA FLJ37654 fis, clone BRHIP2010309, weakly similar to VACUOLAR ATP SYNTHASE SUBUNIT AC45 PRECURSOR (EC 3.6.1.34).																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	82264880	82264880	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82264880delA								ATP6AP1L (650734 upstream) : TMEM167A (83787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	82275278	82275278	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82275278delA								ATP6AP1L (661132 upstream) : TMEM167A (73389 downstream)																																			---	---	---	---
XRCC4	7518	broad.mit.edu	37	5	82526738	82526738	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82526738delT	uc003kib.2	+						XRCC4_uc003kia.1_Intron|XRCC4_uc003kid.2_Intron|XRCC4_uc003kic.2_Intron|XRCC4_uc003kie.2_Intron|XRCC4_uc003kif.1_Intron|XRCC4_uc003kig.2_Intron	NM_022406	NP_071801			X-ray repair cross complementing protein 4						DNA ligation involved in DNA repair|double-strand break repair via nonhomologous end joining|initiation of viral infection|positive regulation of ligase activity|provirus integration|response to X-ray	cytosol|DNA ligase IV complex|DNA-dependent protein kinase-DNA ligase 4 complex|nucleoplasm	DNA binding|protein C-terminus binding			skin(3)	3		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)									NHEJ					---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82842062	82842062	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82842062delA	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	83395788	83395788	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83395788delA	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	84046377	84046377	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84046377delA								EDIL3 (365766 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84158981	84158981	+	IGR	DEL	T	-	-	rs113714413		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84158981delT								EDIL3 (478370 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84223778	84223779	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84223778_84223779delTG								EDIL3 (543167 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84852785	84852786	+	IGR	INS	-	CAA	CAA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84852785_84852786insCAA								None (None upstream) : NBPF22P (725476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	85045143	85045143	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85045143delT								None (None upstream) : NBPF22P (533119 downstream)																																			---	---	---	---
RASA1	5921	broad.mit.edu	37	5	86669978	86669978	+	Splice_Site	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86669978delA	uc003kiw.2	+	14	1895	c.1777_splice	c.e14-2	p.V593_splice	RASA1_uc010jav.2_Splice_Site|RASA1_uc003kix.2_Splice_Site_p.V416_splice|RASA1_uc011ctv.1_Splice_Site_p.V426_splice|RASA1_uc011ctw.1_Splice_Site_p.V427_splice|RASA1_uc010jaw.2_Splice_Site_p.V415_splice	NM_002890	NP_002881			RAS p21 protein activator 1 isoform 1						cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(3)|ovary(1)|lung(1)	5		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)														---	---	---	---
RASA1	5921	broad.mit.edu	37	5	86675571	86675571	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86675571delA	uc003kiw.2	+	19	2625	c.2507delA	c.(2506-2508)GAAfs	p.E836fs	RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Frame_Shift_Del_p.E659fs|RASA1_uc011ctv.1_Frame_Shift_Del_p.E669fs|RASA1_uc011ctw.1_Frame_Shift_Del_p.E670fs|RASA1_uc010jaw.2_Frame_Shift_Del_p.E658fs	NM_002890	NP_002881	P20936	RASA1_HUMAN	RAS p21 protein activator 1 isoform 1	836	Ras-GAP.				cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(3)|ovary(1)|lung(1)	5		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)														---	---	---	---
CCNH	902	broad.mit.edu	37	5	86705006	86705007	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86705006_86705007delTC	uc003kjb.2	-						CCNH_uc003kiy.1_5'Flank|CCNH_uc003kiz.1_Intron|CCNH_uc003kja.2_Intron	NM_001239	NP_001230			cyclin H						G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cyclin-dependent protein kinase activating kinase holoenzyme complex|holo TFIIH complex	protein kinase binding			ovary(2)|kidney(1)	3		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;9.01e-39)|Epithelial(54;5.08e-33)|all cancers(79;4.28e-28)									Direct_reversal_of_damage|NER					---	---	---	---
Unknown	0	broad.mit.edu	37	5	86751779	86751779	+	IGR	DEL	A	-	-	rs34918106		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86751779delA								CCNH (42943 upstream) : TMEM161B (739245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	87232931	87232934	+	IGR	DEL	CTTC	-	-	rs72449897		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87232931_87232934delCTTC								CCNH (524095 upstream) : TMEM161B (258090 downstream)																																			---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87491918	87491918	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87491918delT	uc003kjc.2	-	12					TMEM161B_uc011cty.1_3'UTR|TMEM161B_uc010jax.2_RNA|TMEM161B_uc011ctx.1_3'UTR	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87536473	87536473	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87536473delA	uc003kjc.2	-						TMEM161B_uc011cty.1_Intron|TMEM161B_uc010jax.2_Intron|TMEM161B_uc011ctz.1_Intron	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	87679162	87679162	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87679162delA	uc003kjd.2	+						uc003kje.2_Intron					Homo sapiens cDNA clone IMAGE:4814828.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	87719872	87719872	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87719872delA	uc003kjd.2	+						uc003kje.2_Intron					Homo sapiens cDNA clone IMAGE:4814828.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	87723555	87723556	+	Intron	INS	-	AC	AC	rs144941858	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87723555_87723556insAC	uc003kjd.2	+						uc003kje.2_Intron					Homo sapiens cDNA clone IMAGE:4814828.																														---	---	---	---
MEF2C	4208	broad.mit.edu	37	5	88018306	88018306	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88018306delT	uc003kjj.2	-	11					MEF2C_uc003kji.2_3'UTR|MEF2C_uc003kjk.2_3'UTR|MEF2C_uc003kjm.2_3'UTR|MEF2C_uc003kjl.2_3'UTR	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	88146525	88146526	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88146525_88146526delAC	uc003kjj.2	-						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	88215000	88215000	+	Intron	DEL	T	-	-	rs75521163		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88215000delT	uc003kjn.1	+											Homo sapiens mRNA; cDNA DKFZp586I041 (from clone DKFZp586I041).																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	88260124	88260124	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88260124delC	uc003kjn.1	+											Homo sapiens mRNA; cDNA DKFZp586I041 (from clone DKFZp586I041).																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	89717951	89717952	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89717951_89717952delTT								CETN3 (12348 upstream) : MBLAC2 (36070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	91531816	91531816	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91531816delT	uc003kkb.1	+											Homo sapiens cDNA FLJ31923 fis, clone NT2RP7005323.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	91721991	91721991	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91721991delT	uc003kkb.1	+											Homo sapiens cDNA FLJ31923 fis, clone NT2RP7005323.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	91799180	91799180	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91799180delA								None (None upstream) : FLJ42709 (945885 downstream)																																			---	---	---	---
FLJ42709	441094	broad.mit.edu	37	5	92818262	92818262	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92818262delT	uc003kkc.2	-						FLJ42709_uc003kkd.2_Intron|FLJ42709_uc011cud.1_Intron|FLJ42709_uc003kke.2_Intron|FLJ42709_uc011cue.1_Intron|FLJ42709_uc010jbb.1_Intron|FLJ42709_uc003kkf.2_Intron|FLJ42709_uc003kkg.2_Intron					Homo sapiens cDNA FLJ38400 fis, clone FEBRA2008159.												0																		---	---	---	---
NR2F1	7025	broad.mit.edu	37	5	92929174	92929174	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92929174delA	uc003kkj.2	+							NM_005654	NP_005645			nuclear receptor subfamily 2, group F, member 1						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)														---	---	---	---
FAM172A	83989	broad.mit.edu	37	5	93198343	93198344	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93198343_93198344delTG	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	93386303	93386303	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93386303delA	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	93417568	93417569	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93417568_93417569delAA	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron|FAM172A_uc003kkm.3_Intron	NM_032042	NP_114431			hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0																		---	---	---	---
C5orf36	285600	broad.mit.edu	37	5	93911067	93911069	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93911067_93911069delAAA	uc011cuk.1	-						C5orf36_uc003kkp.2_Intron	NM_001145678	NP_001139150			hypothetical protein LOC285600 isoform 1												0		all_cancers(142;2.12e-08)|all_epithelial(76;5.95e-11)|all_lung(232;0.000996)|Lung NSC(167;0.0108)|Ovarian(174;0.0218)|Colorectal(57;0.0329)|Breast(839;0.214)|Lung SC(612;0.236)		all cancers(79;3.96e-19)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	94040555	94040555	+	IGR	DEL	T	-	-	rs36041113		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94040555delT								ANKRD32 (8984 upstream) : MCTP1 (1734 downstream)																																			---	---	---	---
MCTP1	79772	broad.mit.edu	37	5	94491499	94491499	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94491499delT	uc003kkx.2	-							NM_024717	NP_078993			multiple C2 domains, transmembrane 1 isoform L						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)														---	---	---	---
MCTP1	79772	broad.mit.edu	37	5	94540094	94540094	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94540094delA	uc003kkx.2	-							NM_024717	NP_078993			multiple C2 domains, transmembrane 1 isoform L						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)														---	---	---	---
FAM81B	153643	broad.mit.edu	37	5	94743096	94743097	+	Intron	DEL	AC	-	-	rs72457462		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94743096_94743097delAC	uc003kla.1	+						FAM81B_uc010jbe.1_Intron	NM_152548	NP_689761			hypothetical protein LOC153643											ovary(1)|skin(1)	2		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)														---	---	---	---
RHOBTB3	22836	broad.mit.edu	37	5	95099121	95099121	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95099121delA	uc003klm.2	+							NM_014899	NP_055714			rho-related BTB domain containing 3						retrograde transport, endosome to Golgi	Golgi apparatus	ATP binding|ATPase activity|Rab GTPase binding			lung(1)|skin(1)	2		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	95175713	95175714	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95175713_95175714delAG								GLRX (17136 upstream) : C5orf27 (12222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	95966640	95966640	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95966640delA								PCSK1 (197688 upstream) : CAST (31137 downstream)																																			---	---	---	---
CAST	831	broad.mit.edu	37	5	96084161	96084162	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96084161_96084162insT	uc003klz.1	+						CAST_uc003klt.2_Intron|CAST_uc003klu.2_Intron|CAST_uc003klv.2_Intron|CAST_uc003klw.2_Intron|CAST_uc003klx.2_Intron|CAST_uc003kly.2_Intron|CAST_uc011cuo.1_Intron|CAST_uc011cuq.1_Intron|CAST_uc011cur.1_Intron|CAST_uc011cus.1_Intron|CAST_uc003kma.1_Intron|CAST_uc011cut.1_Intron|CAST_uc003kmb.2_Intron|CAST_uc003kmc.2_Intron|CAST_uc003kmd.2_Intron|CAST_uc003kme.2_Intron|CAST_uc003kmf.2_Intron|CAST_uc003kmh.2_Intron|CAST_uc010jbj.2_Intron|CAST_uc010jbk.2_Intron|CAST_uc010jbl.1_Intron|CAST_uc003kmi.2_Intron|CAST_uc003kmj.2_Intron	NM_001042443	NP_001035908			calpastatin isoform i								calcium-dependent cysteine-type endopeptidase inhibitor activity|protein binding			central_nervous_system(3)|ovary(1)|kidney(1)	5		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)														---	---	---	---
RIOK2	55781	broad.mit.edu	37	5	96503730	96503730	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96503730delA	uc003kmz.2	-						RIOK2_uc003kna.3_Intron	NM_018343	NP_060813			RIO kinase 2 isoform 1								ATP binding|protein serine/threonine kinase activity			kidney(1)	1		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	96971231	96971231	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96971231delA								RIOK2 (452226 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97696126	97696128	+	IGR	DEL	CAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97696126_97696128delCAG								None (None upstream) : RGMB (408871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97793415	97793415	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97793415delT								None (None upstream) : RGMB (311584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97859322	97859322	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97859322delT								None (None upstream) : RGMB (245677 downstream)																																			---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98228483	98228483	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	99159524	99159525	+	IGR	DEL	TA	-	-	rs2123815	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99159524_99159525delTA								CHD1 (897286 upstream) : LOC100133050 (555684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99450876	99450877	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99450876_99450877insA								None (None upstream) : LOC100133050 (264332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99664550	99664550	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99664550delA								None (None upstream) : LOC100133050 (50659 downstream)																																			---	---	---	---
ST8SIA4	7903	broad.mit.edu	37	5	100192193	100192193	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100192193delT	uc003knk.2	-							NM_005668	NP_005659			ST8 alpha-N-acetyl-neuraminide						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	100306105	100306105	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100306105delT								ST8SIA4 (67118 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	100416786	100416786	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100416786delA								ST8SIA4 (177799 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101565682	101565682	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101565682delA								None (None upstream) : SLCO4C1 (4012 downstream)																																			---	---	---	---
PPIP5K2	23262	broad.mit.edu	37	5	102484798	102484799	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102484798_102484799delAC	uc003kod.3	+						PPIP5K2_uc011cva.1_Intron|PPIP5K2_uc003koe.2_Intron|PPIP5K2_uc010jbo.1_Intron	NM_015216	NP_056031			Histidine acid phosphatase domain containing 1						inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity			ovary(1)|skin(1)	2																		---	---	---	---
PPIP5K2	23262	broad.mit.edu	37	5	102518823	102518823	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102518823delT	uc003kod.3	+						PPIP5K2_uc011cva.1_Intron|PPIP5K2_uc003koe.2_Intron|PPIP5K2_uc003kof.2_Intron	NM_015216	NP_056031			Histidine acid phosphatase domain containing 1						inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	102630406	102630406	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102630406delT								C5orf30 (16045 upstream) : NUDT12 (254151 downstream)																																			---	---	---	---
NUDT12	83594	broad.mit.edu	37	5	102896591	102896591	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102896591delG	uc003koi.2	-						NUDT12_uc011cvb.1_Intron|NUDT12_uc010jbq.1_Intron	NM_031438	NP_113626			nudix-type motif 12							nucleus|peroxisome	metal ion binding|NAD+ diphosphatase activity				0		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	104150375	104150375	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104150375delT								None (None upstream) : RAB9BP1 (284800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	104402352	104402352	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104402352delA								None (None upstream) : RAB9BP1 (32823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105448147	105448148	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105448147_105448148delCA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105608828	105608829	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105608828_105608829insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105729198	105729198	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105729198delG								None (None upstream) : EFNA5 (983393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106091775	106091776	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106091775_106091776delAG								None (None upstream) : EFNA5 (620815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106288681	106288681	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106288681delT								None (None upstream) : EFNA5 (423910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106323903	106323903	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106323903delT								None (None upstream) : EFNA5 (388688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106579400	106579400	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106579400delA								None (None upstream) : EFNA5 (133191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106626829	106626829	+	IGR	DEL	A	-	-	rs68069747		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106626829delA								None (None upstream) : EFNA5 (85762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	107145287	107145287	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107145287delA								EFNA5 (138691 upstream) : FBXL17 (49453 downstream)																																			---	---	---	---
FBXL17	64839	broad.mit.edu	37	5	107379134	107379135	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107379134_107379135insT	uc011cvc.1	-						FBXL17_uc003kon.3_Intron	NM_001163315	NP_001156787			F-box and leucine-rich repeat protein 17												0		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	108015061	108015062	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108015061_108015062delTC								FBXL17 (297262 upstream) : FER (68461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	108621264	108621264	+	IGR	DEL	A	-	-	rs147837618		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108621264delA								FER (97891 upstream) : PJA2 (49147 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	110285977	110285977	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110285977delT								SLC25A46 (187495 upstream) : TSLP (119801 downstream)																																			---	---	---	---
C5orf13	9315	broad.mit.edu	37	5	111112711	111112712	+	Intron	INS	-	GGA	GGA	rs147009924		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111112711_111112712insGGA	uc011cvr.1	-						C5orf13_uc011cvs.1_Intron	NM_001142475	NP_001135947			neuronal protein 3.1 isoform c							cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	112033572	112033573	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112033572_112033573insT								FLJ11235 (276899 upstream) : APC (9645 downstream)																																			---	---	---	---
REEP5	7905	broad.mit.edu	37	5	112249838	112249839	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112249838_112249839insA	uc003kqe.1	-						REEP5_uc011cvw.1_Intron|REEP5_uc011cvx.1_Intron|REEP5_uc011cvy.1_Intron|REEP5_uc011cvz.1_Intron	NM_005669	NP_005660			receptor accessory protein 5							integral to membrane	protein binding				0		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		Epithelial(69;1.3e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.26e-08)|all cancers(49;3.56e-07)|Colorectal(14;0.00778)|COAD - Colon adenocarcinoma(37;0.013)														---	---	---	---
MCC	4163	broad.mit.edu	37	5	112644505	112644505	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112644505delA	uc003kql.3	-						MCC_uc003kqk.3_Intron	NM_001085377	NP_001078846			mutated in colorectal cancers isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)														---	---	---	---
TSSK1B	83942	broad.mit.edu	37	5	112769462	112769462	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112769462delG	uc003kqm.2	-	1	1267	c.1075delC	c.(1075-1077)CAAfs	p.Q359fs	MCC_uc003kql.3_Intron	NM_032028	NP_114417	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1	359					cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|skin(2)|stomach(1)	5		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)														---	---	---	---
YTHDC2	64848	broad.mit.edu	37	5	112853392	112853392	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112853392delT	uc003kqn.2	+						YTHDC2_uc010jce.1_Intron|YTHDC2_uc010jcf.1_Intron	NM_022828	NP_073739			YTH domain containing 2								ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	113124125	113124125	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113124125delA								YTHDC2 (193146 upstream) : KCNN2 (573891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	113637870	113637870	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113637870delT								YTHDC2 (706891 upstream) : KCNN2 (60146 downstream)																																			---	---	---	---
KCNN2	3781	broad.mit.edu	37	5	113822813	113822813	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113822813delA	uc003kqo.2	+	6	1778	c.1321delA	c.(1321-1323)AAAfs	p.K441fs	KCNN2_uc003kqp.2_Frame_Shift_Del_p.K93fs|KCNN2_uc010jcg.2_RNA|uc003kqr.1_Intron	NM_021614	NP_067627	Q9H2S1	KCNN2_HUMAN	small conductance calcium-activated potassium	441	Calmodulin-binding (By similarity).					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)														---	---	---	---
TMED7-TICAM2	100302736	broad.mit.edu	37	5	114945793	114945793	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114945793delA	uc003krd.2	-						TMED7-TICAM2_uc003kre.2_Intron	NM_021649	NP_067681			toll-like receptor adaptor molecule 2						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 4 signaling pathway	Golgi apparatus|intrinsic to membrane|plasma membrane	protein binding|transmembrane receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	115106723	115106723	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115106723delA								TMED7-TICAM2 (144853 upstream) : CDO1 (33709 downstream)																																			---	---	---	---
AQPEP	206338	broad.mit.edu	37	5	115351174	115351174	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115351174delA	uc003kro.2	+						AQPEP_uc003krp.2_Intron|AQPEP_uc003krq.2_Intron|AQPEP_uc003krr.2_Intron|AQPEP_uc003krs.2_Intron	NM_173800	NP_776161			laeverin						proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0																		---	---	---	---
COMMD10	51397	broad.mit.edu	37	5	115428220	115428221	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115428220_115428221insT	uc003krt.1	+							NM_016144	NP_057228			COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)														---	---	---	---
COMMD10	51397	broad.mit.edu	37	5	115612566	115612566	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115612566delG	uc003krt.1	+							NM_016144	NP_057228			COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)														---	---	---	---
SEMA6A	57556	broad.mit.edu	37	5	115901498	115901498	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115901498delT	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	116113432	116113432	+	IGR	DEL	A	-	-	rs77585149	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116113432delA								SEMA6A (202881 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	117728262	117728262	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117728262delT								None (None upstream) : DTWD2 (444309 downstream)																																			---	---	---	---
DMXL1	1657	broad.mit.edu	37	5	118445749	118445749	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118445749delT	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	118510897	118510897	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118510897delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	119172045	119172045	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119172045delT								FAM170A (200529 upstream) : PRR16 (627974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	120135565	120135566	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120135565_120135566delAA								PRR16 (112603 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	120923643	120923643	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120923643delA								PRR16 (900681 upstream) : FTMT (264007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	120952552	120952552	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120952552delA								PRR16 (929590 upstream) : FTMT (235098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121092794	121092795	+	IGR	DEL	AC	-	-	rs112246942	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121092794_121092795delAC								None (None upstream) : FTMT (94855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121178779	121178780	+	IGR	DEL	GG	-	-	rs67515319		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121178779_121178780delGG								None (None upstream) : FTMT (8870 downstream)																																			---	---	---	---
FTMT	94033	broad.mit.edu	37	5	121188521	121188522	+	3'UTR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121188521_121188522insA	uc003kss.2	+	1						NM_177478	NP_803431			ferritin mitochondrial precursor						cellular iron ion homeostasis|iron ion transport|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity	mitochondrion	ferric iron binding|ferroxidase activity			ovary(1)	1		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	121611050	121611050	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121611050delT								ZNF474 (121793 upstream) : SNCAIP (36336 downstream)																																			---	---	---	---
SNCAIP	9627	broad.mit.edu	37	5	121731797	121731797	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121731797delT	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_Intron|SNCAIP_uc010jcv.1_Intron|SNCAIP_uc010jcw.1_Intron|SNCAIP_uc010jcx.1_Intron	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)														---	---	---	---
SNCAIP	9627	broad.mit.edu	37	5	121747262	121747262	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121747262delA	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_Intron|SNCAIP_uc010jcv.1_Intron|SNCAIP_uc010jcw.1_Intron|SNCAIP_uc010jcx.1_Intron	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)														---	---	---	---
SNCAIP	9627	broad.mit.edu	37	5	121787400	121787400	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121787400delA	uc003ksw.1	+						SNCAIP_uc011cwl.1_Intron|SNCAIP_uc003ksx.1_Intron|SNCAIP_uc003ksy.1_Intron|SNCAIP_uc003ksz.1_Intron|SNCAIP_uc010jcu.2_Intron|uc003ktb.1_Intron|SNCAIP_uc003ktc.1_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	122546748	122546748	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122546748delT								PRDM6 (23004 upstream) : CEP120 (133832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	122783260	122783261	+	IGR	INS	-	AA	AA	rs34649751		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122783260_122783261insAA								CEP120 (24008 upstream) : CSNK1G3 (64532 downstream)																																			---	---	---	---
CSNK1G3	1456	broad.mit.edu	37	5	122940395	122940396	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122940395_122940396insA	uc003ktm.2	+						CSNK1G3_uc003ktl.2_Intron|CSNK1G3_uc003ktn.2_Intron|CSNK1G3_uc003kto.2_Intron|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_Intron|CSNK1G3_uc010jda.2_Intron	NM_004384	NP_004375			casein kinase 1, gamma 3 isoform 1						Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	122977816	122977816	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122977816delT								CSNK1G3 (25354 upstream) : ZNF608 (994794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123147428	123147428	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123147428delT								CSNK1G3 (194966 upstream) : ZNF608 (825182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123556070	123556073	+	IGR	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123556070_123556073delAAAA								CSNK1G3 (603608 upstream) : ZNF608 (416537 downstream)																																			---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	123981185	123981186	+	Intron	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123981185_123981186insTG	uc003ktq.1	-						ZNF608_uc003ktr.1_Intron|ZNF608_uc003ktp.1_5'Flank	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)														---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	124035775	124035775	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124035775delA	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	124166041	124166042	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124166041_124166042delCA								ZNF608 (81541 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124187225	124187228	+	IGR	DEL	CTTT	-	-	rs111256114		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124187225_124187228delCTTT								ZNF608 (102725 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	125842815	125842815	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125842815delT								GRAMD3 (12964 upstream) : ALDH7A1 (36103 downstream)																																			---	---	---	---
PHAX	51808	broad.mit.edu	37	5	125939712	125939712	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125939712delA	uc003kua.1	+	2	569	c.547delA	c.(547-549)AAAfs	p.K183fs		NM_032177	NP_115553	Q9H814	PHAX_HUMAN	RNA U, small nuclear RNA export adaptor	183	Necessary for interaction with CBP80 (By similarity).				ncRNA metabolic process|protein transport|snRNA export from nucleus|spliceosomal snRNP assembly	Cajal body|cytosol	RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	126055556	126055557	+	IGR	DEL	AA	-	-	rs113286464		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126055556_126055557delAA								C5orf48 (83582 upstream) : LMNB1 (57276 downstream)																																			---	---	---	---
LMNB1	4001	broad.mit.edu	37	5	126156844	126156844	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126156844delT	uc003kud.1	+						LMNB1_uc010jdb.1_Intron|LMNB1_uc011cxb.1_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	126376046	126376046	+	IGR	DEL	T	-	-	rs144313032		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126376046delT								MARCH3 (9606 upstream) : FLJ44606 (5005 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	126515625	126515625	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126515625delA								FLJ44606 (106453 upstream) : MEGF10 (110831 downstream)																																			---	---	---	---
MEGF10	84466	broad.mit.edu	37	5	126743568	126743568	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126743568delT	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)														---	---	---	---
PRRC1	133619	broad.mit.edu	37	5	126866120	126866121	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126866120_126866121delTT	uc003kuk.2	+						PRRC1_uc003kuj.3_Intron	NM_130809	NP_570721			proline-rich coiled-coil 1							Golgi apparatus					0		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)														---	---	---	---
SLC12A2	6558	broad.mit.edu	37	5	127493887	127493887	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127493887delT	uc003kus.2	+						SLC12A2_uc010jdf.2_Intron|SLC12A2_uc010jdg.2_Intron|SLC12A2_uc003kut.1_Intron	NM_001046	NP_001037			solute carrier family 12						potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)													---	---	---	---
FBN2	2201	broad.mit.edu	37	5	127605151	127605151	+	Intron	DEL	A	-	-	rs80131799		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127605151delA	uc003kuu.2	-							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	127954317	127954317	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127954317delC								FBN2 (80401 upstream) : SLC27A6 (346893 downstream)																																			---	---	---	---
ISOC1	51015	broad.mit.edu	37	5	128440485	128440485	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128440485delT	uc003kva.2	+							NM_016048	NP_057132			isochorismatase domain containing 1							peroxisome	catalytic activity				0		all_cancers(142;0.0813)|Prostate(80;0.0865)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.138)|OV - Ovarian serous cystadenocarcinoma(64;0.164)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	128513191	128513191	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128513191delA								ISOC1 (63474 upstream) : ADAMTS19 (282912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	128741595	128741595	+	IGR	DEL	A	-	-	rs11333385		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128741595delA								ISOC1 (291878 upstream) : ADAMTS19 (54508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	129111240	129111240	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129111240delA								ADAMTS19 (36864 upstream) : CHSY3 (129283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	129201291	129201291	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129201291delA								ADAMTS19 (126915 upstream) : CHSY3 (39232 downstream)																																			---	---	---	---
CDC42SE2	56990	broad.mit.edu	37	5	130678414	130678414	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130678414delT	uc003kvh.2	+						CDC42SE2_uc003kvi.2_Intron|CDC42SE2_uc003kvj.2_Intron|CDC42SE2_uc003kvk.2_Intron|CDC42SE2_uc003kvl.2_Intron	NM_020240	NP_064625			CDC42 small effector 2						phagocytosis|regulation of cell shape|regulation of signal transduction	cell projection|cytoplasm|cytoskeleton|phagocytic cup	protein binding|structural molecule activity				0		all_cancers(142;0.0525)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130940937	130940938	+	Intron	INS	-	AAC	AAC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130940937_130940938insAAC	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_Intron|RAPGEF6_uc003kvr.2_Intron|RAPGEF6_uc011cxe.1_Intron|RAPGEF6_uc010jdk.2_Intron	NM_016340	NP_057424			PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)														---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	131006382	131006382	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131006382delA	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	131101802	131101802	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131101802delT	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	131501817	131501817	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131501817delA								CSF2 (89959 upstream) : P4HA2 (26489 downstream)																																			---	---	---	---
RAD50	10111	broad.mit.edu	37	5	131974178	131974178	+	Intron	DEL	C	-	-	rs11308531		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131974178delC	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					---	---	---	---
KIF3A	11127	broad.mit.edu	37	5	132035887	132035887	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132035887delT	uc003kxo.2	-						KIF3A_uc003kxm.2_Intron|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)															---	---	---	---
LEAP2	116842	broad.mit.edu	37	5	132207200	132207202	+	5'Flank	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132207200_132207202delTTT	uc003kyc.2	+						LEAP2_uc003kyb.1_5'Flank	NM_052971	NP_443203			liver-expressed antimicrobial peptide 2						defense response to bacterium	extracellular region					0		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	132378827	132378827	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132378827delT								ZCCHC10 (16587 upstream) : HSPA4 (8835 downstream)																																			---	---	---	---
FSTL4	23105	broad.mit.edu	37	5	132565215	132565216	+	Intron	DEL	AA	-	-	rs67140806		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132565215_132565216delAA	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	132689871	132689871	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132689871delA	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	132773616	132773616	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132773616delT	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	132783625	132783625	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132783625delT	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	132825826	132825826	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132825826delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	133064918	133064921	+	IGR	DEL	ACAC	-	-	rs141110393		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133064918_133064921delACAC								FSTL4 (116695 upstream) : C5orf15 (226278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	133121320	133121320	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133121320delA								FSTL4 (173097 upstream) : C5orf15 (169879 downstream)																																			---	---	---	---
C5orf15	56951	broad.mit.edu	37	5	133295086	133295086	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133295086delT	uc003kyo.2	-							NM_020199	NP_064584			keratinocytes associated transmembrane protein 2							integral to membrane					0			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)															---	---	---	---
VDAC1	7416	broad.mit.edu	37	5	133316708	133316710	+	Intron	DEL	TTT	-	-	rs76341281		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133316708_133316710delTTT	uc003kyp.1	-						VDAC1_uc003kyq.1_Intron|VDAC1_uc003kyr.1_Intron	NM_003374	NP_003365			voltage-dependent anion channel 1						apoptosis|interspecies interaction between organisms	mitochondrial nucleoid|mitochondrial outer membrane|plasma membrane|pore complex	porin activity|protein binding|voltage-gated anion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)		Dihydroxyaluminium(DB01375)													---	---	---	---
CDKL3	51265	broad.mit.edu	37	5	133698210	133698210	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133698210delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	133797186	133797186	+	IGR	DEL	A	-	-	rs75407351		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133797186delA								CDKN2AIPNL (49597 upstream) : PHF15 (62880 downstream)																																			---	---	---	---
SEC24A	10802	broad.mit.edu	37	5	133984645	133984646	+	5'UTR	DEL	CT	-	-	rs61421945		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133984645_133984646delCT	uc003kzs.2	+	1					SEC24A_uc011cxu.1_5'UTR	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	134383014	134383015	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134383014_134383015delCA	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	134501861	134501861	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134501861delA	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																														---	---	---	---
CXCL14	9547	broad.mit.edu	37	5	134908732	134908732	+	Intron	DEL	A	-	-	rs111277613		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134908732delA	uc003lay.2	-							NM_004887	NP_004878			small inducible cytokine B14 precursor						cell-cell signaling|chemotaxis|immune response|signal transduction	extracellular space|Golgi apparatus	chemokine activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
TRPC7	57113	broad.mit.edu	37	5	135654532	135654533	+	Intron	INS	-	T	T	rs146859082	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135654532_135654533insT	uc003lbn.1	-						TRPC7_uc010jef.1_Intron|TRPC7_uc010jeg.1_Intron|TRPC7_uc010jeh.1_Intron|TRPC7_uc010jei.1_Intron|TRPC7_uc010jej.1_Intron	NM_020389	NP_065122			transient receptor potential cation channel,						axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136557986	136557986	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136557986delA	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	136908697	136908698	+	IGR	INS	-	AC	AC	rs142324504	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136908697_136908698insAC								SPOCK1 (73679 upstream) : KLHL3 (44492 downstream)																																			---	---	---	---
MYOT	9499	broad.mit.edu	37	5	137217571	137217571	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
FAM13B	51306	broad.mit.edu	37	5	137281528	137281528	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137281528delT	uc003lbz.2	-						FAM13B_uc003lcb.2_Intron|FAM13B_uc003lca.2_Intron	NM_016603	NP_057687			hypothetical protein LOC51306 isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
BRD8	10902	broad.mit.edu	37	5	137437205	137437205	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137437205delA	uc003lcc.1	-							NM_001164326				bromodomain containing 8 isoform 4						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	137503496	137503496	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137503496delA	uc003lcf.1	-						BRD8_uc003lcc.1_Intron|BRD8_uc011cyl.1_5'Flank|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_3'UTR	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)															---	---	---	---
REEP2	51308	broad.mit.edu	37	5	137778917	137778917	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137778917delG	uc003lcz.2	+						REEP2_uc003lda.2_Intron|REEP2_uc011cyt.1_Intron	NM_016606	NP_057690			receptor accessory protein 2							integral to membrane					0			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	137810441	137810442	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137810441_137810442delAA								EGR1 (5437 upstream) : ETF1 (31346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	137980825	137980825	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137980825delA								HSPA9 (69710 upstream) : CTNNA1 (108282 downstream)																																			---	---	---	---
SPATA24	202051	broad.mit.edu	37	5	138740489	138740491	+	5'Flank	DEL	TTT	-	-	rs74750855		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138740489_138740491delTTT	uc003lel.3	-						SPATA24_uc003lek.2_5'Flank|SPATA24_uc003lem.2_5'Flank	NM_194296	NP_919272			spermatogenesis associated 24						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleolus|nucleoplasm	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	139107443	139107443	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139107443delT								CXXC5 (44763 upstream) : PSD2 (67963 downstream)																																			---	---	---	---
NRG2	9542	broad.mit.edu	37	5	139244342	139244343	+	Intron	DEL	CA	-	-	rs111734532		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139244342_139244343delCA	uc003lex.1	-						NRG2_uc003lev.1_Intron|NRG2_uc003lew.1_Intron|NRG2_uc003ley.1_Intron	NM_004883	NP_004874			neuregulin 2 isoform 1						embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)													OREG0016838	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PFDN1	5201	broad.mit.edu	37	5	139659844	139659845	+	Intron	INS	-	T	T	rs142439684	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139659844_139659845insT	uc003lff.1	-						C5orf32_uc010jfi.2_Intron|PFDN1_uc003lfe.1_Intron|PFDN1_uc003lfg.1_Intron	NM_002622	NP_002613			prefoldin subunit 1						'de novo' posttranslational protein folding|cell cycle	prefoldin complex	sequence-specific DNA binding transcription factor activity|unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139779127	139779127	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139779127delT	uc003lfs.1	+						ANKHD1_uc003lfq.1_5'Flank|ANKHD1_uc003lfr.2_5'Flank|ANKHD1_uc003lfp.2_5'Flank|ANKHD1_uc003lfo.2_5'Flank|ANKHD1_uc010jfk.2_5'Flank	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-EIF4EBP3	404734	broad.mit.edu	37	5	139892956	139892957	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139892956_139892957insA	uc003lfs.1	+	24	4333_4334	c.4209_4210insA	c.(4207-4212)TTGAAAfs	p.L1403fs	ANKHD1_uc003lfq.1_Frame_Shift_Ins_p.L1422fs|ANKHD1_uc003lfr.2_Frame_Shift_Ins_p.L1403fs|ANKHD1_uc003lft.1_Frame_Shift_Ins_p.L614fs|ANKHD1_uc003lfu.1_Frame_Shift_Ins_p.L883fs|ANKHD1_uc003lfv.1_Frame_Shift_Ins_p.L480fs|ANKHD1-EIF4EBP3_uc011czh.1_Frame_Shift_Ins_p.L142fs|ANKHD1_uc003lfw.2_Frame_Shift_Ins_p.L41fs	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein	1403_1404						cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
APBB3	10307	broad.mit.edu	37	5	139939752	139939752	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139939752delA	uc003lgd.1	-						SRA1_uc003lfz.2_5'Flank|SRA1_uc010jfm.2_5'Flank|SRA1_uc003lga.2_5'Flank|APBB3_uc003lgb.1_Intron|APBB3_uc003lgc.1_Intron|APBB3_uc003lge.1_Intron|APBB3_uc003lgf.1_Intron|APBB3_uc010jfp.1_Intron|APBB3_uc011czi.1_Intron	NM_133172	NP_573418			amyloid beta precursor protein-binding, family							actin cytoskeleton|cytoplasm				ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
IK	3550	broad.mit.edu	37	5	140035711	140035711	+	Intron	DEL	C	-	-	rs5871748		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140035711delC	uc003lgq.2	+						IK_uc011czk.1_Intron	NM_006083	NP_006074			RED protein						cell-cell signaling|immune response	extracellular space|nucleus|soluble fraction				large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ZMAT2	153527	broad.mit.edu	37	5	140083649	140083649	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140083649delT	uc003lgy.1	+							NM_144723	NP_653324			zinc finger, matrin type 2							nucleus	DNA binding|zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHAC2	56134	broad.mit.edu	37	5	140358994	140358994	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140358994delT	uc003lii.2	+						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_Intron	NM_018899	NP_061722			protocadherin alpha subfamily C, 2 isoform 1						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	140495481	140495482	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140495481_140495482insA								PCDHB3 (12076 upstream) : PCDHB4 (6099 downstream)																																			---	---	---	---
PCDHB14	56122	broad.mit.edu	37	5	140601349	140601349	+	5'Flank	DEL	T	-	-	rs140834468	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140601349delT	uc003ljb.2	+						PCDHB14_uc011dal.1_5'Flank	NM_018934	NP_061757			protocadherin beta 14 precursor						calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB19P	84054	broad.mit.edu	37	5	140620222	140620225	+	3'UTR	DEL	CCAC	-	-	rs146891747		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140620222_140620225delCCAC	uc011dam.1	+	1						NR_001282				Homo sapiens protocadherin-beta (PCDHpsi-5) pseudogene, mRNA sequence.												0																		---	---	---	---
PCDHGA11	56105	broad.mit.edu	37	5	140803318	140803319	+	Intron	DEL	GG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140803318_140803319delGG	uc003lkq.1	+						PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_3'UTR|PCDHGA11_uc003lkp.1_Intron|PCDHGB8P_uc011daz.1_5'Flank	NM_018914	NP_061737			protocadherin gamma subfamily A, 11 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGC3	5098	broad.mit.edu	37	5	140858191	140858191	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140858191delT	uc003lkv.1	+						PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lku.1_Frame_Shift_Del_p.C836fs|PCDHGC3_uc003lkw.1_Intron	NM_002588	NP_002579			protocadherin gamma subfamily C, 3 isoform 1						calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)													OREG0016865	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DIAPH1	1729	broad.mit.edu	37	5	140996873	140996873	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140996873delA	uc003llb.3	-						DIAPH1_uc003llc.3_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)															---	---	---	---
FGF1	2246	broad.mit.edu	37	5	141975874	141975874	+	Intron	DEL	T	-	-	rs113375357		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141975874delT	uc003lmm.2	-						FGF1_uc011dbi.1_Intron|FGF1_uc003lmn.3_Intron|FGF1_uc003lmp.3_Intron|FGF1_uc003lmq.2_Intron|FGF1_uc010jgj.2_Intron|FGF1_uc003lmr.2_Intron|FGF1_uc003lms.3_Intron	NM_001144892	NP_001138364			fibroblast growth factor 1 (acidic) isoform 1						angiogenesis|cellular response to heat|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of angiogenesis|positive regulation of cell division|positive regulation of cell migration|positive regulation of cholesterol biosynthetic process|positive regulation of intracellular protein kinase cascade|positive regulation of transcription from RNA polymerase II promoter	cell cortex|cytosol|extracellular space	fibroblast growth factor receptor binding|growth factor activity|heparin binding|S100 alpha binding				0		all_neural(839;0.0416)|Ovarian(839;0.0955)|all_hematologic(541;0.1)|Prostate(461;0.157)|Lung NSC(810;0.21)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00032)	Pentosan Polysulfate(DB00686)													---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142203178	142203178	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142203178delA	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886			GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	142874798	142874798	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142874798delA								NR3C1 (59721 upstream) : HMHB1 (316928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	142956804	142956804	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142956804delA								NR3C1 (141727 upstream) : HMHB1 (234922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	143154482	143154482	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143154482delA								NR3C1 (339405 upstream) : HMHB1 (37244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	143511639	143511640	+	IGR	INS	-	T	T	rs72541288		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143511639_143511640insT								HMHB1 (311357 upstream) : YIPF5 (26091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	144183329	144183329	+	IGR	DEL	A	-	-	rs142062138	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144183329delA								KCTD16 (326385 upstream) : PRELID2 (955253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	144416874	144416874	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144416874delT								KCTD16 (559930 upstream) : PRELID2 (721708 downstream)																																			---	---	---	---
LARS	51520	broad.mit.edu	37	5	145550449	145550450	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145550449_145550450delAA	uc003lnx.1	-						LARS_uc011dbq.1_Intron|LARS_uc011dbr.1_Intron|LARS_uc011dbs.1_Intron	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	145581532	145581532	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145581532delT	uc003lnz.3	+						RBM27_uc003lny.2_5'Flank	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)															---	---	---	---
RBM27	54439	broad.mit.edu	37	5	145598511	145598512	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145598511_145598512insT	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)															---	---	---	---
TCERG1	10915	broad.mit.edu	37	5	145854335	145854335	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145854335delT	uc003lob.2	+						TCERG1_uc003loc.2_Intron|TCERG1_uc011dbt.1_Intron	NM_006706	NP_006697			transcription elongation regulator 1 isoform 1						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
TCERG1	10915	broad.mit.edu	37	5	145888688	145888688	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145888688delT	uc003lob.2	+						TCERG1_uc003loc.2_Intron	NM_006706	NP_006697			transcription elongation regulator 1 isoform 1						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	145956744	145956744	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145956744delT								GPR151 (61068 upstream) : PPP2R2B (12326 downstream)																																			---	---	---	---
JAKMIP2	9832	broad.mit.edu	37	5	147117721	147117721	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147117721delT	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	147201781	147201781	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147201781delT								JAKMIP2 (39529 upstream) : SPINK1 (2362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	147382404	147382404	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147382404delT								C5orf46 (96303 upstream) : SPINK5 (61131 downstream)																																			---	---	---	---
SPINK5	11005	broad.mit.edu	37	5	147497577	147497577	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147497577delT	uc003lox.2	+						SPINK5_uc010jgs.1_Intron|SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837			serine peptidase inhibitor, Kazal type 5 isoform						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)															---	---	---	---
SPINK13	153218	broad.mit.edu	37	5	147649399	147649399	+	Intron	DEL	A	-	-	rs71764680		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147649399delA	uc003lpc.2	+						uc003lpb.1_Intron|SPINK13_uc010jgt.2_Intron	NM_001040129	NP_001035218			serine PI Kazal type 5-like 3 precursor							extracellular region	serine-type endopeptidase inhibitor activity				0																		---	---	---	---
SH3TC2	79628	broad.mit.edu	37	5	148173134	148173134	+	Intron	DEL	C	-	-	rs79293240		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148173134delC	uc003lpp.1	-							NM_024577				SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
SH3TC2	79628	broad.mit.edu	37	5	148253252	148253252	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148253252delG	uc003lpp.1	-							NM_024577				SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	148445814	148445815	+	RNA	INS	-	A	A	rs147455515	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148445814_148445815insA	uc003lpx.1	+	2		c.2357_2358insA								Homo sapiens cDNA FLJ32218 fis, clone PLACE6003796.																														---	---	---	---
PCYOX1L	78991	broad.mit.edu	37	5	148736649	148736650	+	5'Flank	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148736649_148736650delTT	uc003lqk.2	+						PCYOX1L_uc003lql.2_5'Flank|PCYOX1L_uc010jgz.2_5'Flank	NM_024028	NP_076933			prenylcysteine oxidase 1 like precursor						prenylcysteine catabolic process	extracellular region	oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	148769781	148769781	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148769781delC								IL17B (10943 upstream) : LOC728264 (16659 downstream)																																			---	---	---	---
CSNK1A1	1452	broad.mit.edu	37	5	148912917	148912917	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148912917delT	uc003lqx.1	-						CSNK1A1_uc011dcc.1_Intron|CSNK1A1_uc003lqv.1_Intron|CSNK1A1_uc003lqw.1_Intron|CSNK1A1_uc003lqy.1_Intron|CSNK1A1_uc010jha.1_Intron	NM_001892	NP_001883			casein kinase 1, alpha 1 isoform 2						cell division|mitosis|Wnt receptor signaling pathway	centrosome|condensed chromosome kinetochore|cytosol|nuclear speck	ATP binding|protein binding|protein binding|protein serine/threonine kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)														---	---	---	---
CSNK1A1	1452	broad.mit.edu	37	5	148927237	148927238	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148927237_148927238delTT	uc003lqx.1	-						CSNK1A1_uc011dcc.1_Intron|CSNK1A1_uc003lqv.1_Intron|CSNK1A1_uc003lqw.1_Intron|CSNK1A1_uc003lqy.1_Intron|CSNK1A1_uc010jha.1_Intron	NM_001892	NP_001883			casein kinase 1, alpha 1 isoform 2						cell division|mitosis|Wnt receptor signaling pathway	centrosome|condensed chromosome kinetochore|cytosol|nuclear speck	ATP binding|protein binding|protein binding|protein serine/threonine kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	149052360	149052360	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149052360delA								ARHGEF37 (37833 upstream) : PPARGC1B (57504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	149334882	149334882	+	IGR	DEL	C	-	-	rs57228974		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149334882delC								PDE6A (10526 upstream) : SLC26A2 (5418 downstream)																																			---	---	---	---
SLC6A7	6534	broad.mit.edu	37	5	149587760	149587760	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149587760delA	uc003lrr.2	+							NM_014228	NP_055043			solute carrier family 6, member 7							integral to plasma membrane|membrane fraction	neurotransmitter:sodium symporter activity|proline:sodium symporter activity				0		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	149820744	149820744	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149820744delA								CD74 (28412 upstream) : RPS14 (3050 downstream)																																			---	---	---	---
ANXA6	309	broad.mit.edu	37	5	150509363	150509363	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150509363delC	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	150629478	150629480	+	IGR	DEL	TTT	-	-	rs112239274		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150629478_150629480delTTT								CCDC69 (25824 upstream) : GM2A (3133 downstream)																																			---	---	---	---
SLC36A2	153201	broad.mit.edu	37	5	150719678	150719680	+	Intron	DEL	GAG	-	-	rs33954122		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150719678_150719680delGAG	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	150800814	150800814	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150800814delT	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)															---	---	---	---
GM2A	2760	broad.mit.edu	37	5	150806547	150806547	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150806547delG	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)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150887298	150887298	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150887298delA	uc003lue.3	-						GM2A_uc011dcs.1_Intron|FAT2_uc003lud.3_Intron	NM_001447	NP_001438			FAT tumor suppressor 2 precursor						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	151384117	151384117	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151384117delT	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	151487964	151487973	+	Intron	DEL	TTTTTTTTTT	-	-	rs71575118		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151487964_151487973delTTTTTTTTTT	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																														---	---	---	---
GALNT10	55568	broad.mit.edu	37	5	153575491	153575491	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153575491delT	uc003lvh.2	+						GALNT10_uc003lvg.1_Intron|GALNT10_uc010jic.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)															---	---	---	---
GALNT10	55568	broad.mit.edu	37	5	153718077	153718077	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
GALNT10	55568	broad.mit.edu	37	5	153719069	153719069	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153719069delA	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)															---	---	---	---
GALNT10	55568	broad.mit.edu	37	5	153729750	153729751	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153729750_153729751delAA	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)															---	---	---	---
GALNT10	55568	broad.mit.edu	37	5	153794905	153794905	+	Intron	DEL	T	-	-	rs78241319		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153794905delT	uc003lvh.2	+						GALNT10_uc010jic.2_Intron|GALNT10_uc010jid.2_Intron|uc003lvi.2_Intron|GALNT10_uc003lvj.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	153950422	153950423	+	IGR	DEL	AC	-	-	rs72103342		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153950422_153950423delAC								HAND1 (92598 upstream) : MIR1303 (114913 downstream)																																			---	---	---	---
LARP1	23367	broad.mit.edu	37	5	154105118	154105118	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154105118delA	uc003lvo.2	+							NM_015315	NP_056130			la related protein isoform 1								protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
LARP1	23367	broad.mit.edu	37	5	154196588	154196593	+	3'UTR	DEL	TTTTTC	-	-	rs32427	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154196588_154196593delTTTTTC	uc003lvp.2	+	19					LARP1_uc003lvo.2_3'UTR	NM_033551	NP_291029			la related protein isoform 2								protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
C5orf4	10826	broad.mit.edu	37	5	154213074	154213075	+	Intron	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154213074_154213075insTG	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	154445339	154445340	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154445339_154445340insT								KIF4B (47654 upstream) : SGCD (689723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	154832858	154832859	+	IGR	DEL	TT	-	-	rs145947080		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154832858_154832859delTT								KIF4B (435173 upstream) : SGCD (302204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	155029320	155029320	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155029320delA								KIF4B (631635 upstream) : SGCD (105743 downstream)																																			---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155276447	155276456	+	Intron	DEL	TGTGCGCGCG	-	-	rs77280677	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155276447_155276456delTGTGCGCGCG	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	155374944	155374944	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155374944delA	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	155638176	155638177	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155638176_155638177insA	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	155953272	155953272	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155953272delA	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681			delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	156017751	156017751	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156017751delT	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681			delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
PPP1R2P3	153743	broad.mit.edu	37	5	156276548	156276548	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156276548delT	uc003lwf.1	+							NR_002168				RecName: Full=Putative protein phosphatase inhibitor 2-like protein 3; AltName: Full=Protein phosphatase 1, regulatory subunit 2 pseudogene 3;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	157166889	157166889	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157166889delA								THG1L (118 upstream) : LSM11 (3866 downstream)																																			---	---	---	---
CLINT1	9685	broad.mit.edu	37	5	157248079	157248079	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157248079delT	uc003lxj.1	-						CLINT1_uc003lxi.1_Intron|CLINT1_uc011ddv.1_Intron	NM_014666	NP_055481			epsin 4						endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
EBF1	1879	broad.mit.edu	37	5	158314011	158314011	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158314011delA	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-4292-01	TCGA-BR-4292-01									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								---	---	---	---
Unknown	0	broad.mit.edu	37	5	158581092	158581095	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158581092_158581095delTTTT								EBF1 (54304 upstream) : RNF145 (3324 downstream)																																			---	---	---	---
UBLCP1	134510	broad.mit.edu	37	5	158695881	158695881	+	5'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158695881delT	uc003lxq.2	+	2						NM_145049	NP_659486			ubiquitin-like domain containing CTD phosphatase							nucleus	phosphoprotein phosphatase activity			ovary(1)	1	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	158721675	158721676	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158721675_158721676insA								UBLCP1 (8627 upstream) : IL12B (20115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159429992	159429992	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159429992delA								ADRA1B (29975 upstream) : TTC1 (6188 downstream)																																			---	---	---	---
CCNJL	79616	broad.mit.edu	37	5	159738750	159738750	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159738750delA	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	159933652	159933654	+	IGR	DEL	GAA	-	-	rs10525460		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159933652_159933654delGAA								MIR146A (21195 upstream) : ATP10B (56473 downstream)																																			---	---	---	---
ATP10B	23120	broad.mit.edu	37	5	160025551	160025551	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160025551delA	uc003lym.1	-						ATP10B_uc010jit.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)															---	---	---	---
ATP10B	23120	broad.mit.edu	37	5	160257948	160257949	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160257948_160257949delTC	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)															---	---	---	---
ATP10B	23120	broad.mit.edu	37	5	160265656	160265656	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160265656delA	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	160659449	160659450	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160659449_160659450delAA								LOC285629 (293816 upstream) : GABRB2 (55986 downstream)																																			---	---	---	---
GABRB2	2561	broad.mit.edu	37	5	160737493	160737494	+	Intron	INS	-	TC	TC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160737493_160737494insTC	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron	NM_021911	NP_068711			gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
GABRB2	2561	broad.mit.edu	37	5	160873979	160873979	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160873979delA	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron	NM_021911	NP_068711			gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	161211791	161211791	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161211791delA								GABRA6 (82193 upstream) : GABRA1 (62406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162250134	162250135	+	IGR	INS	-	TGT	TGT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162250134_162250135insTGT								GABRG2 (667590 upstream) : CCNG1 (614442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162625536	162625538	+	IGR	DEL	AAA	-	-	rs147465728		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162625536_162625538delAAA								None (None upstream) : CCNG1 (239039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163165722	163165722	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163165722delA								MAT2B (219389 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163331607	163331607	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163331607delA								MAT2B (385274 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163743516	163743516	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163743516delT								MAT2B (797183 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164163110	164163110	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164163110delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164520908	164520908	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164520908delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164818977	164818977	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164818977delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166068822	166068822	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166068822delA								None (None upstream) : ODZ2 (643021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166270372	166270373	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166270372_166270373insA								None (None upstream) : ODZ2 (441470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166406880	166406880	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166406880delT								None (None upstream) : ODZ2 (304963 downstream)																																			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	166911496	166911496	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166911496delT	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167246089	167246090	+	Intron	DEL	GC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167246089_167246090delGC	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	167389300	167389300	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167389300delA	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)														---	---	---	---
WWC1	23286	broad.mit.edu	37	5	167781063	167781063	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167781063delT	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron	NM_015238	NP_056053			WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	167900376	167900376	+	IGR	DEL	A	-	-	rs115459237	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167900376delA								WWC1 (1070 upstream) : RARS (13087 downstream)																																			---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168119505	168119506	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168119505_168119506delGA	uc003mab.2	-						SLIT3_uc010jjg.2_Intron	NM_003062	NP_003053			slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168598027	168598027	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168598027delA	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	168606693	168606694	+	Intron	DEL	TG	-	-	rs35324900		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168606693_168606694delTG	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	168728417	168728417	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168728417delT	uc003mab.2	-						SLIT3_uc010jjg.2_5'Flank|SLIT3_uc010jji.2_5'Flank	NM_003062	NP_003053			slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	168918568	168918569	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168918568_168918569delAA								SLIT3 (190435 upstream) : CCDC99 (92069 downstream)																																			---	---	---	---
CCDC99	54908	broad.mit.edu	37	5	169024236	169024237	+	Intron	INS	-	TG	TG	rs148919065	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169024236_169024237insTG	uc003mae.3	+						CCDC99_uc010jjj.2_Intron|CCDC99_uc011deq.1_Intron|CCDC99_uc010jjk.2_Intron	NM_017785	NP_060255			coiled-coil domain containing 99						cell division|establishment of mitotic spindle orientation|mitotic metaphase plate congression|mitotic prometaphase|protein localization to kinetochore	condensed chromosome outer kinetochore|cytosol|microtubule organizing center|nucleus|spindle pole	kinetochore binding|protein binding			ovary(1)|liver(1)	2	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
CCDC99	54908	broad.mit.edu	37	5	169025658	169025658	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169025658delT	uc003mae.3	+						CCDC99_uc010jjj.2_Intron|CCDC99_uc011deq.1_Intron|CCDC99_uc010jjk.2_Intron	NM_017785	NP_060255			coiled-coil domain containing 99						cell division|establishment of mitotic spindle orientation|mitotic metaphase plate congression|mitotic prometaphase|protein localization to kinetochore	condensed chromosome outer kinetochore|cytosol|microtubule organizing center|nucleus|spindle pole	kinetochore binding|protein binding			ovary(1)|liver(1)	2	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169452852	169452853	+	Intron	INS	-	TTCC	TTCC	rs142164505	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169452852_169452853insTTCC	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)															---	---	---	---
KCNIP1	30820	broad.mit.edu	37	5	169922317	169922317	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169922317delG	uc003map.2	+							NM_001034838	NP_001030010			Kv channel interacting protein 1 isoform 3						detection of calcium ion|signal transduction|synaptic transmission	plasma membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
KCNIP1	30820	broad.mit.edu	37	5	169978623	169978624	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169978623_169978624delTG	uc003mas.2	+						KCNIP1_uc003map.2_Intron|KCNIP1_uc003mat.2_Intron|KCNIP1_uc010jjp.2_Intron|KCNIP1_uc010jjq.2_Intron	NM_001034837	NP_001030009			Kv channel interacting protein 1 isoform 1						detection of calcium ion|signal transduction|synaptic transmission	plasma membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
KCNIP1	30820	broad.mit.edu	37	5	170131048	170131048	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170131048delT	uc003mas.2	+						KCNIP1_uc003map.2_Intron|KCNIP1_uc003mat.2_Intron|KCNIP1_uc010jjp.2_Intron|KCNIP1_uc010jjq.2_Intron	NM_001034837	NP_001030009			Kv channel interacting protein 1 isoform 1						detection of calcium ion|signal transduction|synaptic transmission	plasma membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
RANBP17	64901	broad.mit.edu	37	5	170529797	170529797	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170529797delT	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	170579421	170579422	+	Intron	DEL	AA	-	-	rs76282265		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170579421_170579422delAA	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								---	---	---	---
NPM1	4869	broad.mit.edu	37	5	170819655	170819655	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170819655delT	uc011dex.1	+						NPM1_uc003mbh.2_Intron|NPM1_uc003mbi.2_Intron|NPM1_uc003mbj.2_Intron	NM_002520	NP_002511			nucleophosmin 1 isoform 1						anti-apoptosis|cell aging|CenH3-containing nucleosome assembly at centromere|centrosome cycle|DNA repair|interspecies interaction between organisms|intracellular protein transport|negative regulation of cell proliferation|negative regulation of centrosome duplication|nucleocytoplasmic transport|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|regulation of endodeoxyribonuclease activity|regulation of endoribonuclease activity|ribosome assembly|signal transduction	nucleolus|nucleoplasm|ribonucleoprotein complex|spindle pole centrosome	histone binding|NF-kappaB binding|protein binding|protein heterodimerization activity|protein homodimerization activity|ribosomal large subunit binding|ribosomal small subunit binding|RNA binding|Tat protein binding|transcription coactivator activity|unfolded protein binding		NPM1/ALK(632)	haematopoietic_and_lymphoid_tissue(3109)|skin(1)	3110	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T|F 	ALK|RARA|MLF1	NHL|APL|AML								---	---	---	---
NPM1	4869	broad.mit.edu	37	5	170832424	170832425	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170832424_170832425insA	uc011dex.1	+						NPM1_uc003mbh.2_Intron|NPM1_uc003mbi.2_Intron|NPM1_uc003mbj.2_Intron	NM_002520	NP_002511			nucleophosmin 1 isoform 1						anti-apoptosis|cell aging|CenH3-containing nucleosome assembly at centromere|centrosome cycle|DNA repair|interspecies interaction between organisms|intracellular protein transport|negative regulation of cell proliferation|negative regulation of centrosome duplication|nucleocytoplasmic transport|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|regulation of endodeoxyribonuclease activity|regulation of endoribonuclease activity|ribosome assembly|signal transduction	nucleolus|nucleoplasm|ribonucleoprotein complex|spindle pole centrosome	histone binding|NF-kappaB binding|protein binding|protein heterodimerization activity|protein homodimerization activity|ribosomal large subunit binding|ribosomal small subunit binding|RNA binding|Tat protein binding|transcription coactivator activity|unfolded protein binding		NPM1/ALK(632)	haematopoietic_and_lymphoid_tissue(3109)|skin(1)	3110	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T|F 	ALK|RARA|MLF1	NHL|APL|AML								---	---	---	---
Unknown	0	broad.mit.edu	37	5	171160440	171160440	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171160440delA								FGF18 (276278 upstream) : FBXW11 (128116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	171220958	171220959	+	IGR	INS	-	C	C	rs148129554	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171220958_171220959insC								FGF18 (336796 upstream) : FBXW11 (67597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	171270823	171270823	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171270823delA								FGF18 (386661 upstream) : FBXW11 (17733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	171440622	171440622	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171440622delC								FBXW11 (6745 upstream) : STK10 (28452 downstream)																																			---	---	---	---
UBTD2	92181	broad.mit.edu	37	5	171681760	171681760	+	Intron	DEL	G	-	-	rs146000133	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171681760delG	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)															---	---	---	---
NEURL1B	54492	broad.mit.edu	37	5	172107423	172107423	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172107423delG	uc003mbt.2	+							NM_001142651	NP_001136123			neuralized homolog 1B								ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	172178243	172178244	+	IGR	INS	-	AAGG	AAGG	rs28532090		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172178243_172178244insAAGG								NEURL1B (59712 upstream) : DUSP1 (16858 downstream)																																			---	---	---	---
ATP6V0E1	8992	broad.mit.edu	37	5	172414286	172414288	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172414286_172414288delTTT	uc003mcd.1	+							NM_003945	NP_003936			ATPase, H+ transporting, lysosomal 9kDa, V0						ATP hydrolysis coupled proton transport|cell growth|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport|vacuolar acidification	endosome membrane|integral to membrane|membrane fraction|proton-transporting V-type ATPase, V0 domain|vacuole	proton-transporting ATPase activity, rotational mechanism				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
C5orf41	153222	broad.mit.edu	37	5	172532229	172532230	+	Intron	DEL	TG	-	-	rs113596042		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172532229_172532230delTG	uc003mch.2	+						C5orf41_uc011dfd.1_Intron	NM_153607	NP_705835			luman-recruiting factor								protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	172763848	172763848	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172763848delT								STC2 (7342 upstream) : LOC285593 (242798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173149687	173149688	+	IGR	INS	-	GT	GT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173149687_173149688insGT								BOD1 (106021 upstream) : CPEB4 (165643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173236153	173236153	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173236153delA								BOD1 (192487 upstream) : CPEB4 (79178 downstream)																																			---	---	---	---
C5orf47	133491	broad.mit.edu	37	5	173414204	173414205	+	5'Flank	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173414204_173414205insA	uc003mcw.3	+						C5orf47_uc003mcv.2_Intron	NM_001144954	NP_001138426			hypothetical protein LOC133491												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	173735175	173735175	+	IGR	DEL	G	-	-	rs142184927	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173735175delG								HMP19 (198994 upstream) : MSX2 (416400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173820463	173820463	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173820463delA								HMP19 (284282 upstream) : MSX2 (331112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173845987	173845990	+	IGR	DEL	AGAG	-	-	rs112579786		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173845987_173845990delAGAG								HMP19 (309806 upstream) : MSX2 (305585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174104424	174104424	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174104424delT								HMP19 (568243 upstream) : MSX2 (47151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174280602	174280603	+	IGR	INS	-	G	G	rs142554515	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174280602_174280603insG								MSX2 (122701 upstream) : DRD1 (587073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174540436	174540436	+	IGR	DEL	A	-	-	rs67232912		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174540436delA								MSX2 (382535 upstream) : DRD1 (327240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174812028	174812047	+	IGR	DEL	AAGGAAAGAAGGAAGGAAGA	-	-	rs111559272		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174812028_174812047delAAGGAAAGAAGGAAGGAAGA								MSX2 (654127 upstream) : DRD1 (55629 downstream)																																			---	---	---	---
SFXN1	94081	broad.mit.edu	37	5	174919362	174919362	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174919362delT	uc003mda.2	+						SFXN1_uc003mdb.1_Intron	NM_022754	NP_073591			sideroflexin 1						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity|protein binding			ovary(1)	1	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
CPLX2	10814	broad.mit.edu	37	5	175252408	175252409	+	Intron	DEL	AA	-	-	rs68087789		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175252408_175252409delAA	uc003mde.1	+							NM_006650	NP_006641			complexin 2						mast cell degranulation|positive regulation of synaptic plasticity|vesicle docking involved in exocytosis	cytosol				ovary(1)	1	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	175945059	175945060	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175945059_175945060delTT								FAF2 (7985 upstream) : RNF44 (8640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	176221010	176221013	+	IGR	DEL	TCTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176221010_176221013delTCTC								TSPAN17 (134952 upstream) : UNC5A (16547 downstream)																																			---	---	---	---
HK3	3101	broad.mit.edu	37	5	176313234	176313234	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176313234delA	uc003mfa.2	-						HK3_uc003mez.2_Intron	NM_002115	NP_002106			hexokinase 3						glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	7	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
HK3	3101	broad.mit.edu	37	5	176314899	176314899	+	Intron	DEL	T	-	-	rs113393288		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176314899delT	uc003mfa.2	-						HK3_uc003mez.2_Intron	NM_002115	NP_002106			hexokinase 3						glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	7	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176565077	176565077	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176565077delA	uc003mfr.3	+						NSD1_uc003mft.3_Intron|NSD1_uc003mfs.1_Intron|NSD1_uc011dfx.1_Intron|NSD1_uc003mfp.2_Intron	NM_022455	NP_071900			nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176633859	176633859	+	Intron	DEL	A	-	-	rs11322596		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176633859delA	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	176682306	176682306	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176682306delA	uc003mfr.3	+						NSD1_uc003mft.3_Intron|NSD1_uc003mfs.1_Intron|NSD1_uc011dfx.1_Intron	NM_022455	NP_071900			nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176722543	176722543	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176722543delA	uc003mfr.3	+	23					NSD1_uc003mft.3_3'UTR|NSD1_uc011dfx.1_3'UTR	NM_022455	NP_071900			nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
FAM193B	54540	broad.mit.edu	37	5	176966140	176966140	+	5'UTR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176966140delG	uc003mhs.3	-	3					FAM193B_uc003mht.2_5'Flank|FAM193B_uc003mhu.2_5'Flank|FAM193B_uc003mhv.2_5'UTR|FAM193B_uc003mhw.2_RNA	NM_019057	NP_061930			hypothetical protein LOC54540												0																		---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177688429	177688429	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177688429delA	uc003mje.2	-						COL23A1_uc010jkt.2_Intron	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)														---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177769796	177769799	+	Intron	DEL	AAAC	-	-	rs148149929		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177769796_177769799delAAAC	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)														---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	178000217	178000217	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178000217delA	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)														---	---	---	---
AACSL	729522	broad.mit.edu	37	5	178238892	178238892	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178238892delT	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	178240323	178240323	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178240323delA	uc011dgl.1	-						AACSL_uc003mjk.2_Intron					Homo sapiens acetoacetyl-CoA synthetase-like, mRNA (cDNA clone IMAGE:3945810), partial cds.												0																		---	---	---	---
RUFY1	80230	broad.mit.edu	37	5	178981625	178981625	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178981625delT	uc003mka.1	+							NM_025158	NP_079434			RUN and FYVE domain-containing 1 isoform a						endocytosis|protein transport	early endosome membrane	lipid binding|zinc ion binding			ovary(4)|breast(1)	5	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)												HNSCC(44;0.11)			---	---	---	---
HNRNPH1	3187	broad.mit.edu	37	5	179045524	179045526	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179045524_179045526delAAA	uc003mkf.3	-						HNRNPH1_uc011dgn.1_5'Flank|HNRNPH1_uc003mkg.3_Intron|HNRNPH1_uc003mke.3_Intron|HNRNPH1_uc003mkh.3_Intron	NM_005520	NP_005511			heterogeneous nuclear ribonucleoprotein H1						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																		---	---	---	---
CANX	821	broad.mit.edu	37	5	179127867	179127870	+	Intron	DEL	TTTT	-	-	rs36008216		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179127867_179127870delTTTT	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)													---	---	---	---
CANX	821	broad.mit.edu	37	5	179153578	179153580	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179153578_179153580delAAA	uc003mkk.2	+						CANX_uc011dgp.1_Intron|CANX_uc003mkl.2_Intron|CANX_uc011dgq.1_Intron	NM_001746	NP_001737			calnexin precursor						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein secretion	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane|melanosome	calcium ion binding|sugar binding|unfolded protein binding				0	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
SQSTM1	8878	broad.mit.edu	37	5	179255819	179255820	+	Intron	INS	-	A	A	rs151117985	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179255819_179255820insA	uc003mkw.3	+						SQSTM1_uc011dgr.1_Intron|SQSTM1_uc011dgs.1_Intron|SQSTM1_uc003mkv.3_Intron|SQSTM1_uc003mkx.2_Intron	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	179292028	179292031	+	Intron	DEL	CACT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179292028_179292031delCACT	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)															---	---	---	---
CNOT6	57472	broad.mit.edu	37	5	179980217	179980217	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179980217delT	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)														---	---	---	---
CNOT6	57472	broad.mit.edu	37	5	179999716	179999716	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179999716delT	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)														---	---	---	---
BTNL8	79908	broad.mit.edu	37	5	180365545	180365546	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180365545_180365546delTT	uc003mmp.2	+						BTNL8_uc003mmq.2_Intron|BTNL8_uc011dhg.1_Intron|BTNL8_uc010jll.2_Intron|BTNL8_uc010jlm.2_Intron|BTNL8_uc011dhh.1_Intron	NM_001040462	NP_001035552			butyrophilin-like 8 isoform 2 precursor							integral to membrane				upper_aerodigestive_tract(1)|skin(1)	2	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
DUSP22	56940	broad.mit.edu	37	6	346429	346430	+	Intron	INS	-	AC	AC	rs145451781	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:346429_346430insAC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	360710	360710	+	IGR	DEL	A	-	-	rs66515407		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:360710delA								DUSP22 (9357 upstream) : IRF4 (31042 downstream)																																			---	---	---	---
EXOC2	55770	broad.mit.edu	37	6	637878	637878	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:637878delA	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	1232082	1232082	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1232082delA								LOC285768 (130515 upstream) : FOXQ1 (80593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	1248491	1248491	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1248491delA								LOC285768 (146924 upstream) : FOXQ1 (64184 downstream)																																			---	---	---	---
FOXF2	2295	broad.mit.edu	37	6	1395438	1395439	+	3'UTR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1395438_1395439delTG	uc003mtm.2	+	2					FOXF2_uc003mtn.2_3'UTR	NM_001452	NP_001443			forkhead box F2						epithelial to mesenchymal transition|genitalia development|palate development|pattern specification process|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding				0	Ovarian(93;0.0733)	all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.095)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	2517319	2517321	+	IGR	DEL	AGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2517319_2517321delAGG								GMDS (271473 upstream) : C6orf195 (105651 downstream)																																			---	---	---	---
MYLK4	340156	broad.mit.edu	37	6	2728652	2728654	+	Intron	DEL	AAC	-	-	rs2326027	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2728652_2728654delAAC	uc003mty.3	-							NM_001012418	NP_001012418			myosin light chain kinase family, member 4								ATP binding|protein serine/threonine kinase activity			breast(3)|ovary(1)	4	Ovarian(93;0.0412)	all_hematologic(90;0.0897)																---	---	---	---
RIPK1	8737	broad.mit.edu	37	6	3079323	3079323	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3079323delT	uc010jni.2	+						RIPK1_uc003muv.3_Intron|RIPK1_uc003muw.3_Intron|RIPK1_uc011dhs.1_Intron|RIPK1_uc003mux.2_Intron	NM_003804	NP_003795			receptor (TNFRSF)-interacting serine-threonine						activation of caspase activity|activation of JUN kinase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of necroptosis by extracellular signals|innate immune response|MyD88-independent toll-like receptor signaling pathway|positive regulation of anti-apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of reactive oxygen species metabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|protein autophosphorylation|regulation of ATP:ADP antiporter activity|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|death-inducing signaling complex|endosome membrane|mitochondrion|receptor complex	ATP binding|death domain binding|death receptor binding|protein serine/threonine kinase activity			large_intestine(3)|lung(1)|skin(1)	5	Ovarian(93;0.0386)	all_hematologic(90;0.0895)																---	---	---	---
SLC22A23	63027	broad.mit.edu	37	6	3458774	3458774	+	5'Flank	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3458774delG	uc003mvm.3	-						SLC22A23_uc010jnn.2_5'Flank|SLC22A23_uc010jno.2_5'Flank|uc003mvs.1_Intron	NM_015482	NP_056297			solute carrier family 22, member 23 isoform a						ion transport	integral to membrane	transmembrane transporter activity			ovary(1)	1	Ovarian(93;0.0493)	all_hematologic(90;0.0905)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	3944660	3944660	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3944660delT								FAM50B (93110 upstream) : PRPF4B (76909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4195398	4195398	+	IGR	DEL	A	-	-	rs71540811		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4195398delA								PECI (59567 upstream) : CDYL (510995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4414615	4414615	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4414615delA								PECI (278784 upstream) : CDYL (291778 downstream)																																			---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5606728	5606729	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5606728_5606729insA	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558			phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)													---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5640373	5640374	+	Intron	DEL	GT	-	-	rs71540875		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5640373_5640374delGT	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558			phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	5990013	5990016	+	IGR	DEL	TTTT	-	-	rs77842861		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5990013_5990016delTTTT								FARS2 (218197 upstream) : NRN1 (8219 downstream)																																			---	---	---	---
F13A1	2162	broad.mit.edu	37	6	6152285	6152285	+	Intron	DEL	T	-	-	rs76049652	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6152285delT	uc003mwv.2	-						F13A1_uc011dib.1_Intron	NM_000129	NP_000120			coagulation factor XIII A1 subunit precursor						peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)													---	---	---	---
RREB1	6239	broad.mit.edu	37	6	7148776	7148776	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7148776delG	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	7150229	7150232	+	Intron	DEL	TTTT	-	-	rs71770871		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7150229_7150232delTTTT	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	7247181	7247181	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7247181delC	uc003mxc.2	+	11	4723	c.4333delC	c.(4333-4335)CCCfs	p.P1445fs	RREB1_uc003mxb.2_Frame_Shift_Del_p.P1500fs|RREB1_uc010jnx.2_Intron	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	1445					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	7295544	7295544	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7295544delT	uc003mxf.3	-						SSR1_uc003mxg.3_Intron|SSR1_uc010jny.2_Intron	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)																	---	---	---	---
SSR1	6745	broad.mit.edu	37	6	7310340	7310340	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7310340delA	uc003mxf.3	-						SSR1_uc003mxg.3_Intron|SSR1_uc010jny.2_Intron	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	7506850	7506850	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7506850delA								RIOK1 (88582 upstream) : DSP (35020 downstream)																																			---	---	---	---
DSP	1832	broad.mit.edu	37	6	7582771	7582771	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7582771delT	uc003mxp.1	+						DSP_uc003mxq.1_Intron	NM_004415	NP_004406			desmoplakin isoform I						cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	8178166	8178166	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8178166delC								EEF1E1 (75338 upstream) : SLC35B3 (233567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	8342836	8342837	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8342836_8342837insA								EEF1E1 (240008 upstream) : SLC35B3 (68896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9014817	9014817	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9014817delA								HULC (360740 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9398512	9398513	+	IGR	DEL	TT	-	-	rs33949740		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9398512_9398513delTT								HULC (744435 upstream) : TFAP2A (998404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9439930	9439930	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9439930delA								HULC (785853 upstream) : TFAP2A (956987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9498974	9498975	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9498974_9498975insA								HULC (844897 upstream) : TFAP2A (897942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9910190	9910191	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9910190_9910191insA	uc003myg.1	-						uc010jog.1_Intron|uc003myh.1_Intron|uc003myi.2_5'Flank|uc003myj.1_Intron|uc003myk.1_Intron|uc003myn.2_Intron|uc010joi.1_Intron|uc010joh.1_Intron|uc011dif.1_Intron|uc011dig.1_Intron					Homo sapiens clone 958LR MRDS1 protein (MRDS1) mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	9933333	9933333	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9933333delA	uc003myg.1	-						uc010jog.1_Intron|uc003myh.1_Intron|uc003myj.1_Intron|uc003myk.1_Intron|uc003myn.2_Intron|uc010joi.1_Intron|uc010joh.1_Intron|uc011dif.1_Intron|uc011dig.1_Intron					Homo sapiens clone 958LR MRDS1 protein (MRDS1) mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	10253647	10253647	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10253647delT								None (None upstream) : TFAP2A (143270 downstream)																																			---	---	---	---
PAK1IP1	55003	broad.mit.edu	37	6	10697841	10697841	+	Intron	DEL	A	-	-	rs75540392	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10697841delA	uc003mzg.2	+						C6orf52_uc011dil.1_5'Flank	NM_017906	NP_060376			PAK1 interacting protein 1						negative regulation of signal transduction	nucleolus|plasma membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.117)																---	---	---	---
PAK1IP1	55003	broad.mit.edu	37	6	10698124	10698127	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10698124_10698127delAAAA	uc003mzg.2	+							NM_017906	NP_060376			PAK1 interacting protein 1						negative regulation of signal transduction	nucleolus|plasma membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.117)																---	---	---	---
TMEM14C	51522	broad.mit.edu	37	6	10731012	10731012	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10731012delA	uc003mzh.2	+	6					TMEM14C_uc003mzi.2_3'UTR	NM_016462	NP_057546			transmembrane protein 14C						heme biosynthetic process	integral to membrane|mitochondrial membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)	Epithelial(50;0.246)															---	---	---	---
SYCP2L	221711	broad.mit.edu	37	6	10942593	10942593	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10942593delT	uc003mzo.2	+						SYCP2L_uc010jow.2_Intron	NM_001040274	NP_001035364			synaptonemal complex protein 2-like							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	11396527	11396527	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11396527delT								NEDD9 (13946 upstream) : TMEM170B (141984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	11786244	11786245	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11786244_11786245insG								C6orf105 (6964 upstream) : HIVEP1 (226479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	11826343	11826343	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11826343delG								C6orf105 (47063 upstream) : HIVEP1 (186381 downstream)																																			---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12011157	12011157	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12011157delC	uc003nac.2	+							NM_002114	NP_002105			human immunodeficiency virus type I enhancer						transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)																---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12164716	12164716	+	3'UTR	DEL	T	-	-	rs76772048		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12164716delT	uc003nac.2	+	9					HIVEP1_uc011diq.1_RNA	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	12210336	12210336	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12210336delA								HIVEP1 (45105 upstream) : EDN1 (80193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	12457354	12457355	+	IGR	INS	-	CA	CA	rs117549843	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12457354_12457355insCA								EDN1 (159928 upstream) : PHACTR1 (259533 downstream)																																			---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	12718911	12718911	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12718911delT	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron|PHACTR1_uc003nai.2_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	12866754	12866755	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12866754_12866755delTT	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron|PHACTR1_uc003nai.2_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	13017491	13017491	+	Intron	DEL	T	-	-	rs74950713		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13017491delT	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	13192488	13192488	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13192488delA	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	13206420	13206420	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13206420delG	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	13286469	13286469	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13286469delT	uc010jpc.2	+						PHACTR1_uc003nah.1_Intron|TBC1D7_uc003naj.2_Intron|TBC1D7_uc011dis.1_Intron|uc003nak.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)															---	---	---	---
TBC1D7	51256	broad.mit.edu	37	6	13313788	13313789	+	Intron	INS	-	AGGT	AGGT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13313788_13313789insAGGT	uc003naj.2	-						TBC1D7_uc011dis.1_Intron|TBC1D7_uc003nan.2_Intron|TBC1D7_uc003nal.2_Intron|TBC1D7_uc003nam.2_Intron|TBC1D7_uc003nao.2_Intron|TBC1D7_uc010jpd.2_Intron|TBC1D7_uc003nap.2_Intron	NM_016495	NP_057579			TBC1 domain family, member 7 isoform a						positive regulation of protein ubiquitination	cytoplasmic membrane-bounded vesicle	protein binding|Rab GTPase activator activity			ovary(1)	1	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)															---	---	---	---
NOL7	51406	broad.mit.edu	37	6	13620991	13620992	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13620991_13620992insA	uc003naz.2	+	8	738_739	c.706_707insA	c.(706-708)CAAfs	p.Q236fs		NM_016167	NP_057251	Q9UMY1	NOL7_HUMAN	nucleolar protein 7, 27kDa	236						mitochondrion|nucleolus					0	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.135)	Epithelial(50;0.176)															---	---	---	---
RANBP9	10048	broad.mit.edu	37	6	13704870	13704871	+	Intron	DEL	AA	-	-	rs79478304		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13704870_13704871delAA	uc003nbb.2	-							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	13742076	13742076	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13742076delT								RANBP9 (30280 upstream) : CCDC90A (48945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	13755849	13755850	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13755849_13755850insC								RANBP9 (44053 upstream) : CCDC90A (35171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	13982337	13982337	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13982337delT								RNF182 (2104 upstream) : CD83 (135528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14171491	14171491	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14171491delA								CD83 (34345 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14323857	14323858	+	IGR	DEL	CA	-	-	rs34776080		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14323857_14323858delCA								CD83 (186711 upstream) : JARID2 (921876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14539432	14539432	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14539432delA								CD83 (402286 upstream) : JARID2 (706302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15201155	15201155	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15201155delA								None (None upstream) : JARID2 (44579 downstream)																																			---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15316244	15316244	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15316244delT	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	15428116	15428116	+	Intron	DEL	T	-	-	rs71535041		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15428116delT	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)																---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15496722	15496722	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15496722delG	uc003nbj.2	+	7	1510	c.1266delG	c.(1264-1266)GTGfs	p.V422fs	JARID2_uc011diu.1_Frame_Shift_Del_p.V286fs|JARID2_uc011div.1_Frame_Shift_Del_p.V250fs|JARID2_uc011diw.1_Frame_Shift_Del_p.V384fs	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	422					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)																---	---	---	---
DTNBP1	84062	broad.mit.edu	37	6	15638038	15638038	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15638038delA	uc003nbm.2	-						DTNBP1_uc003nbl.2_Intron|DTNBP1_uc003nbn.2_Intron|DTNBP1_uc003nbo.2_Intron|DTNBP1_uc003nbp.2_Intron|DTNBP1_uc010jph.2_Intron	NM_032122	NP_115498			dystrobrevin binding protein 1 isoform a						actin cytoskeleton reorganization|cellular membrane organization|neuron projection morphogenesis|post-Golgi vesicle-mediated transport|regulation of dopamine receptor signaling pathway	axon part|BLOC-1 complex|cell junction|dendritic spine|endoplasmic reticulum membrane|endosome membrane|growth cone|melanosome membrane|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|synaptic vesicle membrane|synaptosome	identical protein binding				0	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)											Hermansky-Pudlak_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	6	15880250	15880250	+	IGR	DEL	C	-	-	rs71554547		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15880250delC								DTNBP1 (216979 upstream) : MYLIP (249067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15916823	15916825	+	IGR	DEL	AGG	-	-	rs151327040		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15916823_15916825delAGG								DTNBP1 (253552 upstream) : MYLIP (212492 downstream)																																			---	---	---	---
MYLIP	29116	broad.mit.edu	37	6	16141709	16141709	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16141709delT	uc003nbq.2	+						MYLIP_uc003nbr.2_Intron	NM_013262	NP_037394			myosin regulatory light chain interacting						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)															---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16426510	16426510	+	Intron	DEL	G	-	-	rs5874555		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16426510delG	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron	NM_000332	NP_000323			ataxin 1						cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)																---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16731623	16731623	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16731623delA	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	18351712	18351712	+	IGR	DEL	T	-	-	rs113709604		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18351712delT								DEK (86913 upstream) : RNF144B (35882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	18538844	18538844	+	Intron	DEL	T	-	-	rs33915893		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18538844delT	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	18545294	18545295	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18545294_18545295insT	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	19095613	19095613	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19095613delA	uc003ncu.1	-											Homo sapiens cDNA FLJ40266 fis, clone TESTI2026461.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	19198515	19198515	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19198515delA								MIR548A1 (626404 upstream) : ID4 (639102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19295794	19295794	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19295794delT								MIR548A1 (723683 upstream) : ID4 (541823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19534135	19534135	+	IGR	DEL	T	-	-	rs35445709		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19534135delT								MIR548A1 (962024 upstream) : ID4 (303482 downstream)																																			---	---	---	---
MBOAT1	154141	broad.mit.edu	37	6	20186247	20186248	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20186247_20186248insA	uc003ncx.1	-						MBOAT1_uc011dji.1_Intron	NM_001080480	NP_001073949			membrane bound O-acyltransferase domain						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	21299448	21299449	+	IGR	INS	-	TTCT	TTCT	rs142485305	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21299448_21299449insTTCT								CDKAL1 (66816 upstream) : SOX4 (294523 downstream)																																			---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	21701030	21701031	+	Intron	DEL	TT	-	-	rs75650629		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21701030_21701031delTT	uc010jpp.1	+						FLJ22536_uc003ndj.2_Intron|FLJ22536_uc011djk.1_Intron|FLJ22536_uc011djj.1_Intron					Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	23376080	23376080	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23376080delT								HDGFL1 (805331 upstream) : NRSN1 (750334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23693543	23693545	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23693543_23693545delTTT								None (None upstream) : NRSN1 (432869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23950020	23950020	+	IGR	DEL	A	-	-	rs34937220		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23950020delA								None (None upstream) : NRSN1 (176394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	24075683	24075683	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24075683delT								None (None upstream) : NRSN1 (50731 downstream)																																			---	---	---	---
MRS2	57380	broad.mit.edu	37	6	24424667	24424668	+	3'UTR	INS	-	CCCTG	CCCTG	rs142810123	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24424667_24424668insCCCTG	uc003neb.2	+	11					MRS2_uc011djl.1_3'UTR|MRS2_uc011djm.1_RNA|MRS2_uc011djn.1_3'UTR|MRS2_uc003nec.2_3'UTR	NM_020662	NP_065713			MRS2-like, magnesium homeostasis factor						ion transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
KIAA0319	9856	broad.mit.edu	37	6	24565481	24565481	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24565481delA	uc011djo.1	-						KIAA0319_uc011djp.1_Intron|KIAA0319_uc003neh.1_Intron|KIAA0319_uc011djq.1_Intron|KIAA0319_uc011djr.1_Intron|KIAA0319_uc010jpt.1_Intron	NM_014809	NP_055624			KIAA0319 precursor						negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
KIAA0319	9856	broad.mit.edu	37	6	24576991	24576992	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24576991_24576992delAA	uc011djo.1	-						KIAA0319_uc011djp.1_Intron|KIAA0319_uc003neh.1_Intron|KIAA0319_uc011djq.1_Intron|KIAA0319_uc011djr.1_Intron|KIAA0319_uc010jpt.1_Intron	NM_014809	NP_055624			KIAA0319 precursor						negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
KIAA0319	9856	broad.mit.edu	37	6	24596507	24596508	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24596507_24596508insC	uc011djo.1	-	3	631_632	c.394_395insG	c.(394-396)GACfs	p.D132fs	KIAA0319_uc011djp.1_Frame_Shift_Ins_p.D87fs|KIAA0319_uc003neh.1_Frame_Shift_Ins_p.D132fs|KIAA0319_uc011djq.1_Frame_Shift_Ins_p.D123fs|KIAA0319_uc011djr.1_Frame_Shift_Ins_p.D132fs	NM_014809	NP_055624	Q5VV43	K0319_HUMAN	KIAA0319 precursor	132	Extracellular (Potential).				negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
FAM65B	9750	broad.mit.edu	37	6	24833726	24833727	+	Intron	INS	-	A	A	rs145511348	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24833726_24833727insA	uc003neo.1	-						FAM65B_uc011djs.1_Intron	NM_014722	NP_055537			hypothetical protein LOC9750 isoform 1						cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1																		---	---	---	---
SCGN	10590	broad.mit.edu	37	6	25666584	25666584	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25666584delA	uc003nfb.2	+						SCGN_uc010jpz.2_Intron	NM_006998	NP_008929			secretagogin precursor							extracellular region|transport vesicle membrane	calcium ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
SLC17A4	10050	broad.mit.edu	37	6	25769786	25769787	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25769786_25769787delAA	uc003nfe.2	+						SLC17A4_uc011djx.1_Intron|SLC17A4_uc003nff.1_Intron|SLC17A4_uc003nfg.2_Intron	NM_005495	NP_005486			solute carrier family 17 (sodium phosphate),						phosphate metabolic process	integral to plasma membrane|membrane fraction	sodium:phosphate symporter activity			skin(1)	1																		---	---	---	---
HFE	3077	broad.mit.edu	37	6	26090509	26090509	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26090509delA	uc003nfx.1	+						HFE_uc003nfy.1_Intron|HFE_uc010jqe.1_Intron|HFE_uc003nfz.1_Intron|HFE_uc003ngd.1_Intron|HFE_uc003nga.1_Intron|HFE_uc003ngb.1_Intron|HFE_uc003ngc.1_Intron|HFE_uc003nge.1_Intron|HFE_uc003ngf.1_Intron	NM_000410	NP_000401			hemochromatosis protein isoform 1 precursor						antigen processing and presentation of peptide antigen via MHC class I|cellular iron ion homeostasis|immune response|iron ion transport|protein complex assembly|receptor-mediated endocytosis	apical part of cell|basal part of cell|cytoplasmic vesicle|early endosome|integral to plasma membrane|MHC class I protein complex|perinuclear region of cytoplasm|recycling endosome	protein binding				0														Hemochromatosis				---	---	---	---
Unknown	0	broad.mit.edu	37	6	26213271	26213274	+	IGR	DEL	TGTG	-	-	rs35127949		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26213271_26213274delTGTG								HIST1H4E (8023 upstream) : HIST1H2BG (3154 downstream)																																			---	---	---	---
BTN3A2	11118	broad.mit.edu	37	6	26371914	26371914	+	Intron	DEL	T	-	-	rs79766812		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26371914delT	uc010jqh.1	+						BTN3A2_uc003nho.1_Intron|BTN3A2_uc003nhp.2_Intron|BTN3A2_uc011dkd.1_Intron|BTN3A2_uc011dke.1_Intron|BTN3A2_uc010jqi.1_Intron	NM_007047	NP_008978			butyrophilin, subfamily 3, member A2 precursor							integral to membrane					0																		---	---	---	---
BTN3A1	11119	broad.mit.edu	37	6	26410420	26410422	+	Intron	DEL	AAA	-	-	rs75190190		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26410420_26410422delAAA	uc003nhv.2	+						BTN3A1_uc011dkj.1_Intron|BTN3A1_uc011dkk.1_Intron|BTN3A1_uc010jqj.2_Intron	NM_007048	NP_008979			butyrophilin, subfamily 3, member A1 isoform a						lipid metabolic process	integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	26577961	26577961	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26577961delT								HMGN4 (30799 upstream) : ABT1 (19219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	26757934	26757934	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26757934delA								ZNF322A (97971 upstream) : GUSBL1 (81332 downstream)																																			---	---	---	---
HIST1H2BJ	8970	broad.mit.edu	37	6	27099962	27099962	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27099962delA	uc003niu.1	-						HIST1H2AG_uc003niw.2_5'Flank					Homo sapiens histone cluster 1, H2bj, mRNA (cDNA clone IMAGE:4048288), with apparent retained intron.						defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	27258164	27258164	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27258164delA								PRSS16 (33915 upstream) : POM121L2 (18678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27611582	27611583	+	IGR	DEL	AA	-	-	rs77540651		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27611582_27611583delAA								ZNF184 (170685 upstream) : HIST1H2BL (163675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27933333	27933334	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27933333_27933334delGT								OR2B6 (7375 upstream) : ZNF165 (113238 downstream)																																			---	---	---	---
ZNF192	7745	broad.mit.edu	37	6	28120627	28120627	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28120627delT	uc003nkn.1	+						ZNF192_uc010jqx.1_Intron|ZNF192_uc010jqy.1_Intron|ZNF192_uc011dkz.1_Intron	NM_006298	NP_006289			zinc finger protein 192						viral reproduction	cytoplasm|nucleolus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
ZKSCAN3	80317	broad.mit.edu	37	6	28327932	28327932	+	Intron	DEL	T	-	-	rs113424723		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28327932delT	uc003nle.3	+						ZKSCAN3_uc010jrc.2_Intron|ZKSCAN3_uc003nlf.3_Intron	NM_024493	NP_077819			zinc finger with KRAB and SCAN domains 3						positive regulation of transcription, DNA-dependent|viral reproduction	nucleus	chromatin binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	28529774	28529775	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28529774_28529775insA								GPX5 (27046 upstream) : SCAND3 (9633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	28675316	28675321	+	IGR	DEL	AAAAAA	-	-	rs143414094		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28675316_28675321delAAAAAA								SCAND3 (120204 upstream) : TRIM27 (195459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	29225072	29225072	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29225072delA								OR2J2 (82722 upstream) : OR14J1 (49395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	29440908	29440908	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29440908delA								OR2H1 (8811 upstream) : MAS1L (13637 downstream)																																			---	---	---	---
HLA-F	3134	broad.mit.edu	37	6	29688761	29688762	+	5'Flank	DEL	TT	-	-	rs34999981		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29688761_29688762delTT	uc010jrl.2	+						HLA-F_uc003nnm.3_5'Flank|HLA-F_uc003nno.3_5'Flank|HLA-F_uc011dlx.1_5'Flank|HLA-F_uc011dly.1_5'Flank	NM_018950	NP_061823			major histocompatibility complex, class I, F						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-G	3135	broad.mit.edu	37	6	29822780	29822783	+	Intron	DEL	AAAC	-	-	rs72457660		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29822780_29822783delAAAC	uc011dmb.1	+							NM_002127	NP_002118			major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|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			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
NCRNA00171	80862	broad.mit.edu	37	6	29983493	29983493	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29983493delA	uc011dme.1	-						uc011dmf.1_5'Flank	NR_026751				Homo sapiens clone HTEX4 mRNA, complete sequence.												0																		---	---	---	---
TRIM10	10107	broad.mit.edu	37	6	30124272	30124275	+	Intron	DEL	AGAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30124272_30124275delAGAA	uc003npo.3	-						TRIM10_uc003npn.2_Intron	NM_006778	NP_006769			tripartite motif-containing 10 isoform 1							cytoplasm	zinc ion binding				0																		---	---	---	---
DHX16	8449	broad.mit.edu	37	6	30622326	30622327	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30622326_30622327insA	uc003nqz.2	-						DHX16_uc003nqy.2_Intron|DHX16_uc011dmo.1_Intron	NM_003587	NP_003578			DEAH (Asp-Glu-Ala-His) box polypeptide 16						mRNA processing|RNA splicing	nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(2)|kidney(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	30644133	30644133	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30644133delT								DHX16 (3303 upstream) : KIAA1949 (35 downstream)																																			---	---	---	---
MDC1	9656	broad.mit.edu	37	6	30675170	30675172	+	In_Frame_Del	DEL	CTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30675170_30675172delCTT	uc003nrg.3	-	9	3513_3515	c.3073_3075delAAG	c.(3073-3075)AAGdel	p.K1025del	MDC1_uc003nrf.3_In_Frame_Del_p.K415del|MDC1_uc011dmp.1_In_Frame_Del_p.K632del	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1025				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					---	---	---	---
FLOT1	10211	broad.mit.edu	37	6	30698108	30698108	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30698108delC	uc003nrm.2	-						FLOT1_uc011dmr.1_Intron	NM_005803	NP_005794			flotillin 1							centriolar satellite|endosome|integral to membrane|melanosome|membrane fraction					0																		---	---	---	---
FLOT1	10211	broad.mit.edu	37	6	30704271	30704273	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30704271_30704273delAAA	uc003nrm.2	-						FLOT1_uc011dmr.1_Intron	NM_005803	NP_005794			flotillin 1							centriolar satellite|endosome|integral to membrane|melanosome|membrane fraction					0																		---	---	---	---
FLOT1	10211	broad.mit.edu	37	6	30707445	30707445	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30707445delT	uc003nrm.2	-						FLOT1_uc011dmr.1_Intron	NM_005803	NP_005794			flotillin 1							centriolar satellite|endosome|integral to membrane|melanosome|membrane fraction					0																		---	---	---	---
GTF2H4	2968	broad.mit.edu	37	6	30879960	30879960	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30879960delG	uc003nsa.1	+						GTF2H4_uc003nsb.1_Intron|GTF2H4_uc011dmw.1_Intron|VARS2_uc003nsc.1_5'Flank|VARS2_uc003nsd.2_5'Flank|VARS2_uc011dmx.1_5'Flank|VARS2_uc011dmy.1_5'Flank|VARS2_uc011dmz.1_5'Flank|VARS2_uc011dna.1_5'Flank|VARS2_uc011dnb.1_5'Flank|VARS2_uc011dnc.1_5'Flank	NM_001517	NP_001508			general transcription factor IIH, polypeptide 4,						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	holo TFIIH complex	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|breast(1)	3													NER					---	---	---	---
Unknown	0	broad.mit.edu	37	6	31535445	31535462	+	IGR	DEL	ACACACACACGCACGCAT	-	-	rs28993445	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31535445_31535462delACACACACACGCACGCAT								NFKBIL1 (7768 upstream) : LTA (4414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	31572031	31572032	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31572031_31572032delTT								NCR3 (11269 upstream) : AIF1 (10962 downstream)																																			---	---	---	---
MSH5	4439	broad.mit.edu	37	6	31721511	31721513	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31721511_31721513delTTT	uc003nwv.1	+						MSH5_uc003nwt.1_Intron|MSH5_uc003nwu.1_Intron|MSH5_uc003nww.1_Intron|MSH5_uc003nwx.1_Intron|MSH5_uc011dof.1_Intron|MSH5_uc003nwy.1_5'Flank	NM_172166	NP_751898			mutS homolog 5 isoform c						chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			ovary(2)|breast(1)	3													Direct_reversal_of_damage|MMR					---	---	---	---
STK19	8859	broad.mit.edu	37	6	31943380	31943382	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31943380_31943382delTTT	uc003nyv.2	+						STK19_uc003nyt.2_Intron|STK19_uc011dox.1_Intron|STK19_uc003nyw.2_Intron|STK19_uc010jtn.1_Intron	NM_032454	NP_115830			serine/threonine kinase 19 isoform 2							nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			skin(4)	4																		---	---	---	---
ATF6B	1388	broad.mit.edu	37	6	32096442	32096442	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32096442delC	uc003nzn.2	-						ATF6B_uc003nzo.2_5'Flank|ATF6B_uc011dpg.1_5'Flank|ATF6B_uc011dph.1_5'Flank	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																		---	---	---	---
PPT2	9374	broad.mit.edu	37	6	32123888	32123888	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32123888delT	uc003nzx.2	+						uc003nzv.3_5'Flank|PPT2_uc003nzw.2_Intron|PPT2_uc011dpi.1_Intron|PPT2_uc003nzy.1_Intron|PPT2_uc003nzz.2_Intron|PPT2_uc003oaa.2_Intron|PPT2_uc010jtu.1_Intron	NM_005155	NP_005146			palmitoyl-protein thioesterase 2 isoform a						protein modification process	lysosome	palmitoyl-(protein) hydrolase activity				0																		---	---	---	---
NOTCH4	4855	broad.mit.edu	37	6	32183605	32183606	+	Intron	INS	-	TCCT	TCCT	rs144795436	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32183605_32183606insTCCT	uc003obb.2	-						NOTCH4_uc011dpu.1_Intron|NOTCH4_uc011dpv.1_Intron	NM_004557	NP_004548			notch4 preproprotein						cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|protein heterodimerization activity|receptor activity			lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1)	22																		---	---	---	---
C6orf10	10665	broad.mit.edu	37	6	32292392	32292393	+	Intron	INS	-	AACT	AACT	rs149639436	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32292392_32292393insAACT	uc011dpy.1	-							NM_006781	NP_006772			chromosome 6 open reading frame 10							integral to membrane				skin(1)	1																		---	---	---	---
HLA-DRB5	3127	broad.mit.edu	37	6	32512212	32512221	+	Intron	DEL	TATCGACGGG	-	-	rs148460181		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32512212_32512221delTATCGACGGG	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-DQB1	3119	broad.mit.edu	37	6	32636661	32636662	+	5'Flank	INS	-	CTT	CTT	rs143254119	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32636661_32636662insCTT	uc003obw.2	-						HLA-DQB1_uc003obv.2_5'Flank|HLA-DQB1_uc011dqd.1_5'Flank|HLA-DQB1_uc011dqe.1_5'Flank	NM_002123	NP_002114			major histocompatibility complex, class II, DQ						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)									Melanoma_Familial_Clustering_of|ACTH-independent_macronodular_adrenal_hyperplasia|T-cell_Lymphoma_(Cutaneous)__Familial_Clustering_of|Sj_gren_syndrome				---	---	---	---
SYNGAP1	8831	broad.mit.edu	37	6	33397578	33397579	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33397578_33397579delTG	uc011dri.1	+						SYNGAP1_uc003oeo.1_Intron|SYNGAP1_uc010juy.2_Intron	NM_006772	NP_006763			synaptic Ras GTPase activating protein 1						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity|SH3 domain binding			ovary(4)	4																		---	---	---	---
C6orf125	84300	broad.mit.edu	37	6	33677544	33677544	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33677544delA	uc003ofa.1	-						C6orf125_uc010jve.1_Intron	NM_032340	NP_115716			hypothetical protein LOC84300												0																		---	---	---	---
GRM4	2914	broad.mit.edu	37	6	34064692	34064693	+	Intron	INS	-	GTGT	GTGT	rs138509258	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34064692_34064693insGTGT	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)													---	---	---	---
ANKS1A	23294	broad.mit.edu	37	6	34949950	34949950	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34949950delT	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																		---	---	---	---
TCP11	6954	broad.mit.edu	37	6	35108447	35108447	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35108447delG	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																		---	---	---	---
SCUBE3	222663	broad.mit.edu	37	6	35216592	35216592	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35216592delA	uc003okf.1	+	22					SCUBE3_uc003okg.1_3'UTR|SCUBE3_uc003okh.1_3'UTR	NM_152753	NP_689966			signal peptide, CUB domain, EGF-like 3						protein heterooligomerization|protein homooligomerization	cell surface|extracellular region	calcium ion binding|protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	35292910	35292910	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35292910delT								DEF6 (3364 upstream) : PPARD (17425 downstream)																																			---	---	---	---
FANCE	2178	broad.mit.edu	37	6	35424297	35424297	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35424297delT	uc003oko.1	+						FANCE_uc010jvw.1_Intron	NM_021922	NP_068741			Fanconi anemia, complementation group E						DNA repair	nucleoplasm	protein binding			ovary(1)|lung(1)|skin(1)	3								N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
TEAD3	7005	broad.mit.edu	37	6	35442747	35442747	+	3'UTR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35442747delC	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	35554625	35554625	+	Intron	DEL	T	-	-	rs112376611		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35554625delT	uc011dte.1	-						FKBP5_uc003okx.2_Intron|FKBP5_uc011dtf.1_Intron|FKBP5_uc003oky.2_Intron|FKBP5_uc003okz.2_3'UTR	NM_001145776	NP_001139248			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																		---	---	---	---
SRPK1	6732	broad.mit.edu	37	6	35814991	35814991	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35814991delT	uc003olj.2	-						SRPK1_uc011dtg.1_Intron|SRPK1_uc003olh.2_Intron|SRPK1_uc003oli.2_Intron	NM_003137	NP_003128			SFRS protein kinase 1						cell differentiation|chromosome segregation|interspecies interaction between organisms|intracellular protein kinase cascade|mRNA processing|negative regulation of viral genome replication|positive regulation of viral genome replication|regulation of mRNA processing|RNA splicing	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
SRPK1	6732	broad.mit.edu	37	6	35825026	35825026	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35825026delA	uc003olj.2	-						SRPK1_uc011dtg.1_Intron|SRPK1_uc003olh.2_Intron|SRPK1_uc003oli.2_Intron	NM_003137	NP_003128			SFRS protein kinase 1						cell differentiation|chromosome segregation|interspecies interaction between organisms|intracellular protein kinase cascade|mRNA processing|negative regulation of viral genome replication|positive regulation of viral genome replication|regulation of mRNA processing|RNA splicing	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
MAPK14	1432	broad.mit.edu	37	6	36058108	36058108	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36058108delT	uc003olp.2	+						MAPK14_uc011dth.1_Intron|MAPK14_uc003olo.2_Intron|MAPK14_uc003olq.2_Intron|MAPK14_uc003olr.2_Intron|MAPK14_uc011dti.1_Intron	NM_001315	NP_001306			mitogen-activated protein kinase 14 isoform 1						activation of MAPK activity|cellular component movement|cellular response to ionizing radiation|chemotaxis|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|platelet activation|positive regulation of muscle cell differentiation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|signal transduction in response to DNA damage|stress-activated MAPK cascade|stress-induced premature senescence|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|MAP kinase kinase activity|protein binding			ovary(2)|stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
STK38	11329	broad.mit.edu	37	6	36495886	36495887	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36495886_36495887delAA	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	36686689	36686689	+	IGR	DEL	T	-	-	rs34442767		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36686689delT								CDKN1A (31581 upstream) : CPNE5 (21866 downstream)																																			---	---	---	---
CPNE5	57699	broad.mit.edu	37	6	36751300	36751301	+	Intron	DEL	TC	-	-	rs35764239		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36751300_36751301delTC	uc003omr.1	-						CPNE5_uc003oms.1_Intron	NM_020939	NP_065990			copine V											skin(1)	1																		---	---	---	---
TBC1D22B	55633	broad.mit.edu	37	6	37243114	37243114	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37243114delT	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	37308655	37308657	+	IGR	DEL	CTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37308655_37308657delCTG								TBC1D22B (7910 upstream) : RNF8 (13091 downstream)																																			---	---	---	---
RNF8	9025	broad.mit.edu	37	6	37321123	37321128	+	5'Flank	DEL	TTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37321123_37321128delTTTTTT	uc003onq.3	+						RNF8_uc003onr.3_5'Flank|RNF8_uc011dtx.1_5'Flank	NM_003958	NP_003949			ring finger protein 8 isoform 1						cell division|double-strand break repair|histone H2A ubiquitination|histone H2B ubiquitination|mitosis|positive regulation of DNA repair|response to ionizing radiation	midbody|nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	37566582	37566583	+	IGR	INS	-	T	T	rs142910672		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37566582_37566583insT								C6orf129 (98882 upstream) : MDGA1 (33701 downstream)																																			---	---	---	---
MDGA1	266727	broad.mit.edu	37	6	37617647	37617647	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37617647delT	uc003onu.1	-						MDGA1_uc003onv.1_5'Flank	NM_153487	NP_705691			MAM domain containing						brain development|neuron migration|spinal cord association neuron differentiation	anchored to plasma membrane				central_nervous_system(2)	2																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38813268	38813268	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38813268delA	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																		---	---	---	---
KIF6	221458	broad.mit.edu	37	6	39446726	39446727	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39446726_39446727insT	uc003oot.2	-						KIF6_uc010jwz.1_Intron|KIF6_uc010jxa.1_Intron|KIF6_uc011dua.1_Intron|KIF6_uc010jxb.1_Intron	NM_145027	NP_659464			kinesin family member 6						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
KIF6	221458	broad.mit.edu	37	6	39475414	39475415	+	Intron	INS	-	CCTTCCTT	CCTTCCTT	rs62402254		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39475414_39475415insCCTTCCTT	uc003oot.2	-						KIF6_uc010jwz.1_Intron|KIF6_uc010jxa.1_Intron|KIF6_uc011dua.1_Intron|KIF6_uc010jxb.1_Intron	NM_145027	NP_659464			kinesin family member 6						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	39960793	39960793	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39960793delT								MOCS1 (58539 upstream) : TDRG1 (385370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	39993321	39993321	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39993321delA								MOCS1 (91067 upstream) : TDRG1 (352842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40090486	40090487	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40090486_40090487insA								MOCS1 (188232 upstream) : TDRG1 (255676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40121524	40121524	+	IGR	DEL	G	-	-	rs35822270		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40121524delG								MOCS1 (219270 upstream) : TDRG1 (224639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40730604	40730604	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40730604delT								LRFN2 (175478 upstream) : UNC5CL (264168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40843694	40843694	+	IGR	DEL	G	-	-	rs140542162	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40843694delG								LRFN2 (288568 upstream) : UNC5CL (151078 downstream)																																			---	---	---	---
NFYA	4800	broad.mit.edu	37	6	41066126	41066127	+	3'UTR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41066126_41066127delAG	uc003opo.2	+	10					NFYA_uc003opp.2_3'UTR|NFYA_uc003opq.2_3'UTR|LOC221442_uc003ops.2_5'Flank	NM_002505	NP_002496			nuclear transcription factor Y, alpha isoform 1						transcription from RNA polymerase II promoter	CCAAT-binding factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	41276458	41276458	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41276458delT								TREM1 (22001 upstream) : NCR2 (27070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	41599421	41599422	+	IGR	INS	-	A	A	rs142118546	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41599421_41599422insA								FOXP4 (29300 upstream) : MDFI (5508 downstream)																																			---	---	---	---
TFEB	7942	broad.mit.edu	37	6	41694186	41694187	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41694186_41694187insT	uc003oqs.1	-						TFEB_uc003oqt.1_Intron|TFEB_uc003oqu.1_Intron|TFEB_uc003oqv.1_Intron|TFEB_uc010jxo.1_Intron|TFEB_uc003oqx.1_Intron|TFEB_uc003oqy.1_5'Flank|TFEB_uc003oqz.1_Intron|TFEB_uc010jxq.1_Intron	NM_007162	NP_009093			transcription factor EB						embryonic placenta development|humoral immune response|positive regulation of transcription from RNA polymerase II promoter	cytoplasm	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)					T	ALPHA	renal (childhood epithelioid)								---	---	---	---
PGC	5225	broad.mit.edu	37	6	41712724	41712729	+	Intron	DEL	TCTGTC	-	-	rs72336731		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41712724_41712729delTCTGTC	uc003ora.1	-							NM_002630	NP_002621			progastricsin (pepsinogen C) precursor						digestion|proteolysis	extracellular space	aspartic-type endopeptidase activity				0	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)															---	---	---	---
PGC	5225	broad.mit.edu	37	6	41712982	41712982	+	Intron	DEL	T	-	-	rs11304918		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41712982delT	uc003ora.1	-							NM_002630	NP_002621			progastricsin (pepsinogen C) precursor						digestion|proteolysis	extracellular space	aspartic-type endopeptidase activity				0	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)															---	---	---	---
CCND3	896	broad.mit.edu	37	6	41943590	41943590	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41943590delT	uc003orp.2	-						CCND3_uc011duk.1_Intron|CCND3_uc011dum.1_Intron	NM_001136017	NP_001129489			cyclin D3 isoform 1						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				0	Colorectal(47;0.121)		Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)					T	IGH@	MM								---	---	---	---
CCND3	896	broad.mit.edu	37	6	41982104	41982108	+	Intron	DEL	AAACA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41982104_41982108delAAACA	uc003orp.2	-						CCND3_uc011duk.1_Intron|CCND3_uc011dum.1_Intron	NM_001136017	NP_001129489			cyclin D3 isoform 1						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				0	Colorectal(47;0.121)		Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)					T	IGH@	MM								---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42610142	42610142	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	42696259	42696260	+	5'Flank	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42696259_42696260delAG	uc011duv.1	-											DQ588041																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	42720352	42720352	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42720352delT								TBCC (6468 upstream) : KIAA0240 (29438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	42731981	42731982	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42731981_42731982insA								TBCC (18097 upstream) : KIAA0240 (17808 downstream)																																			---	---	---	---
PTCRA	171558	broad.mit.edu	37	6	42885994	42885996	+	Intron	DEL	AAA	-	-	rs76300598		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42885994_42885996delAAA	uc003osx.2	+						PTCRA_uc011duz.1_Intron|PTCRA_uc010jxx.1_Intron|PTCRA_uc010jxy.2_Intron|PTCRA_uc010jxz.2_Intron	NM_138296	NP_612153			pre T-cell antigen receptor alpha precursor							integral to membrane	receptor activity			ovary(2)	2	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)															---	---	---	---
PPP2R5D	5528	broad.mit.edu	37	6	42953344	42953344	+	Intron	DEL	T	-	-	rs111692462		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42953344delT	uc003oth.2	+						MEA1_uc010jyc.1_Intron|PPP2R5D_uc003otg.2_Intron|PPP2R5D_uc010jyd.2_Intron|PPP2R5D_uc011dva.1_Intron|PPP2R5D_uc003oti.2_Intron	NM_006245	NP_006236			delta isoform of regulatory subunit B56, protein						nervous system development|signal transduction	cytoplasm|nucleus|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			breast(1)|central_nervous_system(1)	2			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
C6orf153	88745	broad.mit.edu	37	6	42994811	42994812	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42994811_42994812delTG	uc003otp.1	+							NM_033112	NP_149103			hypothetical protein LOC88745						ribosomal small subunit biogenesis|rRNA processing	nucleolus					0			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)															---	---	---	---
POLH	5429	broad.mit.edu	37	6	43571761	43571761	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43571761delT	uc003ovq.3	+						POLH_uc010jyu.2_Intron|POLH_uc011dvl.1_Intron|POLH_uc003ovr.3_Intron	NM_006502	NP_006493			DNA-directed DNA polymerase eta						DNA replication|DNA synthesis involved in DNA repair|regulation of DNA repair|response to UV-C	cytoplasm|nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			breast(2)	2	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)										DNA_polymerases_(catalytic_subunits)	Xeroderma_Pigmentosum				---	---	---	---
RSPH9	221421	broad.mit.edu	37	6	43616903	43616904	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43616903_43616904insT	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				---	---	---	---
RSPH9	221421	broad.mit.edu	37	6	43623774	43623782	+	Intron	DEL	CCCTTCTTT	-	-	rs70993404		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43623774_43623782delCCCTTCTTT	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				---	---	---	---
MRPL14	64928	broad.mit.edu	37	6	44093097	44093097	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44093097delA	uc003owp.2	-						TMEM63B_uc003owq.1_5'Flank|TMEM63B_uc003owr.2_5'Flank|TMEM63B_uc010jyy.1_5'Flank	NM_032111	NP_115487			mitochondrial ribosomal protein L14 precursor						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0181)															---	---	---	---
TMEM63B	55362	broad.mit.edu	37	6	44117575	44117575	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44117575delC	uc003owr.2	+						TMEM63B_uc003ows.2_Intron|TMEM63B_uc010jyz.2_Intron	NM_018426	NP_060896			transmembrane protein 63B							integral to membrane	nucleotide binding|protein binding			pancreas(2)|central_nervous_system(1)	3	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)															---	---	---	---
CDC5L	988	broad.mit.edu	37	6	44371468	44371468	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44371468delT	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)															---	---	---	---
CDC5L	988	broad.mit.edu	37	6	44398314	44398315	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44398314_44398315delTT	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)															---	---	---	---
CLIC5	53405	broad.mit.edu	37	6	46036327	46036327	+	Intron	DEL	C	-	-	rs73448525	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46036327delC	uc003oxv.3	-							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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	46469770	46469770	+	Intron	DEL	C	-	-	rs5875968		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46469770delC	uc003oye.2	+											Homo sapiens cDNA clone IMAGE:4821026.																														---	---	---	---
SLC25A27	9481	broad.mit.edu	37	6	46623926	46623926	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46623926delT	uc003oyh.2	+						SLC25A27_uc011dwb.1_Intron|SLC25A27_uc003oyg.2_Intron|SLC25A27_uc011dwc.1_Intron|SLC25A27_uc003oyi.2_5'Flank	NM_004277	NP_004268			solute carrier family 25, member 27						generation of precursor metabolites and energy|transport	integral to membrane|mitochondrial inner membrane					0			Lung(136;0.192)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	47402638	47402638	+	IGR	DEL	T	-	-	rs112266031		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47402638delT								TNFRSF21 (124958 upstream) : CD2AP (42887 downstream)																																			---	---	---	---
CD2AP	23607	broad.mit.edu	37	6	47446461	47446461	+	Intron	DEL	T	-	-	rs57471454		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47446461delT	uc003oyw.2	+							NM_012120	NP_036252			CD2-associated protein						cell division|mitosis|protein complex assembly|signal transduction|substrate-dependent cell migration, cell extension	cytoplasm|filamentous actin|nucleolus|plasma membrane|ruffle	SH3 domain binding|structural constituent of cytoskeleton			ovary(1)|skin(1)	2			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)															---	---	---	---
C6orf138	442213	broad.mit.edu	37	6	47893481	47893481	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47893481delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	48616266	48616266	+	IGR	DEL	C	-	-	rs68126837		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48616266delC								C6orf138 (537323 upstream) : MUT (782728 downstream)																																			---	---	---	---
CENPQ	55166	broad.mit.edu	37	6	49459995	49459995	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49459995delT	uc003ozh.1	+	9						NM_018132	NP_060602			centromere protein Q						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2	Lung NSC(77;0.0128)																	---	---	---	---
CRISP3	10321	broad.mit.edu	37	6	49701364	49701364	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	50365854	50365855	+	IGR	INS	-	TG	TG	rs141016863	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50365854_50365855insTG								DEFB112 (349490 upstream) : TFAP2D (315402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	50530242	50530242	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50530242delA								DEFB112 (513878 upstream) : TFAP2D (151015 downstream)																																			---	---	---	---
TFAP2D	83741	broad.mit.edu	37	6	50723312	50723312	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50723312delT	uc003paf.2	+						TFAP2D_uc011dwt.1_Intron	NM_172238	NP_758438			transcription factor AP-2 beta-like 1								DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|breast(1)	7	Lung NSC(77;0.0334)																	---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51846287	51846287	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51846287delT	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)																	---	---	---	---
GSTA5	221357	broad.mit.edu	37	6	52701179	52701179	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52701179delA	uc003pba.1	-							NM_153699	NP_714543			glutathione S-transferase alpha 5						glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity			ovary(1)	1	Lung NSC(77;0.0912)				Glutathione(DB00143)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	52984513	52984513	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52984513delT								FBXO9 (18845 upstream) : GCM1 (7249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	53421915	53421915	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53421915delT								GCLC (12084 upstream) : KLHL31 (90785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	53598207	53598207	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53598207delT								KLHL31 (67701 upstream) : LRRC1 (61571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	53608914	53608915	+	IGR	INS	-	A	A	rs145510940	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53608914_53608915insA								KLHL31 (78408 upstream) : LRRC1 (50863 downstream)																																			---	---	---	---
LRRC1	55227	broad.mit.edu	37	6	53784268	53784269	+	Intron	INS	-	T	T	rs142498215		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53784268_53784269insT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	53817888	53817888	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53817888delT	uc003pce.2	+											Homo sapiens cDNA FLJ32022 fis, clone NTONG1000161.																														---	---	---	---
C6orf142	90523	broad.mit.edu	37	6	54119525	54119525	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54119525delT	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	54270435	54270435	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54270435delA								TINAG (15485 upstream) : FAM83B (441134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	54519536	54519541	+	IGR	DEL	TGTCTG	-	-	rs35114607		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54519536_54519541delTGTCTG								TINAG (264586 upstream) : FAM83B (192028 downstream)																																			---	---	---	---
HCRTR2	3062	broad.mit.edu	37	6	55128706	55128706	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	55499194	55499195	+	IGR	DEL	CT	-	-	rs111578661		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55499194_55499195delCT								HMGCLL1 (55182 upstream) : BMP5 (121045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	55504717	55504717	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55504717delA								HMGCLL1 (60705 upstream) : BMP5 (115523 downstream)																																			---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	56139526	56139526	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56139526delA	uc003pcu.1	-							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	56675511	56675512	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56675511_56675512delAA	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc011dxl.1_Intron	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
RAB23	51715	broad.mit.edu	37	6	57058002	57058003	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57058002_57058003delAA	uc003pds.2	-						RAB23_uc003pdt.2_Intron|RAB23_uc010kac.2_Intron|RAB23_uc010kad.2_Intron	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)															---	---	---	---
RAB23	51715	broad.mit.edu	37	6	57074850	57074850	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57074850delA	uc003pds.2	-						RAB23_uc003pdt.2_Intron|RAB23_uc010kac.2_Intron|RAB23_uc010kad.2_Intron	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	57218373	57218374	+	Intron	INS	-	A	A	rs138912611	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57218373_57218374insA	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	57219137	57219138	+	Intron	INS	-	TCTTA	TCTTA	rs143003076	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57219137_57219138insTCTTA	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	57241773	57241774	+	Intron	INS	-	A	A	rs142182279	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57241773_57241774insA	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	57245082	57245091	+	Intron	DEL	GCTATCCCCT	-	-	rs140533781		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57245082_57245091delGCTATCCCCT	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	57261527	57261528	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57261527_57261528insT	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	57386410	57386410	+	Intron	DEL	A	-	-	rs66841422		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57386410delA	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	57387177	57387178	+	Intron	INS	-	T	T	rs145242761		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57387177_57387178insT	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	57390108	57390114	+	Intron	DEL	ATCTGTT	-	-	rs12209515		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57390108_57390114delATCTGTT	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	57392834	57392836	+	Intron	DEL	AAC	-	-	rs33971467		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57392834_57392836delAAC	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	57402197	57402197	+	Intron	DEL	T	-	-	rs68138830		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57402197delT	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	57418137	57418138	+	Intron	INS	-	TAC	TAC	rs142042320		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57418137_57418138insTAC	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	57436081	57436082	+	Intron	INS	-	T	T	rs149176852	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57436081_57436082insT	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	57443140	57443141	+	Intron	INS	-	TT	TT	rs141096105	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57443140_57443141insTT	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	57474000	57474001	+	Intron	DEL	TC	-	-	rs113450576		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57474000_57474001delTC	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	57476061	57476062	+	Intron	INS	-	T	T	rs5876643	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57476061_57476062insT	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	57485672	57485673	+	Intron	INS	-	C	C	rs151109620	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57485672_57485673insC	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	57488800	57488800	+	Intron	DEL	G	-	-	rs111409818		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57488800delG	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	57509525	57509525	+	Intron	DEL	T	-	-	rs11307740		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57509525delT	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	57516345	57516346	+	IGR	INS	-	T	T	rs151188373		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57516345_57516346insT								PRIM2 (2970 upstream) : GUSBL2 (729813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57518368	57518369	+	IGR	INS	-	TGTT	TGTT	rs146375109		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57518368_57518369insTGTT								PRIM2 (4993 upstream) : GUSBL2 (727790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57541213	57541214	+	IGR	INS	-	A	A	rs78776821		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57541213_57541214insA								PRIM2 (27838 upstream) : GUSBL2 (704945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57577557	57577558	+	IGR	INS	-	A	A	rs150323846	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57577557_57577558insA								PRIM2 (64182 upstream) : GUSBL2 (668601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57591634	57591636	+	IGR	DEL	TTG	-	-	rs36091874		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57591634_57591636delTTG								PRIM2 (78259 upstream) : GUSBL2 (654523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57606558	57606558	+	IGR	DEL	T	-	-	rs74398707		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57606558delT								PRIM2 (93183 upstream) : GUSBL2 (639601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57844588	57844588	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57844588delC								PRIM2 (331213 upstream) : GUSBL2 (401571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	58159479	58159480	+	IGR	INS	-	GAAGGAAG	GAAGGAAG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58159479_58159480insGAAGGAAG								PRIM2 (646104 upstream) : GUSBL2 (86679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	58169015	58169015	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58169015delA								PRIM2 (655640 upstream) : GUSBL2 (77144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	58356016	58356016	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58356016delG								GUSBL2 (68292 upstream) : None (None downstream)																																			---	---	---	---
KHDRBS2	202559	broad.mit.edu	37	6	62661808	62661809	+	Intron	INS	-	T	T	rs151224787	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62661808_62661809insT	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	62867228	62867229	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62867228_62867229insA	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	63002918	63002919	+	IGR	INS	-	CA	CA	rs138287299	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63002918_63002919insCA								KHDRBS2 (6818 upstream) : LGSN (982938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63097707	63097707	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63097707delT								KHDRBS2 (101607 upstream) : LGSN (888150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63161825	63161825	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63161825delT								KHDRBS2 (165725 upstream) : LGSN (824032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63454374	63454374	+	IGR	DEL	A	-	-	rs140343378		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63454374delA								KHDRBS2 (458274 upstream) : LGSN (531483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63620234	63620235	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63620234_63620235insA								KHDRBS2 (624134 upstream) : LGSN (365622 downstream)																																			---	---	---	---
EYS	346007	broad.mit.edu	37	6	64951509	64951509	+	Intron	DEL	A	-	-	rs77999060		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64951509delA	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	65087594	65087595	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65087594_65087595insT	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	66375964	66375964	+	Intron	DEL	T	-	-	rs78356109		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66375964delT	uc011dxu.1	-						EYS_uc003peq.2_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	66874800	66874801	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66874800_66874801insT								MCART3P (375425 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	66919899	66919899	+	IGR	DEL	T	-	-	rs143891525		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66919899delT								MCART3P (420524 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67506815	67506815	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67506815delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67883213	67883214	+	IGR	INS	-	AGG	AGG	rs62418728		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67883213_67883214insAGG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68014016	68014016	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68014016delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68044814	68044814	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68044814delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68556576	68556576	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68556576delT								None (None upstream) : BAI3 (789056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68734209	68734209	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68734209delT								None (None upstream) : BAI3 (611423 downstream)																																			---	---	---	---
BAI3	577	broad.mit.edu	37	6	69785876	69785876	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69785876delT	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)																---	---	---	---
COL19A1	1310	broad.mit.edu	37	6	70610813	70610814	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70610813_70610814delAA	uc003pfc.1	+							NM_001858	NP_001849			alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4																		---	---	---	---
COL19A1	1310	broad.mit.edu	37	6	70810552	70810552	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70810552delT	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849			alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4																		---	---	---	---
COL19A1	1310	broad.mit.edu	37	6	70825718	70825721	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70825718_70825721delTTTT	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849			alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4																		---	---	---	---
COL9A1	1297	broad.mit.edu	37	6	70966529	70966529	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70966529delA	uc003pfg.3	-						COL9A1_uc003pfe.3_Intron|COL9A1_uc003pff.3_Intron	NM_001851	NP_001842			alpha 1 type IX collagen isoform 1 precursor						axon guidance|cell adhesion|organ morphogenesis	collagen type IX	metal ion binding			ovary(4)	4																		---	---	---	---
COL9A1	1297	broad.mit.edu	37	6	70984766	70984767	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70984766_70984767insA	uc003pfg.3	-						COL9A1_uc003pfe.3_Intron|COL9A1_uc003pff.3_Intron	NM_001851	NP_001842			alpha 1 type IX collagen isoform 1 precursor						axon guidance|cell adhesion|organ morphogenesis	collagen type IX	metal ion binding			ovary(4)	4																		---	---	---	---
B3GAT2	135152	broad.mit.edu	37	6	71612038	71612039	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71612038_71612039delAA	uc003pfv.2	-						B3GAT2_uc011dxz.1_Intron|B3GAT2_uc003pfw.2_Intron	NM_080742	NP_542780			beta-1,3-glucuronyltransferase 2						carbohydrate biosynthetic process	Golgi membrane|integral to membrane	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity|metal ion binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	71679433	71679433	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71679433delT								B3GAT2 (12645 upstream) : OGFRL1 (319044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	72466712	72466712	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72466712delA								C6orf155 (336264 upstream) : RIMS1 (129938 downstream)																																			---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72960181	72960181	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	73038351	73038351	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73038351delT	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	NM_014989	NP_055804			regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	73264759	73264759	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73264759delC								RIMS1 (152252 upstream) : KCNQ5 (66812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	73308513	73308513	+	IGR	DEL	T	-	-	rs1147570	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73308513delT								RIMS1 (196006 upstream) : KCNQ5 (23058 downstream)																																			---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73418549	73418549	+	Intron	DEL	T	-	-	rs113215587		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73418549delT	uc003pgk.2	+						KCNQ5_uc003pgj.3_Intron|KCNQ5_uc011dyh.1_Intron|KCNQ5_uc011dyi.1_Intron|KCNQ5_uc010kat.2_Intron|KCNQ5_uc011dyj.1_Intron|KCNQ5_uc011dyk.1_Intron	NM_019842	NP_062816			potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)														---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73787656	73787656	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73787656delT	uc003pgk.2	+						KCNQ5_uc003pgj.3_Intron|KCNQ5_uc011dyh.1_Intron|KCNQ5_uc011dyi.1_Intron|KCNQ5_uc010kat.2_Intron|KCNQ5_uc011dyj.1_Intron|KCNQ5_uc011dyk.1_Intron	NM_019842	NP_062816			potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)														---	---	---	---
SLC17A5	26503	broad.mit.edu	37	6	74320415	74320415	+	Intron	DEL	A	-	-	rs10707321		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74320415delA	uc003phn.3	-						SLC17A5_uc010kax.2_Intron|SLC17A5_uc010kay.2_Intron|SLC17A5_uc011dyo.1_Intron	NM_012434	NP_036566			sialin						anion transport	integral to plasma membrane|lysosomal membrane|membrane fraction	sialic acid:hydrogen symporter activity			skin(5)|central_nervous_system(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	74876543	74876543	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74876543delT	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	75343488	75343489	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75343488_75343489delTC	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75827329	75827329	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75827329delA	uc003phs.2	-						COL12A1_uc003pht.2_Intron	NM_004370	NP_004361			collagen, type XII, alpha 1 long isoform						cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
FILIP1	27145	broad.mit.edu	37	6	76195713	76195714	+	Intron	DEL	AT	-	-	rs150985944	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76195713_76195714delAT	uc003pia.2	-						FILIP1_uc003phy.1_Intron|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	76385140	76385140	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76385140delT	uc003pid.3	+						SENP6_uc003pie.3_Intron|SENP6_uc010kbf.2_Intron|SENP6_uc003pic.2_Intron|SENP6_uc003pif.1_Intron	NM_015571	NP_056386			SUMO1/sentrin specific peptidase 6 isoform 1						proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)																---	---	---	---
MYO6	4646	broad.mit.edu	37	6	76471351	76471351	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76471351delT	uc003pih.1	+						MYO6_uc003pig.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	76842523	76842524	+	IGR	DEL	GG	-	-	rs72063395		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76842523_76842524delGG								IMPG1 (60188 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	77277606	77277606	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77277606delT								IMPG1 (495271 upstream) : HTR1B (894342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78234206	78234206	+	IGR	DEL	A	-	-	rs34248429		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78234206delA								HTR1B (61086 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79250672	79250674	+	IGR	DEL	TCC	-	-	rs111944340		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79250672_79250674delTCC								None (None upstream) : IRAK1BP1 (326515 downstream)																																			---	---	---	---
PHIP	55023	broad.mit.edu	37	6	79708254	79708254	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79708254delA	uc003pir.2	-						PHIP_uc011dyp.1_Intron	NM_017934	NP_060404			pleckstrin homology domain interacting protein						insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)														---	---	---	---
HMGN3	9324	broad.mit.edu	37	6	79947223	79947224	+	5'Flank	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79947223_79947224delAC	uc003pit.2	-						HMGN3_uc003pis.2_5'Flank|HMGN3_uc003piu.1_5'Flank	NM_004242	NP_004233			high mobility group nucleosomal binding domain 3						chromatin modification	chromatin|cytoplasm|nucleus	DNA binding|thyroid hormone receptor binding				0		all_cancers(76;0.000116)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0393)		BRCA - Breast invasive adenocarcinoma(397;0.125)														---	---	---	---
SH3BGRL2	83699	broad.mit.edu	37	6	80409424	80409424	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	80415865	80415866	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80415865_80415866delTT								SH3BGRL2 (2496 upstream) : RNY4 (35770 downstream)																																			---	---	---	---
TTK	7272	broad.mit.edu	37	6	80741972	80741972	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80741972delT	uc003pjc.2	+						TTK_uc003pjb.3_Intron	NM_003318	NP_003309			TTK protein kinase						mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1)	11		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)														---	---	---	---
TTK	7272	broad.mit.edu	37	6	80751897	80751897	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80751897delA	uc003pjc.2	+	22	2626	c.2552delA	c.(2551-2553)GAAfs	p.E851fs	TTK_uc003pjb.3_Frame_Shift_Del_p.E850fs	NM_003318	NP_003309	P33981	TTK_HUMAN	TTK protein kinase	851					mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.R838fs*4(3)		ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1)	11		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)														---	---	---	---
BCKDHB	594	broad.mit.edu	37	6	80878328	80878329	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80878328_80878329insG	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)														---	---	---	---
BCKDHB	594	broad.mit.edu	37	6	80955093	80955093	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80955093delA	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	81113940	81113940	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81113940delT								BCKDHB (57953 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	81218010	81218012	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81218010_81218012delTTT								BCKDHB (162023 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	81920880	81920880	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81920880delA								BCKDHB (864893 upstream) : FAM46A (534568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82190328	82190328	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82190328delT								None (None upstream) : FAM46A (265120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82478358	82478359	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82478358_82478359delTT								FAM46A (15930 upstream) : IBTK (401597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82671488	82671489	+	IGR	DEL	AA	-	-	rs141726594		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82671488_82671489delAA								FAM46A (209060 upstream) : IBTK (208467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82778802	82778802	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82778802delA								FAM46A (316374 upstream) : IBTK (101154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82843485	82843485	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82843485delA								FAM46A (381057 upstream) : IBTK (36471 downstream)																																			---	---	---	---
IBTK	25998	broad.mit.edu	37	6	82923674	82923674	+	Intron	DEL	T	-	-	rs9443970	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82923674delT	uc003pjl.1	-						IBTK_uc011dyv.1_Intron|IBTK_uc011dyw.1_Intron|IBTK_uc010kbi.1_Intron|IBTK_uc003pjm.2_Intron	NM_015525	NP_056340			inhibitor of Bruton's tyrosine kinase						negative regulation of protein phosphorylation|release of sequestered calcium ion into cytosol	cytoplasm|membrane|nucleus	protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(2)|central_nervous_system(2)	4		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	83595237	83595237	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83595237delT								TPBG (518623 upstream) : UBE2CBP (6949 downstream)																																			---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83782811	83782811	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83782811delT	uc003pjs.1	+							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)														---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83839311	83839311	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83858737	83858738	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83858737_83858738insG	uc003pjs.1	+						DOPEY1_uc011dyy.1_Intron|DOPEY1_uc010kbl.1_Intron|DOPEY1_uc003pjt.2_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)														---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83863211	83863212	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83863211_83863212insT	uc003pjs.1	+						DOPEY1_uc011dyy.1_Intron|DOPEY1_uc010kbl.1_Intron|DOPEY1_uc003pjt.2_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)														---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83876278	83876278	+	Intron	DEL	A	-	-	rs77456516		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83876278delA	uc003pjs.1	+						DOPEY1_uc011dyy.1_Intron|DOPEY1_uc010kbl.1_Intron|DOPEY1_uc003pjt.2_Intron|uc003pju.1_RNA	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	84056672	84056672	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84056672delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	84185674	84185674	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84185674delT								ME1 (44895 upstream) : PRSS35 (36600 downstream)																																			---	---	---	---
SNAP91	9892	broad.mit.edu	37	6	84358473	84358474	+	Intron	INS	-	T	T	rs144960491	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84358473_84358474insT	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)														---	---	---	---
SNAP91	9892	broad.mit.edu	37	6	84359464	84359466	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84359464_84359466delTTT	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	84944490	84944491	+	IGR	INS	-	TG	TG	rs145197722	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84944490_84944491insTG								KIAA1009 (7155 upstream) : TBX18 (452590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	85194213	85194213	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85194213delA								KIAA1009 (256878 upstream) : TBX18 (202868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86012274	86012274	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86012274delT								TBX18 (538375 upstream) : NT5E (147028 downstream)																																			---	---	---	---
SYNCRIP	10492	broad.mit.edu	37	6	86346559	86346559	+	Intron	DEL	A	-	-	rs116240890	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86346559delA	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	86554913	86554913	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86554913delT								SNHG5 (166462 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86744796	86744796	+	IGR	DEL	A	-	-	rs139033149		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86744796delA								SNHG5 (356345 upstream) : HTR1E (902228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86817382	86817382	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86817382delT								SNHG5 (428931 upstream) : HTR1E (829642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87171480	87171482	+	IGR	DEL	AGG	-	-	rs72087188		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87171480_87171482delAGG								SNHG5 (783029 upstream) : HTR1E (475542 downstream)																																			---	---	---	---
AKIRIN2	55122	broad.mit.edu	37	6	88397846	88397846	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88397846delT	uc003pmk.2	-							NM_018064	NP_060534			akirin 2						innate immune response|transcription, DNA-dependent	transcriptional repressor complex					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	88506652	88506659	+	Intron	DEL	GTGTGTGA	-	-	rs143085933		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88506652_88506659delGTGTGTGA	uc003pmm.2	+											Homo sapiens mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	88949657	88949657	+	IGR	DEL	A	-	-	rs34778175		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88949657delA								CNR1 (73890 upstream) : RNGTT (370332 downstream)																																			---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90361861	90361861	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90361861delA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90451056	90451056	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90451056delA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90454853	90454854	+	Intron	INS	-	AA	AA	rs71556527		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90454853_90454854insAA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90491072	90491072	+	Intron	DEL	A	-	-	rs80223670		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90491072delA	uc003pnn.1	-						MDN1_uc003pno.1_Intron|MDN1_uc003pnp.1_Frame_Shift_Del_p.F563fs	NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90505161	90505161	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90505161delA	uc003pnn.1	-						MDN1_uc003pnp.1_Intron	NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90583372	90583372	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90583372delT	uc003pnr.2	+						CASP8AP2_uc003pnt.2_Intron|CASP8AP2_uc011dzz.1_Intron	NM_001137667	NP_001131139			caspase 8 associated protein 2						cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)														---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90928226	90928226	+	Intron	DEL	T	-	-	rs148823934		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90928226delT	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	90950410	90950410	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90950410delC	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	91518774	91518774	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91518774delA								MAP3K7 (221867 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91606507	91606507	+	IGR	DEL	T	-	-	rs63056660		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91606507delT								MAP3K7 (309600 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93536193	93536193	+	IGR	DEL	G	-	-	rs9351327	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93536193delG								None (None upstream) : EPHA7 (413549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93886236	93886237	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93886236_93886237delTT								None (None upstream) : EPHA7 (63505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	94638627	94638628	+	IGR	DEL	GG	-	-	rs113329165		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94638627_94638628delGG								TSG1 (152428 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	94686895	94686896	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94686895_94686896delAA								TSG1 (200696 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	94723973	94723974	+	IGR	DEL	AC	-	-	rs71793514		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94723973_94723974delAC								TSG1 (237774 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	94881692	94881693	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94881692_94881693insA								TSG1 (395493 upstream) : None (None downstream)																																			---	---	---	---
FHL5	9457	broad.mit.edu	37	6	97055283	97055284	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97055283_97055284delAC	uc003pos.1	+						FHL5_uc003pot.1_Intron	NM_020482	NP_065228			activator of cAMP-responsive element modulator							nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	97236655	97236655	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97236655delT								FHL5 (172143 upstream) : GPR63 (9234 downstream)																																			---	---	---	---
C6orf167	253714	broad.mit.edu	37	6	97615689	97615689	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97615689delA	uc003ppb.2	-						C6orf167_uc011eaf.1_Intron	NM_198468	NP_940870			hypothetical protein LOC253714						double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)														---	---	---	---
C6orf167	253714	broad.mit.edu	37	6	97660917	97660918	+	Intron	INS	-	TG	TG	rs139266677	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97660917_97660918insTG	uc003ppb.2	-						C6orf167_uc011eaf.1_Intron	NM_198468	NP_940870			hypothetical protein LOC253714						double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)														---	---	---	---
C6orf167	253714	broad.mit.edu	37	6	97730435	97730438	+	Intron	DEL	GGGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97730435_97730438delGGGG	uc003ppb.2	-						C6orf167_uc011eaf.1_5'Flank|C6orf167_uc010kcn.1_Intron|C6orf167_uc010kco.1_5'Flank|C6orf167_uc003ppc.2_5'Flank	NM_198468	NP_940870			hypothetical protein LOC253714						double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	97917028	97917031	+	Intron	DEL	TTGT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97917028_97917031delTTGT	uc003ppd.1	+											Homo sapiens cDNA FLJ34046 fis, clone FCBBF2007610.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	98184743	98184743	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98184743delT								C6orf167 (453682 upstream) : MIR2113 (287664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	98210430	98210430	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98210430delT								C6orf167 (479369 upstream) : MIR2113 (261977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	98356380	98356380	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98356380delT								C6orf167 (625319 upstream) : MIR2113 (116027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	98715362	98715377	+	IGR	DEL	TCCTTCCTTCCTTCCT	-	-	rs72178118		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98715362_98715377delTCCTTCCTTCCTTCCT								MIR2113 (242865 upstream) : POU3F2 (567203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	99679233	99679233	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99679233delA								FBXL4 (283384 upstream) : C6orf168 (41561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	99716714	99716714	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99716714delT								FBXL4 (320865 upstream) : C6orf168 (4080 downstream)																																			---	---	---	---
COQ3	51805	broad.mit.edu	37	6	99844858	99844861	+	5'Flank	DEL	AAAA	-	-	rs72152369		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99844858_99844861delAAAA	uc003ppk.2	-							NM_017421	NP_059117			hexaprenyldihydroxybenzoate methyltransferase						glycerol metabolic process|ubiquinone biosynthetic process	mitochondrial matrix	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity|3-demethylubiquinone-9 3-O-methyltransferase activity|hexaprenyldihydroxybenzoate methyltransferase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101332031	101332031	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101332031delA	uc003pqk.2	-						ASCC3_uc011eai.1_5'Flank|ASCC3_uc003pql.2_5'Flank|ASCC3_uc010kcv.2_5'Flank|ASCC3_uc003pqm.2_5'Flank	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	101757077	101757080	+	IGR	DEL	TCTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101757077_101757080delTCTC								ASCC3 (427853 upstream) : GRIK2 (89825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	101823426	101823426	+	IGR	DEL	A	-	-	rs66930823		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101823426delA								ASCC3 (494202 upstream) : GRIK2 (23479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	102566381	102566382	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102566381_102566382delTT								GRIK2 (48424 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	102977029	102977030	+	IGR	INS	-	GTG	GTG	rs151105146	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102977029_102977030insGTG								GRIK2 (459072 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	103065464	103065464	+	IGR	DEL	G	-	-	rs113501376		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103065464delG								GRIK2 (547507 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	103855609	103855610	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103855609_103855610delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104133062	104133063	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104133062_104133063insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104474027	104474027	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104474027delT								None (None upstream) : HACE1 (701941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104484964	104484967	+	IGR	DEL	TTTT	-	-	rs143449945		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104484964_104484967delTTTT								None (None upstream) : HACE1 (691001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104801054	104801054	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104801054delT								None (None upstream) : HACE1 (374914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104981762	104981763	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104981762_104981763delCT								None (None upstream) : HACE1 (194205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	105052361	105052361	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105052361delA								None (None upstream) : HACE1 (123607 downstream)																																			---	---	---	---
PREP	5550	broad.mit.edu	37	6	105725779	105725779	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105725779delA	uc003prc.2	-	15						NM_002726	NP_002717			prolyl endopeptidase						proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	105877426	105877426	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105877426delT								PREP (26457 upstream) : PRDM1 (656769 downstream)																																			---	---	---	---
QRSL1	55278	broad.mit.edu	37	6	107087000	107087001	+	Intron	INS	-	G	G	rs13203777		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107087000_107087001insG	uc003prm.2	+						QRSL1_uc003prl.2_Intron	NM_018292	NP_060762			glutaminyl-tRNA synthase						translation		ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)														---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107553650	107553650	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107553650delT	uc003prt.2	-						PDSS2_uc011eak.1_Intron|PDSS2_uc011eal.1_Intron|PDSS2_uc003pru.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)														---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107569227	107569227	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107569227delA	uc003prt.2	-						PDSS2_uc011eak.1_Intron|PDSS2_uc011eal.1_Intron|PDSS2_uc003pru.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)														---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107738092	107738092	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107738092delA	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)														---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107773874	107773875	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107773874_107773875delTT	uc003prt.2	-						PDSS2_uc011eak.1_Intron|PDSS2_uc011eal.1_Intron|PDSS2_uc003pru.2_Intron|PDSS2_uc003prv.2_Intron	NM_020381	NP_065114			prenyl diphosphate synthase, subunit 2						isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)														---	---	---	---
SOBP	55084	broad.mit.edu	37	6	107905999	107905999	+	Intron	DEL	T	-	-	rs33984957		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107905999delT	uc003prx.2	+						SOBP_uc003prw.1_Intron	NM_018013	NP_060483			sine oculis binding protein homolog								metal ion binding			ovary(1)	1		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)														---	---	---	---
SEC63	11231	broad.mit.edu	37	6	108232516	108232516	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108232516delA	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)														---	---	---	---
SNX3	8724	broad.mit.edu	37	6	108549902	108549902	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108549902delA	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	108717253	108717253	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108717253delT	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)														---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108807467	108807468	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108807467_108807468insT	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	108887776	108887776	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108887776delT	uc003psk.2	+						FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_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)														---	---	---	---
FOXO3	2309	broad.mit.edu	37	6	108888342	108888342	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108888342delT	uc003psk.2	+						FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_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	109037976	109037976	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109037976delT								FOXO3 (32005 upstream) : ARMC2 (131643 downstream)																																			---	---	---	---
ARMC2	84071	broad.mit.edu	37	6	109294600	109294600	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109294600delA	uc003pss.3	+	18	2661	c.2487delA	c.(2485-2487)CTAfs	p.L829fs	ARMC2_uc011eao.1_Frame_Shift_Del_p.L664fs	NM_032131	NP_115507	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	829							binding				0		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)														---	---	---	---
SESN1	27244	broad.mit.edu	37	6	109366227	109366229	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109366227_109366229delAAA	uc003psu.2	-							NM_014454	NP_055269			sestrin 1						cell cycle arrest|negative regulation of cell proliferation|response to DNA damage stimulus	nucleus				ovary(1)	1		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)														---	---	---	---
AKD1	221264	broad.mit.edu	37	6	109818586	109818589	+	Intron	DEL	CTCA	-	-	rs71018346		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109818586_109818589delCTCA	uc003ptn.2	-						AKD1_uc011eas.1_Intron	NM_001145128	NP_001138600			adenylate kinase domain containing 1 isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	110319190	110319191	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110319190_110319191delAA								GPR6 (17269 upstream) : WASF1 (101831 downstream)																																			---	---	---	---
CDC40	51362	broad.mit.edu	37	6	110523272	110523273	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110523272_110523273delCT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	110832556	110832556	+	IGR	DEL	A	-	-	rs78567166		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110832556delA								SLC22A16 (34712 upstream) : CDK19 (98625 downstream)																																			---	---	---	---
CDK19	23097	broad.mit.edu	37	6	110962843	110962844	+	Intron	INS	-	GAAA	GAAA	rs66614793		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110962843_110962844insGAAA	uc003puh.1	-						CDK19_uc003pui.1_Intron|CDK19_uc011eax.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																		---	---	---	---
RPF2	84154	broad.mit.edu	37	6	111301292	111301292	+	5'Flank	DEL	C	-	-	rs35346583		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111301292delC	uc003pun.2	+						RPF2_uc003puo.2_5'Flank	NM_032194	NP_115570			brix domain containing 1							nucleolus	protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	111375880	111375895	+	IGR	DEL	ATACACACACACACAC	-	-	rs9374256	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111375880_111375895delATACACACACACACAC								GSTM2P1 (7123 upstream) : SLC16A10 (32886 downstream)																																			---	---	---	---
KIAA1919	91749	broad.mit.edu	37	6	111583373	111583373	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111583373delT	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	111692172	111692172	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111692172delT	uc003puy.3	-						REV3L_uc003pux.3_Intron|REV3L_uc003puz.3_Intron|REV3L_uc003pva.1_5'Flank	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	111714246	111714247	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111714246_111714247delTT	uc003puy.3	-						REV3L_uc003pux.3_Intron|REV3L_uc003puz.3_Intron	NM_002912	NP_002903			DNA polymerase zeta						DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
FYN	2534	broad.mit.edu	37	6	112034746	112034746	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112034746delC	uc003pvj.2	-						FYN_uc003pvi.2_Intron|FYN_uc003pvk.2_Intron|FYN_uc003pvh.2_Intron	NM_002037	NP_002028			protein-tyrosine kinase fyn isoform a						axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	112218694	112218694	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112218694delC								FYN (24067 upstream) : WISP3 (156584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	113180456	113180456	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113180456delA								RFPL4B (507958 upstream) : MARCKS (998071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114136911	114136915	+	IGR	DEL	AAAAA	-	-	rs141193629		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114136911_114136915delAAAAA								None (None upstream) : MARCKS (41612 downstream)																																			---	---	---	---
MARCKS	4082	broad.mit.edu	37	6	114181210	114181210	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114181210delA	uc003pvy.3	+	2	849	c.454delA	c.(454-456)AAAfs	p.K152fs		NM_002356	NP_002347	P29966	MARCS_HUMAN	myristoylated alanine-rich protein kinase C	152	Calmodulin-binding (PSD).				energy reserve metabolic process|regulation of insulin secretion	actin cytoskeleton|plasma membrane	actin filament binding|calmodulin binding				0		all_cancers(87;7.65e-05)|all_epithelial(87;0.000296)|all_hematologic(75;0.0172)|Colorectal(196;0.0317)|all_lung(197;0.198)		Epithelial(106;1.59e-07)|all cancers(137;9.85e-07)|OV - Ovarian serous cystadenocarcinoma(136;0.000322)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	114813096	114813099	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114813096_114813099delTTTT								HS3ST5 (149556 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115108212	115108213	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115108212_115108213insTG								HS3ST5 (444672 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115807922	115807923	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115807922_115807923insA								None (None upstream) : FRK (454770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116406877	116406878	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116406877_116406878delGT								FRK (24956 upstream) : NT5DC1 (15121 downstream)																																			---	---	---	---
DSE	29940	broad.mit.edu	37	6	116758559	116758559	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116758559delA	uc003pws.2	+	6					DSE_uc011ebg.1_3'UTR|DSE_uc003pwt.2_3'UTR|DSE_uc003pwu.2_3'UTR	NM_001080976	NP_001074445			dermatan sulfate epimerase precursor						dermatan sulfate biosynthetic process	endoplasmic reticulum|Golgi apparatus|integral to membrane	chondroitin-glucuronate 5-epimerase activity			ovary(1)	1		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)														---	---	---	---
BET3L	100128327	broad.mit.edu	37	6	116843175	116843176	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116843175_116843176delGA	uc011ebh.1	-							NM_001139444	NP_001132916			BET3 like						vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0																		---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117706684	117706684	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117706684delA	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	117798942	117798942	+	Intron	DEL	T	-	-	rs76654178		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117798942delT	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-4292-01	TCGA-BR-4292-01									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	117986502	117986502	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117986502delA								GOPC (62821 upstream) : NUS1 (10115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	118129978	118129978	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118129978delT								NUS1 (98094 upstream) : SLC35F1 (98711 downstream)																																			---	---	---	---
SLC35F1	222553	broad.mit.edu	37	6	118315365	118315366	+	Intron	INS	-	C	C	rs140654593	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118315365_118315366insC	uc003pxx.3	+							NM_001029858	NP_001025029			solute carrier family 35, member F1						transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)														---	---	---	---
SLC35F1	222553	broad.mit.edu	37	6	118509714	118509715	+	Intron	DEL	AA	-	-	rs76971722		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118509714_118509715delAA	uc003pxx.3	+							NM_001029858	NP_001025029			solute carrier family 35, member F1						transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)														---	---	---	---
MCM9	254394	broad.mit.edu	37	6	119259160	119259160	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119259160delA	uc003pyh.2	-							NM_153255	NP_694987			minichromosome maintenance complex component 9						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)														---	---	---	---
FAM184A	79632	broad.mit.edu	37	6	119289430	119289430	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119289430delA	uc003pyj.2	-						FAM184A_uc003pyk.3_Intron|FAM184A_uc003pyl.3_Intron|FAM184A_uc003pyi.2_Intron	NM_024581	NP_078857			hypothetical protein LOC79632 isoform 1											ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	120011066	120011067	+	IGR	DEL	TT	-	-	rs5879515		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120011066_120011067delTT								MAN1A1 (340140 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	120119243	120119244	+	IGR	INS	-	TTCC	TTCC	rs142572854	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120119243_120119244insTTCC								MAN1A1 (448317 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	120721559	120721559	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120721559delT								None (None upstream) : C6orf170 (679068 downstream)																																			---	---	---	---
C6orf170	221322	broad.mit.edu	37	6	121643100	121643101	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121643100_121643101delTT	uc003pyo.1	-						C6orf170_uc003pyq.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	122350631	122350632	+	IGR	INS	-	TG	TG	rs148303337	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122350631_122350632insTG								GJA1 (579759 upstream) : HSF2 (370064 downstream)																																			---	---	---	---
HSF2	3298	broad.mit.edu	37	6	122744704	122744704	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122744704delA	uc003pyu.2	+						HSF2_uc003pyv.2_Intron	NM_004506	NP_004497			heat shock transcription factor 2 isoform a						response to stress|transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0				OV - Ovarian serous cystadenocarcinoma(136;0.00371)|all cancers(137;0.0299)|GBM - Glioblastoma multiforme(226;0.0586)														---	---	---	---
FABP7	2173	broad.mit.edu	37	6	123101679	123101679	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123101679delT	uc003pzf.2	+						FABP7_uc003pzd.2_Intron|FABP7_uc003pze.1_3'UTR	NM_001446	NP_001437			fatty acid binding protein 7, brain						negative regulation of cell proliferation	cytoplasm	lipid binding|transporter activity				0				GBM - Glioblastoma multiforme(226;0.226)	Alpha-Linolenic Acid(DB00132)|gamma-Homolinolenic acid(DB00154)|Icosapent(DB00159)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	123306623	123306624	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123306623_123306624insA								SMPDL3A (175761 upstream) : CLVS2 (10958 downstream)																																			---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123673672	123673673	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123673672_123673673insT	uc003pzj.1	-						TRDN_uc003pzk.1_Frame_Shift_Ins_p.K461fs|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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	124058139	124058140	+	IGR	DEL	CG	-	-	rs71021461		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124058139_124058140delCG								TRDN (100197 upstream) : NKAIN2 (66929 downstream)																																			---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124216209	124216209	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124216209delT	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	124260950	124260950	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124260950delT	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	125120615	125120616	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125120615_125120616delAC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	125471751	125471752	+	IGR	INS	-	T	T	rs148166757	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125471751_125471752insT								RNF217 (67094 upstream) : TPD52L1 (3127 downstream)																																			---	---	---	---
TPD52L1	7164	broad.mit.edu	37	6	125490191	125490192	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125490191_125490192delTC	uc003pzu.1	+						TPD52L1_uc003pzv.1_Intron|TPD52L1_uc003pzw.1_Intron|TPD52L1_uc003pzx.1_Intron|TPD52L1_uc003pzy.1_Intron	NM_003287	NP_003278			tumor protein D52-like 1 isoform 1						DNA fragmentation involved in apoptotic nuclear change|G2/M transition of mitotic cell cycle|induction of apoptosis|positive regulation of JNK cascade|positive regulation of MAP kinase activity	perinuclear region of cytoplasm	caspase activator activity|protein heterodimerization activity|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)														---	---	---	---
TPD52L1	7164	broad.mit.edu	37	6	125577500	125577501	+	Intron	INS	-	A	A	rs113832248		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125577500_125577501insA	uc003pzu.1	+						TPD52L1_uc003pzv.1_Intron|TPD52L1_uc003pzw.1_Intron|TPD52L1_uc003pzy.1_Intron|TPD52L1_uc003pzz.1_Intron	NM_003287	NP_003278			tumor protein D52-like 1 isoform 1						DNA fragmentation involved in apoptotic nuclear change|G2/M transition of mitotic cell cycle|induction of apoptosis|positive regulation of JNK cascade|positive regulation of MAP kinase activity	perinuclear region of cytoplasm	caspase activator activity|protein heterodimerization activity|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	125838422	125838423	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125838422_125838423delTT								HDDC2 (215140 upstream) : HEY2 (230357 downstream)																																			---	---	---	---
NCOA7	135112	broad.mit.edu	37	6	126176145	126176145	+	Intron	DEL	T	-	-	rs72530341		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126176145delT	uc010kes.2	+						NCOA7_uc003qae.3_Intron|NCOA7_uc003qah.2_Intron|NCOA7_uc003qai.2_Intron|NCOA7_uc010ket.2_Intron|NCOA7_uc003qaf.2_Intron|NCOA7_uc003qag.2_Intron|NCOA7_uc003qaj.2_Intron	NM_181782	NP_861447			nuclear receptor coactivator 7 isoform 1						cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)														---	---	---	---
TRMT11	60487	broad.mit.edu	37	6	126320096	126320096	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126320096delT	uc003qam.2	+						TRMT11_uc003qan.2_Intron|TRMT11_uc010kev.2_Intron	NM_001031712	NP_001026882			tRNA methyltransferase 11						tRNA processing		methyltransferase activity|nucleic acid binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0356)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	126565322	126565322	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126565322delA								TRMT11 (204904 upstream) : CENPW (95931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	126605541	126605541	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126605541delA								TRMT11 (245123 upstream) : CENPW (55712 downstream)																																			---	---	---	---
CENPW	387103	broad.mit.edu	37	6	126660355	126660356	+	5'Flank	INS	-	AGG	AGG	rs140564891	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126660355_126660356insAGG	uc003qao.2	+						CENPW_uc003qap.3_5'Flank	NM_001012507	NP_001012525			hypothetical protein LOC387103							chromosome, centromeric region|nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	127428830	127428830	+	Intron	DEL	A	-	-	rs77986909		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127428830delA	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
RSPO3	84870	broad.mit.edu	37	6	127513921	127513922	+	Intron	INS	-	TA	TA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127513921_127513922insTA	uc003qar.2	+						RSPO3_uc003qas.1_Intron	NM_032784	NP_116173			R-spondin 3 precursor							extracellular region	heparin binding				0				GBM - Glioblastoma multiforme(226;0.0555)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127557400	127557400	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127557400delT								RSPO3 (38490 upstream) : RNF146 (30620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	127683600	127683600	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127683600delA								ECHDC1 (18846 upstream) : C6orf174 (75952 downstream)																																			---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128290201	128290201	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128290201delA	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	128665679	128665679	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128665679delT	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron|PTPRK_uc003qbm.3_Intron	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128752086	128752087	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128752086_128752087delTT	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc011ebv.1_Intron|PTPRK_uc003qbm.3_Intron	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129573211	129573211	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129573211delT	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	129650512	129650512	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129650512delT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
ARHGAP18	93663	broad.mit.edu	37	6	129958380	129958380	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129958380delT	uc003qbr.2	-						ARHGAP18_uc011ebw.1_Intron	NM_033515	NP_277050			Rho GTPase activating protein 18						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)														---	---	---	---
ARHGAP18	93663	broad.mit.edu	37	6	129959603	129959603	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129959603delT	uc003qbr.2	-	3	577	c.488delA	c.(487-489)AACfs	p.N163fs	ARHGAP18_uc011ebw.1_Frame_Shift_Del_p.N163fs	NM_033515	NP_277050	Q8N392	RHG18_HUMAN	Rho GTPase activating protein 18	163					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)														---	---	---	---
ARHGAP18	93663	broad.mit.edu	37	6	129963597	129963598	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129963597_129963598delTT	uc003qbr.2	-						ARHGAP18_uc011ebw.1_Intron	NM_033515	NP_277050			Rho GTPase activating protein 18						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)														---	---	---	---
L3MBTL3	84456	broad.mit.edu	37	6	130423247	130423248	+	Intron	DEL	AA	-	-	rs146098025		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130423247_130423248delAA	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-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	131049896	131049896	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131049896delA								TMEM200A (285688 upstream) : LOC285733 (98428 downstream)																																			---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131199492	131199492	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131199492delA	uc003qch.2	-						EPB41L2_uc003qce.1_Intron|EPB41L2_uc003qcf.1_Intron|EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc010kfl.1_Intron|EPB41L2_uc003qcj.1_5'Flank	NM_001431	NP_001422			erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)														---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131372593	131372593	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131372593delA	uc003qch.2	-						EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron	NM_001431	NP_001422			erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)														---	---	---	---
AKAP7	9465	broad.mit.edu	37	6	131466397	131466397	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131466397delT	uc003qck.2	+						AKAP7_uc011ebz.1_5'Flank	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)														---	---	---	---
AKAP7	9465	broad.mit.edu	37	6	131520530	131520530	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131520530delT	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)														---	---	---	---
AKAP7	9465	broad.mit.edu	37	6	131594367	131594367	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131594367delT	uc003qcm.1	+						AKAP7_uc003qck.2_Intron|AKAP7_uc011ebz.1_Intron|AKAP7_uc003qcl.1_Intron|AKAP7_uc003qcn.1_Intron	NM_138633	NP_619539			A-kinase anchor protein 7 isoform beta						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)														---	---	---	---
ENPP1	5167	broad.mit.edu	37	6	132179792	132179792	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132179792delT	uc011ecf.1	+						ENPP1_uc003qcy.2_5'Flank	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	132189068	132189068	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132189068delT	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)													---	---	---	---
ENPP1	5167	broad.mit.edu	37	6	132215430	132215432	+	3'UTR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132215430_132215432delTTT	uc011ecf.1	+	25						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	132280847	132280847	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132280847delA								CTGF (8329 upstream) : MOXD1 (336348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	132735041	132735041	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132735041delA								MOXD1 (12377 upstream) : STX7 (43622 downstream)																																			---	---	---	---
STX7	8417	broad.mit.edu	37	6	132824037	132824037	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132824037delA	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)														---	---	---	---
TAAR2	9287	broad.mit.edu	37	6	132946598	132946598	+	5'Flank	DEL	C	-	-	rs146565055		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132946598delC	uc003qdl.1	-							NM_001033080	NP_001028252			trace amine associated receptor 2 isoform 1							plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)														---	---	---	---
EYA4	2070	broad.mit.edu	37	6	133677196	133677197	+	Intron	DEL	AG	-	-	rs113841856		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133677196_133677197delAG	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	135028413	135028414	+	IGR	INS	-	T	T	rs58945279	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135028413_135028414insT								SGK1 (389217 upstream) : ALDH8A1 (210115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	135107829	135107830	+	IGR	INS	-	T	T	rs143671043	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135107829_135107830insT								SGK1 (468633 upstream) : ALDH8A1 (130699 downstream)																																			---	---	---	---
ALDH8A1	64577	broad.mit.edu	37	6	135267900	135267901	+	Intron	INS	-	CACAGGTGCGCATGTGTGCGCGCGTG	CACAGGTGCGCATGTGTGCGCGCGTG	rs67708020		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135267900_135267901insCACAGGTGCGCATGTGTGCGCGCGTG	uc003qew.2	-						ALDH8A1_uc003qex.2_Intron|ALDH8A1_uc010kgh.2_Intron|ALDH8A1_uc011ecx.1_Intron	NM_022568	NP_072090			aldehyde dehydrogenase 8A1 isoform 1						retinal metabolic process	cytoplasm	retinal dehydrogenase activity			ovary(2)|pancreas(1)|skin(1)	4	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	135581208	135581209	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135581208_135581209delAA								MIR548A2 (20814 upstream) : AHI1 (23903 downstream)																																			---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	136883493	136883495	+	Intron	DEL	TTT	-	-	rs11322947		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136883493_136883495delTTT	uc003qhc.2	-						MAP3K5_uc011edj.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)														---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	136955726	136955726	+	Intron	DEL	T	-	-	rs71848610		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136955726delT	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)														---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	137002770	137002771	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137002770_137002771insA	uc003qhc.2	-						MAP3K5_uc011edk.1_Intron|MAP3K5_uc010kgw.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)														---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	137028696	137028698	+	Intron	DEL	GGG	-	-	rs140155309	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137028696_137028698delGGG	uc003qhc.2	-						MAP3K5_uc011edk.1_Intron|MAP3K5_uc010kgw.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	137118116	137118117	+	IGR	DEL	GT	-	-	rs111874250		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137118116_137118117delGT								MAP3K5 (4460 upstream) : PEX7 (25585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	137292802	137292802	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137292802delA								SLC35D3 (46028 upstream) : NHEG1 (7570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	137428104	137428105	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137428104_137428105delTT								IL20RA (61806 upstream) : IL22RA2 (36853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	137869900	137869901	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137869900_137869901insT								OLIG3 (54369 upstream) : TNFAIP3 (318680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138085776	138085778	+	IGR	DEL	ATG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138085776_138085778delATG								OLIG3 (270245 upstream) : TNFAIP3 (102803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138243606	138243606	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138243606delT								TNFAIP3 (39161 upstream) : PERP (166036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138267147	138267147	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138267147delA								TNFAIP3 (62702 upstream) : PERP (142495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138301383	138301384	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138301383_138301384delCA								TNFAIP3 (96938 upstream) : PERP (108258 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138403230	138403230	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138403230delT								TNFAIP3 (198785 upstream) : PERP (6412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138404752	138404777	+	IGR	DEL	AAGAGCTGGATAATATATCCAGCAGG	-	-	rs11270264		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138404752_138404777delAAGAGCTGGATAATATATCCAGCAGG								TNFAIP3 (200307 upstream) : PERP (4865 downstream)																																			---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138628599	138628600	+	Intron	DEL	AA	-	-	rs80147113		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138628599_138628600delAA	uc003qhu.2	+							NM_020340	NP_065073			brefeldin A-inhibited guanine						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	139010924	139010924	+	5'Flank	DEL	T	-	-	rs67022766		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139010924delT	uc003qhz.1	+						uc003qia.1_5'Flank|uc003qib.1_5'Flank|uc003qic.1_5'Flank					Homo sapiens cDNA FLJ46906 fis, clone BRHIP2020930.																														---	---	---	---
CCDC28A	25901	broad.mit.edu	37	6	139097330	139097330	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139097330delA	uc003qie.2	+	2	498	c.343delA	c.(343-345)AAAfs	p.K115fs	uc003qid.1_5'Flank	NM_015439	NP_056254	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A	115											0				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)														---	---	---	---
CCDC28A	25901	broad.mit.edu	37	6	139112624	139112624	+	Intron	DEL	T	-	-	rs77009482		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139112624delT	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)														---	---	---	---
ECT2L	345930	broad.mit.edu	37	6	139208361	139208362	+	Intron	INS	-	TTTTT	TTTTT	rs139275505	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139208361_139208362insTTTTT	uc003qif.1	+						ECT2L_uc011edq.1_Intron	NM_001077706	NP_001071174			epithelial cell transforming sequence 2						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	140624699	140624700	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140624699_140624700insT								CITED2 (928914 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141211415	141211416	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141211415_141211416insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141817379	141817379	+	IGR	DEL	T	-	-	rs66481558		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141817379delT								None (None upstream) : NMBR (579367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141999364	141999365	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141999364_141999365delTT	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																														---	---	---	---
LOC153910	153910	broad.mit.edu	37	6	142891214	142891214	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142891214delA	uc003qjc.1	-						LOC153910_uc010khg.1_Intron	NR_027312				Homo sapiens cDNA FLJ31371 fis, clone NB9N42000196.												0																		---	---	---	---
LOC153910	153910	broad.mit.edu	37	6	142949435	142949435	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142949435delC	uc003qjc.1	-						LOC153910_uc010khg.1_Intron	NR_027312				Homo sapiens cDNA FLJ31371 fis, clone NB9N42000196.												0																		---	---	---	---
HIVEP2	3097	broad.mit.edu	37	6	143090598	143090599	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143090598_143090599delTT	uc003qjd.2	-							NM_006734	NP_006725			human immunodeficiency virus type I enhancer						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)														---	---	---	---
AIG1	51390	broad.mit.edu	37	6	143478575	143478575	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143478575delT	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	143838250	143838253	+	IGR	DEL	AGAG	-	-	rs10605071		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143838250_143838253delAGAG								FUCA2 (5387 upstream) : LOC285740 (37214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	144154167	144154168	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144154167_144154168delAA								PHACTR2 (1846 upstream) : LTV1 (10340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	144522213	144522213	+	IGR	DEL	A	-	-	rs10782292	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144522213delA								STX11 (9138 upstream) : UTRN (85277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	144523462	144523462	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144523462delA								STX11 (10387 upstream) : UTRN (84028 downstream)																																			---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144775019	144775019	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144775019delT	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144796037	144796038	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144796037_144796038delAA	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	144811164	144811164	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144811164delA	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	145234469	145234469	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145234469delA								UTRN (60301 upstream) : EPM2A (711977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	145709985	145709985	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145709985delT								UTRN (535817 upstream) : EPM2A (236461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	145759235	145759236	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145759235_145759236delGT								UTRN (585067 upstream) : EPM2A (187210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	145821147	145821147	+	IGR	DEL	T	-	-	rs66978931		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145821147delT								UTRN (646979 upstream) : EPM2A (125299 downstream)																																			---	---	---	---
EPM2A	7957	broad.mit.edu	37	6	145976910	145976910	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145976910delA	uc003qkw.2	-						EPM2A_uc003qkv.2_Intron|EPM2A_uc010khr.2_Intron|EPM2A_uc003qkx.2_Intron|EPM2A_uc003qku.2_Intron	NM_005670	NP_005661			laforin isoform a						glycogen metabolic process	cytosol|endoplasmic reticulum|nucleus|plasma membrane|polysome	carbohydrate binding|identical protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146209042	146209043	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146209042_146209043insA	uc003qlf.2	-						SHPRH_uc003qld.2_Intron|SHPRH_uc003qle.2_Intron	NM_001042683	NP_001036148			SNF2 histone linker PHD RING helicase isoform a						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)														---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146421182	146421182	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146421182delT	uc010khw.1	+						GRM1_uc010khu.1_Intron|GRM1_uc010khv.1_Intron|GRM1_uc003qll.2_Intron|GRM1_uc011edz.1_Intron|GRM1_uc011eea.1_Intron	NM_000838	NP_000829			glutamate receptor, metabotropic 1 isoform alpha						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	147264795	147264795	+	Intron	DEL	A	-	-	rs112173564		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147264795delA	uc003qlt.1	-						uc003qlu.1_Intron|uc003qlv.2_Intron					Homo sapiens cDNA FLJ34275 fis, clone FEBRA2003454.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	147961015	147961015	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147961015delT								SAMD5 (69858 upstream) : SASH1 (702714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	148212925	148212926	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148212925_148212926insA								SAMD5 (321768 upstream) : SASH1 (450803 downstream)																																			---	---	---	---
SASH1	23328	broad.mit.edu	37	6	148846157	148846158	+	Intron	INS	-	A	A	rs147777430	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148846157_148846158insA	uc003qme.1	+						SASH1_uc011eeb.1_Intron|SASH1_uc003qmf.1_5'UTR	NM_015278	NP_056093			SAM and SH3 domain containing 1								protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)														---	---	---	---
UST	10090	broad.mit.edu	37	6	149297973	149297973	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149297973delT	uc003qmg.2	+							NM_005715	NP_005706			uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	149486809	149486809	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149486809delA								UST (88684 upstream) : TAB2 (52950 downstream)																																			---	---	---	---
TAB2	23118	broad.mit.edu	37	6	149662919	149662919	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149662919delT	uc003qmj.2	+						TAB2_uc011eec.1_Intron|TAB2_uc010kia.1_Intron|TAB2_uc010kib.1_Intron|TAB2_uc003qmk.3_5'Flank	NM_015093	NP_055908			mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|heart development|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	K63-linked polyubiquitin binding|zinc ion binding				0																		---	---	---	---
PPIL4	85313	broad.mit.edu	37	6	149832534	149832535	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149832534_149832535delTG	uc003qmo.1	-						PPIL4_uc010kic.2_Intron	NM_139126	NP_624311			peptidylprolyl isomerase-like 4						protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)														---	---	---	---
NUP43	348995	broad.mit.edu	37	6	150045887	150045887	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150045887delT	uc003qmz.2	-	8					NUP43_uc003qmx.3_Intron|NUP43_uc011eee.1_Intron	NM_198887	NP_942590			nucleoporin 43kDa						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			upper_aerodigestive_tract(1)	1		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;4.71e-13)|GBM - Glioblastoma multiforme(68;0.101)														---	---	---	---
PCMT1	5110	broad.mit.edu	37	6	150094153	150094160	+	Intron	DEL	AAAAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150094153_150094160delAAAAAAAA	uc003qne.2	+						PCMT1_uc003qna.2_Intron|PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)														---	---	---	---
PCMT1	5110	broad.mit.edu	37	6	150114900	150114900	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150114900delT	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)														---	---	---	---
PPP1R14C	81706	broad.mit.edu	37	6	150472184	150472185	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150472184_150472185insT	uc003qnt.2	+							NM_030949	NP_112211			protein phosphatase 1, regulatory (inhibitor)						regulation of phosphorylation	cytoplasm|membrane					0		Ovarian(120;0.0284)	BRCA - Breast invasive adenocarcinoma(37;0.215)	OV - Ovarian serous cystadenocarcinoma(155;9.14e-12)														---	---	---	---
PLEKHG1	57480	broad.mit.edu	37	6	151066819	151066819	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151066819delA	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron|PLEKHG1_uc011eem.1_Intron|PLEKHG1_uc003qnz.2_Intron	NM_001029884	NP_001025055			pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)														---	---	---	---
PLEKHG1	57480	broad.mit.edu	37	6	151141344	151141347	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151141344_151141347delAAAA	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron|PLEKHG1_uc011eem.1_Intron|PLEKHG1_uc003qnz.2_Intron	NM_001029884	NP_001025055			pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)														---	---	---	---
MTHFD1L	25902	broad.mit.edu	37	6	151218080	151218081	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151218080_151218081delAA	uc003qob.2	+						MTHFD1L_uc011een.1_Intron|MTHFD1L_uc011eeo.1_Intron|MTHFD1L_uc003qoc.2_Intron|MTHFD1L_uc003qoa.1_Intron|MTHFD1L_uc010kil.1_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)														---	---	---	---
MTHFD1L	25902	broad.mit.edu	37	6	151413789	151413789	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151413789delT	uc003qob.2	+						MTHFD1L_uc003qoc.2_Intron	NM_015440	NP_056255			methylenetetrahydrofolate dehydrogenase (NADP+						folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)														---	---	---	---
ESR1	2099	broad.mit.edu	37	6	152055759	152055759	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152055759delT	uc003qom.3	+							NM_001122742	NP_001116214			estrogen receptor alpha isoform 4						positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)													---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152620823	152620824	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152620823_152620824delTT	uc010kiw.2	-						SYNE1_uc010kiv.2_Intron|SYNE1_uc003qos.3_Intron|SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kiy.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	152863092	152863092	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152863092delA	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	153545652	153545655	+	IGR	DEL	AAAA	-	-	rs74971163		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153545652_153545655delAAAA								RGS17 (93263 upstream) : OPRM1 (785981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153626515	153626517	+	IGR	DEL	CTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153626515_153626517delCTC								RGS17 (174126 upstream) : OPRM1 (705119 downstream)																																			---	---	---	---
IPCEF1	26034	broad.mit.edu	37	6	154598995	154598995	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154598995delT	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																OREG0017742	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	6	154925890	154925891	+	IGR	INS	-	TGTTT	TGTTT	rs150363410	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154925890_154925891insTGTTT								CNKSR3 (94137 upstream) : RBM16 (128621 downstream)																																			---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155186164	155186165	+	Intron	DEL	TT	-	-	rs68160515		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155186164_155186165delTT	uc003qqb.2	+						uc003qqc.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	155935466	155935466	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155935466delA								NOX3 (158429 upstream) : MIR1202 (332465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156898576	156898576	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156898576delT								MIR1202 (630563 upstream) : ARID1B (200510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	157768430	157768431	+	IGR	DEL	AC	-	-	rs34940761		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157768430_157768431delAC								C6orf35 (23637 upstream) : ZDHHC14 (34126 downstream)																																			---	---	---	---
SNX9	51429	broad.mit.edu	37	6	158363958	158363958	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158363958delA	uc003qqv.1	+	18						NM_016224	NP_057308			sorting nexin 9						cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	158376769	158376770	+	IGR	INS	-	TCA	TCA	rs144462402	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158376769_158376770insTCA								SNX9 (10660 upstream) : SYNJ2 (26149 downstream)																																			---	---	---	---
SERAC1	84947	broad.mit.edu	37	6	158545817	158545822	+	Intron	DEL	ACACAT	-	-	rs827670		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158545817_158545822delACACAT	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)														---	---	---	---
SERAC1	84947	broad.mit.edu	37	6	158551577	158551578	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158551577_158551578insA	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)														---	---	---	---
SERAC1	84947	broad.mit.edu	37	6	158579538	158579538	+	Intron	DEL	A	-	-	rs111829898		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158579538delA	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)														---	---	---	---
GTF2H5	404672	broad.mit.edu	37	6	158605276	158605276	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158605276delA	uc003qrd.2	+							NM_207118	NP_997001			general transcription factor IIH, polypeptide 5						nucleotide-excision repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;5.98e-18)|BRCA - Breast invasive adenocarcinoma(81;2.83e-05)									Direct_reversal_of_damage|NER					---	---	---	---
Unknown	0	broad.mit.edu	37	6	158952200	158952201	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158952200_158952201delAA								TULP4 (19346 upstream) : TMEM181 (5267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	159481766	159481766	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159481766delA								TAGAP (15582 upstream) : FNDC1 (108663 downstream)																																			---	---	---	---
WTAP	9589	broad.mit.edu	37	6	160145892	160145892	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160145892delA	uc003qsl.2	+						WTAP_uc010kjx.2_5'Flank|WTAP_uc003qsk.2_5'Flank|WTAP_uc003qsm.1_5'Flank|WTAP_uc003qsn.2_5'Flank	NM_004906	NP_004897			Wilms' tumour 1-associating protein isoform 1						cell cycle|mRNA processing|RNA splicing	nuclear membrane|nucleolus					0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)														---	---	---	---
TCP1	6950	broad.mit.edu	37	6	160200861	160200861	+	Intron	DEL	A	-	-	rs147097290	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160200861delA	uc003qsr.2	-						TCP1_uc003qss.2_Intron|TCP1_uc010kjz.2_Intron|TCP1_uc003qst.2_Intron	NM_030752	NP_110379			T-complex protein 1 isoform a						'de novo' posttranslational protein folding|tubulin complex assembly	cell junction|Golgi apparatus	ATP binding|unfolded protein binding			breast(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(65;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)														---	---	---	---
SLC22A3	6581	broad.mit.edu	37	6	160830048	160830050	+	Intron	DEL	TTT	-	-	rs147640016		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160830048_160830050delTTT	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)														---	---	---	---
LPAL2	80350	broad.mit.edu	37	6	160887595	160887595	+	RNA	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160887595delT	uc003qtj.2	-	10		c.1960delA				NR_028093				Homo sapiens cDNA FLJ43922 fis, clone TESTI4012406.												0		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.214)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	161091425	161091425	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161091425delA								LPA (4018 upstream) : PLG (31849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	161395328	161395328	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161395328delT								PLG (220983 upstream) : MAP3K4 (17494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	161546012	161546012	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161546012delT								MAP3K4 (7596 upstream) : AGPAT4 (5045 downstream)																																			---	---	---	---
AGPAT4	56895	broad.mit.edu	37	6	161586755	161586756	+	Intron	DEL	AA	-	-	rs112552218		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161586755_161586756delAA	uc003qtr.1	-						AGPAT4_uc003qts.1_Intron|AGPAT4_uc011egb.1_Intron|AGPAT4_uc003qtt.1_Intron|AGPAT4_uc011egc.1_Intron|AGPAT4_uc011egd.1_Intron|AGPAT4_uc011ege.1_Intron	NM_020133	NP_064518			1-acylglycerol-3-phosphate O-acyltransferase 4						phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)														---	---	---	---
AGPAT4	56895	broad.mit.edu	37	6	161683506	161683506	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161683506delT	uc003qtr.1	-						AGPAT4_uc003qts.1_Intron|AGPAT4_uc011egb.1_Intron|AGPAT4_uc011egc.1_Intron|AGPAT4_uc011egd.1_Intron|AGPAT4_uc011ege.1_Intron	NM_020133	NP_064518			1-acylglycerol-3-phosphate O-acyltransferase 4						phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	161838481	161838484	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161838481_161838484delAAAA	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-4292-01	TCGA-BR-4292-01									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	161849750	161849751	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161849750_161849751insT	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	162034400	162034400	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162034400delT	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	162532738	162532738	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162532738delA	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	162730308	162730308	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162730308delT	uc003qtx.3	-						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	164240573	164240574	+	IGR	INS	-	TG	TG	rs146833153	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164240573_164240574insTG								QKI (245681 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164523377	164523378	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164523377_164523378delCT								QKI (528485 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164586696	164586696	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164586696delT								QKI (591804 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164970011	164970011	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164970011delA								QKI (975119 upstream) : C6orf118 (723144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	165080222	165080223	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165080222_165080223delAC								None (None upstream) : C6orf118 (612932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	166495479	166495480	+	IGR	INS	-	CA	CA	rs141622854	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166495479_166495480insCA								LOC441177 (92376 upstream) : T (75606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	166606510	166606510	+	IGR	DEL	T	-	-	rs72084915		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166606510delT								T (24379 upstream) : PRR18 (112658 downstream)																																			---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	167268918	167268920	+	Intron	DEL	GAA	-	-	rs13215333		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167268918_167268920delGAA	uc003qvd.1	-						RPS6KA2_uc003qvc.1_Intron	NM_021135	NP_066958			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)														---	---	---	---
FGFR1OP	11116	broad.mit.edu	37	6	167426850	167426850	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167426850delA	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								---	---	---	---
UNC93A	54346	broad.mit.edu	37	6	167729089	167729090	+	3'UTR	INS	-	T	T	rs141621248	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167729089_167729090insT	uc003qvq.2	+	8					UNC93A_uc003qvr.2_3'UTR	NM_018974	NP_061847			unc-93 homolog A isoform 1							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	168084693	168084695	+	5'Flank	DEL	AAA	-	-	rs113243510		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168084693_168084695delAAA	uc010kkq.1	-						uc003qvy.1_RNA					Homo sapiens cDNA FLJ32038 fis, clone NTONG2000583.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	168107688	168107690	+	IGR	DEL	AAC	-	-	rs72245219		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168107688_168107690delAAC								TCP10 (309690 upstream) : C6orf123 (77531 downstream)																																			---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168271459	168271459	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168271459delT	uc003qwd.2	+						MLLT4_uc003qwb.1_Intron|MLLT4_uc003qwc.1_Intron	NM_001040001	NP_001035090			myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168319288	168319289	+	Intron	INS	-	TG	TG	rs143827994	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168319288_168319289insTG	uc003qwd.2	+						MLLT4_uc003qwb.1_Intron|MLLT4_uc003qwc.1_Intron|MLLT4_uc003qwg.1_Intron	NM_001040001	NP_001035090			myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168355107	168355108	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168355107_168355108insT	uc003qwd.2	+						MLLT4_uc003qwc.1_Intron|MLLT4_uc003qwg.1_Intron	NM_001040001	NP_001035090			myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168370286	168370286	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168370286delT	uc003qwd.2	+							NM_001040001	NP_001035090			myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
Unknown	0	broad.mit.edu	37	6	168547340	168547342	+	IGR	DEL	TTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168547340_168547342delTTG								FRMD1 (67501 upstream) : DACT2 (160244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	169084296	169084296	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169084296delA								SMOC2 (15625 upstream) : THBS2 (531580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	169516655	169516656	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169516655_169516656delTT								SMOC2 (447984 upstream) : THBS2 (99220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	169719117	169719118	+	IGR	INS	-	TT	TT	rs35418322		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169719117_169719118insTT								THBS2 (64980 upstream) : WDR27 (138189 downstream)																																			---	---	---	---
WDR27	253769	broad.mit.edu	37	6	169939611	169939612	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169939611_169939612insA	uc003qwx.2	-						WDR27_uc003qwv.1_Intron|WDR27_uc010kkw.1_Intron|WDR27_uc003qwy.2_Intron					RecName: Full=WD repeat-containing protein 27;											pancreas(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)														---	---	---	---
WDR27	253769	broad.mit.edu	37	6	169941229	169941229	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169941229delA	uc003qwx.2	-						WDR27_uc003qwv.1_Intron|WDR27_uc010kkw.1_Intron|WDR27_uc003qwy.2_Intron					RecName: Full=WD repeat-containing protein 27;											pancreas(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)														---	---	---	---
C6orf120	387263	broad.mit.edu	37	6	170104189	170104190	+	3'UTR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170104189_170104190insA	uc003qxb.2	+	1					WDR27_uc010kkw.1_5'Flank|WDR27_uc003qwx.2_5'Flank|WDR27_uc003qwy.2_5'Flank|WDR27_uc011egw.1_5'Flank|WDR27_uc010kkx.2_5'Flank|PHF10_uc011egy.1_Intron|PHF10_uc011egz.1_Intron	NM_001029863	NP_001025034			hypothetical protein LOC387263 precursor							extracellular region					0		Breast(66;0.000338)		OV - Ovarian serous cystadenocarcinoma(33;9.65e-22)|BRCA - Breast invasive adenocarcinoma(81;1.29e-07)|GBM - Glioblastoma multiforme(31;0.0015)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	170468595	170468595	+	IGR	DEL	G	-	-	rs77249139		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170468595delG								C6orf208 (265626 upstream) : LOC154449 (94827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	170762262	170762263	+	IGR	INS	-	GT	GT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170762262_170762263insGT								FAM120B (48026 upstream) : PSMB1 (17844 downstream)																																			---	---	---	---
TBP	6908	broad.mit.edu	37	6	170881390	170881391	+	3'UTR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170881390_170881391delTT	uc003qxt.2	+	8					TBP_uc003qxu.2_3'UTR|TBP_uc011ehf.1_3'UTR	NM_003194	NP_003185			TATA box binding protein						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	152877	152878	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152877_152878insC	uc003sio.1	+						uc010kry.1_Intron					Homo sapiens cDNA FLJ14181 fis, clone NT2RP2004300.																														---	---	---	---
PRKAR1B	5575	broad.mit.edu	37	7	621806	621807	+	Intron	INS	-	A	A	rs35955005		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:621806_621807insA	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron|PRKAR1B_uc003six.1_Intron	NM_002735	NP_002726			protein kinase, cAMP-dependent, regulatory, type						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)														---	---	---	---
PRKAR1B	5575	broad.mit.edu	37	7	671425	671426	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:671425_671426delAA	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron	NM_002735	NP_002726			protein kinase, cAMP-dependent, regulatory, type						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)														---	---	---	---
CYP2W1	54905	broad.mit.edu	37	7	1027483	1027483	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1027483delG	uc003sjq.1	+						CYP2W1_uc003sjr.1_Intron	NM_017781	NP_060251			cytochrome P450, family 2, subfamily W,						xenobiotic metabolic process	endoplasmic reticulum membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	1562234	1562234	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1562234delA								INTS1 (18216 upstream) : MAFK (8134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1566060	1566061	+	IGR	INS	-	GGA	GGA	rs137939492	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1566060_1566061insGGA								INTS1 (22042 upstream) : MAFK (4307 downstream)																																			---	---	---	---
ELFN1	392617	broad.mit.edu	37	7	1763538	1763538	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1763538delT	uc010ksg.2	+							NM_001128636	NP_001122108			extracellular leucine-rich repeat and												0																		---	---	---	---
MAD1L1	8379	broad.mit.edu	37	7	2177824	2177824	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2177824delT	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc010ksj.2_Intron	NM_001013836	NP_001013858			MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)														---	---	---	---
SNX8	29886	broad.mit.edu	37	7	2331246	2331248	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2331246_2331248delAAA	uc003slw.2	-							NM_013321	NP_037453			sorting nexin 8						cell communication|early endosome to Golgi transport|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)														---	---	---	---
C7orf27	221927	broad.mit.edu	37	7	2586809	2586809	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2586809delA	uc003smi.2	-						C7orf27_uc003smj.1_Intron	NM_152743	NP_689956			hypothetical protein LOC221927 precursor						response to ionizing radiation	nucleus	protein binding				0		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;2.91e-14)														---	---	---	---
GNA12	2768	broad.mit.edu	37	7	2853213	2853213	+	Intron	DEL	A	-	-	rs144292839	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2853213delA	uc003smu.2	-						GNA12_uc011jwb.1_Intron|GNA12_uc003smt.2_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	2926872	2926873	+	IGR	INS	-	A	A	rs141109174	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2926872_2926873insA								GNA12 (42913 upstream) : CARD11 (18896 downstream)																																	OREG0017842	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	3309476	3309477	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3309476_3309477delAG								CARD11 (225897 upstream) : SDK1 (31603 downstream)																																			---	---	---	---
SDK1	221935	broad.mit.edu	37	7	4068847	4068849	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4068847_4068849delTTT	uc003smx.2	+						SDK1_uc010kso.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)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	4304121	4304122	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4304121_4304122delCT	uc003smx.2	+						SDK1_uc010kso.2_Intron|SDK1_uc003smy.2_Intron|SDK1_uc003smz.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)														---	---	---	---
WIPI2	26100	broad.mit.edu	37	7	5244615	5244615	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5244615delT	uc003snv.2	+						WIPI2_uc003snw.2_Intron|WIPI2_uc003snx.2_Intron|WIPI2_uc003sny.2_Intron|WIPI2_uc010ksv.2_Intron	NM_015610	NP_056425			WD repeat domain, phosphoinositide interacting 2						autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)														---	---	---	---
TNRC18	84629	broad.mit.edu	37	7	5363200	5363200	+	Intron	DEL	T	-	-	rs68168751		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5363200delT	uc003soi.3	-							NM_001080495	NP_001073964			trinucleotide repeat containing 18								DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5780522	5780522	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5780522delT	uc003soy.1	-						RNF216_uc010ksz.1_Intron|RNF216_uc010kta.1_Intron|RNF216_uc011jwj.1_Intron|RNF216_uc003sox.1_Intron	NM_207116	NP_996999			ring finger protein 216 isoform b						apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)														---	---	---	---
USP42	84132	broad.mit.edu	37	7	6158172	6158172	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6158172delA	uc011jwo.1	+						USP42_uc011jwn.1_Intron|USP42_uc010kth.1_Intron|USP42_uc011jwp.1_Intron|USP42_uc011jwq.1_Intron|USP42_uc011jwr.1_Intron	NM_032172	NP_115548			ubiquitin specific peptidase 42						cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	6444074	6444075	+	IGR	DEL	AA	-	-	rs67922824		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6444074_6444075delAA								RAC1 (477 upstream) : DAGLB (4673 downstream)																																			---	---	---	---
DAGLB	221955	broad.mit.edu	37	7	6470059	6470059	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6470059delT	uc003sqa.2	-						DAGLB_uc011jwt.1_Intron|DAGLB_uc011jwu.1_Intron|DAGLB_uc003sqb.2_Intron|DAGLB_uc003sqc.2_Intron|DAGLB_uc011jwv.1_Intron|DAGLB_uc003sqd.3_Intron|DAGLB_uc011jww.1_Intron	NM_139179	NP_631918			diacylglycerol lipase, beta isoform 1						lipid catabolic process|platelet activation	integral to membrane|plasma membrane	acylglycerol lipase activity|metal ion binding|triglyceride lipase activity			ovary(2)|central_nervous_system(1)	3		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	6954621	6954621	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6954621delT								C7orf28B (88760 upstream) : C1GALT1 (267625 downstream)																																			---	---	---	---
C1GALT1	56913	broad.mit.edu	37	7	7248170	7248170	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7248170delA	uc010ktn.2	+						C1GALT1_uc010ktm.1_Intron	NM_020156	NP_064541			core 1 synthase,						angiogenesis|cell differentiation|kidney development	integral to membrane	glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity|metal ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (126;0.177)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	7359507	7359508	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7359507_7359508insA								C1GALT1 (75528 upstream) : COL28A1 (38736 downstream)																																			---	---	---	---
COL28A1	340267	broad.mit.edu	37	7	7469621	7469621	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7469621delT	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	7578372	7578372	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7578372delA	uc003src.1	-						COL28A1_uc011jxe.1_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)														---	---	---	---
RPA3	6119	broad.mit.edu	37	7	7713342	7713344	+	Intron	DEL	CTT	-	-	rs71010996		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7713342_7713344delCTT	uc003sri.2	-						uc011jxf.1_Intron	NM_002947	NP_002938			replication protein A3, 14kDa						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	cytoplasm|DNA replication factor A complex|nucleoplasm	protein binding|single-stranded DNA binding			large_intestine(1)	1		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.202)									Direct_reversal_of_damage|NER					---	---	---	---
GLCCI1	113263	broad.mit.edu	37	7	8043518	8043518	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8043518delT	uc003srk.2	+							NM_138426	NP_612435			glucocorticoid induced transcript 1												0		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)														---	---	---	---
GLCCI1	113263	broad.mit.edu	37	7	8110186	8110186	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8110186delT	uc003srk.2	+							NM_138426	NP_612435			glucocorticoid induced transcript 1												0		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)														---	---	---	---
NXPH1	30010	broad.mit.edu	37	7	8496126	8496126	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8496126delG	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)														---	---	---	---
NXPH1	30010	broad.mit.edu	37	7	8790526	8790526	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8790526delA	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	9258199	9258199	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9258199delA								NXPH1 (465607 upstream) : PER4 (415701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9770250	9770250	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9770250delT								PER4 (94803 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10179204	10179205	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10179204_10179205delTT								PER4 (503757 upstream) : NDUFA4 (793610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10221052	10221052	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10221052delA								PER4 (545605 upstream) : NDUFA4 (751763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10837672	10837672	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10837672delT								None (None upstream) : NDUFA4 (135143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10933031	10933032	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10933031_10933032delTC								None (None upstream) : NDUFA4 (39783 downstream)																																			---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11041667	11041667	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11041667delT	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)														---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11074738	11074738	+	Intron	DEL	A	-	-	rs34240680		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11074738delA	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)														---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11205744	11205744	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11205744delT	uc003srz.2	+						PHF14_uc011jxj.1_Intron|PHF14_uc003ssa.2_Intron	NM_001007157	NP_001007158			PHD finger protein 14 isoform 1								zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	11226850	11226851	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11226850_11226851insT								PHF14 (17609 upstream) : THSD7A (187322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	11397301	11397301	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11397301delG	uc003ssb.2	+											Homo sapiens cDNA clone IMAGE:4830466.																														---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11441364	11441364	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	12218321	12218321	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12218321delA								THSD7A (346497 upstream) : TMEM106B (32527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	12546630	12546630	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12546630delA								VWDE (102778 upstream) : SCIN (49557 downstream)																																			---	---	---	---
SCIN	85477	broad.mit.edu	37	7	12667658	12667663	+	Intron	DEL	GTGTGT	-	-	rs66633095		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12667658_12667663delGTGTGT	uc003ssn.3	+						SCIN_uc010ktt.2_Intron|SCIN_uc003sso.3_Intron	NM_001112706	NP_001106177			scinderin isoform 1						actin filament capping|actin filament severing|actin nucleation|calcium ion-dependent exocytosis|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of megakaryocyte differentiation|positive regulation of secretion|regulation of chondrocyte differentiation	cell cortex|cytoskeleton	1-phosphatidylinositol binding|actin filament binding|calcium ion binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	13391437	13391437	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13391437delA								ARL4A (660881 upstream) : ETV1 (539421 downstream)																																			---	---	---	---
ETV1	2115	broad.mit.edu	37	7	14027675	14027675	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	14105297	14105298	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14105297_14105298insT								ETV1 (74247 upstream) : DGKB (79377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	14109097	14109097	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14109097delA								ETV1 (78047 upstream) : DGKB (75578 downstream)																																			---	---	---	---
DGKB	1607	broad.mit.edu	37	7	14421914	14421914	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14421914delA	uc003ssz.2	-						DGKB_uc011jxt.1_Intron|DGKB_uc003sta.2_Intron|DGKB_uc011jxu.1_Intron	NM_004080	NP_004071			diacylglycerol kinase, beta isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	15622931	15622931	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15622931delT								TMEM195 (21291 upstream) : MEOX2 (27908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	15869321	15869321	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15869321delA								MEOX2 (143013 upstream) : ISPD (257831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	16620935	16620936	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16620935_16620936insT								SOSTDC1 (50730 upstream) : ANKMY2 (18477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	16772117	16772120	+	IGR	DEL	CCTC	-	-	rs1626439		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16772117_16772120delCCTC								BZW2 (25969 upstream) : TSPAN13 (21231 downstream)																																			---	---	---	---
AGR3	155465	broad.mit.edu	37	7	16905487	16905487	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16905487delT	uc003sts.2	-							NM_176813	NP_789783			breast cancer membrane protein 11 precursor							extracellular region					0	Lung NSC(10;0.0376)|all_lung(11;0.0721)|all_epithelial(12;0.202)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	17228287	17228288	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17228287_17228288delTT								AGR3 (306674 upstream) : AHR (109988 downstream)																																			---	---	---	---
AHR	196	broad.mit.edu	37	7	17374493	17374493	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17374493delT	uc011jxz.1	+						AHR_uc003stt.3_Intron	NM_001621	NP_001612			aryl hydrocarbon receptor precursor						apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)																	---	---	---	---
AHR	196	broad.mit.edu	37	7	17374829	17374829	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17374829delA	uc011jxz.1	+						AHR_uc003stt.3_Intron	NM_001621	NP_001612			aryl hydrocarbon receptor precursor						apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	17687319	17687319	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17687319delA								AHR (301544 upstream) : SNX13 (143067 downstream)																																			---	---	---	---
SNX13	23161	broad.mit.edu	37	7	17855827	17855827	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17855827delT	uc003stw.1	-	19	2177	c.1964delA	c.(1963-1965)AAGfs	p.K655fs	SNX13_uc003stv.2_Frame_Shift_Del_p.K644fs|SNX13_uc010kuc.2_Frame_Shift_Del_p.K441fs|SNX13_uc010kub.2_Frame_Shift_Del_p.K50fs			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;	655	PX.				cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)																	---	---	---	---
SNX13	23161	broad.mit.edu	37	7	17953829	17953829	+	Intron	DEL	A	-	-	rs141714375		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17953829delA	uc003stw.1	-						SNX13_uc003stv.2_Intron|SNX13_uc010kuc.2_Intron|SNX13_uc003stx.1_Intron|SNX13_uc003sty.2_Intron					SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;						cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)																	---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18389113	18389113	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18389113delG	uc003sua.1	+						HDAC9_uc011jya.1_Intron	NM_014707	NP_055522			histone deacetylase 9 isoform 3						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	19147013	19147013	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19147013delT								HDAC9 (110029 upstream) : TWIST1 (8080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	19426738	19426738	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19426738delT								FERD3L (241694 upstream) : TWISTNB (308347 downstream)																																			---	---	---	---
MACC1	346389	broad.mit.edu	37	7	20178175	20178175	+	3'UTR	DEL	C	-	-	rs112585387		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20178175delC	uc003sus.3	-	7					MACC1_uc010kug.2_3'UTR	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	20808626	20808626	+	IGR	DEL	G	-	-	rs59683536	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20808626delG								ABCB5 (11990 upstream) : SP8 (13269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20880807	20880807	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20880807delT								RPL23P8 (13368 upstream) : SP4 (586882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20884648	20884648	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20884648delT								RPL23P8 (17209 upstream) : SP4 (583041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20954298	20954298	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20954298delA								RPL23P8 (86859 upstream) : SP4 (513391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	21228919	21228921	+	IGR	DEL	TCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21228919_21228921delTCT								RPL23P8 (361480 upstream) : SP4 (238768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	21563134	21563135	+	IGR	INS	-	TC	TC	rs112796756		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21563134_21563135insTC								SP4 (8985 upstream) : DNAH11 (19698 downstream)																																			---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21721381	21721382	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21721381_21721382insT	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				---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22259366	22259366	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22259366delA	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	22632294	22632294	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22632294delA								MGC87042 (92496 upstream) : IL6 (133209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	22887598	22887598	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22887598delT								TOMM7 (25177 upstream) : SNORD93 (8634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	22906680	22906681	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22906680_22906681insA								SNORD93 (10376 upstream) : FAM126A (74206 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	22959801	22959801	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22959801delA								SNORD93 (63497 upstream) : FAM126A (21086 downstream)																																			---	---	---	---
KLHL7	55975	broad.mit.edu	37	7	23155171	23155171	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23155171delT	uc003svs.3	+						KLHL7_uc003svr.3_Intron|KLHL7_uc011jys.1_Intron|KLHL7_uc011jyt.1_Intron|KLHL7_uc003svt.2_Intron|KLHL7_uc003svp.2_Intron|KLHL7_uc003svq.2_Intron|KLHL7_uc011jyu.1_Intron	NM_001031710	NP_001026880			kelch-like 7 isoform 1							Golgi apparatus|nucleolus|plasma membrane					0																		---	---	---	---
IGF2BP3	10643	broad.mit.edu	37	7	23422012	23422013	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23422012_23422013delTT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	23541792	23541792	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23541792delT								RPS2P32 (10763 upstream) : TRA2A (2610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	23579170	23579171	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23579170_23579171insT								TRA2A (7514 upstream) : CLK2P (45164 downstream)																																			---	---	---	---
STK31	56164	broad.mit.edu	37	7	23883299	23883300	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23883299_23883300delTC	uc003swv.1	+											SubName: Full=Putative uncharacterized protein STK31;								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	24819186	24819186	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24819186delA								DFNA5 (21547 upstream) : OSBPL3 (16979 downstream)																																			---	---	---	---
C7orf31	136895	broad.mit.edu	37	7	25200833	25200833	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25200833delT	uc003sxn.1	-	4	919	c.358delA	c.(358-360)AGTfs	p.S120fs	C7orf31_uc003sxm.1_5'Flank	NM_138811	NP_620166	Q8N865	CG031_HUMAN	hypothetical protein LOC136895	120											0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	25862643	25862644	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25862643_25862644delAA								NPVF (594538 upstream) : MIR148A (126895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25925031	25925031	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25925031delT								NPVF (656926 upstream) : MIR148A (64508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	26092727	26092727	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26092727delA								MIR148A (103121 upstream) : NFE2L3 (99120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	26105098	26105098	+	IGR	DEL	A	-	-	rs34645000		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26105098delA								MIR148A (115492 upstream) : NFE2L3 (86749 downstream)																																			---	---	---	---
HNRNPA2B1	3181	broad.mit.edu	37	7	26231982	26231982	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26231982delA	uc003sxr.3	-						HNRNPA2B1_uc003sxs.3_Intron	NM_031243	NP_112533			heterogeneous nuclear ribonucleoprotein A2/B1						RNA transport	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	nucleotide binding|protein binding|protein binding|RNA binding|single-stranded telomeric DNA binding			ovary(1)|central_nervous_system(1)|skin(1)	3								T	ETV1	prostate								---	---	---	---
SNX10	29887	broad.mit.edu	37	7	26352404	26352404	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26352404delA	uc003sxx.2	+						SNX10_uc011jzg.1_Intron|SNX10_uc010kuu.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	26551344	26551344	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26551344delT								LOC441204 (12750 upstream) : KIAA0087 (21396 downstream)																																			---	---	---	---
SKAP2	8935	broad.mit.edu	37	7	26764976	26764977	+	Intron	INS	-	AC	AC	rs112271894		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26764976_26764977insAC	uc003syc.2	-						SKAP2_uc011jzi.1_Intron|SKAP2_uc011jzj.1_Intron	NM_003930	NP_003921			src kinase associated phosphoprotein 2						B cell activation|cell junction assembly|protein complex assembly|signal transduction	cytosol|plasma membrane	SH3/SH2 adaptor activity			pancreas(1)	1																		---	---	---	---
SKAP2	8935	broad.mit.edu	37	7	26809225	26809226	+	Intron	INS	-	T	T	rs144178232	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26809225_26809226insT	uc003syc.2	-						SKAP2_uc011jzi.1_Intron|SKAP2_uc011jzj.1_Intron	NM_003930	NP_003921			src kinase associated phosphoprotein 2						B cell activation|cell junction assembly|protein complex assembly|signal transduction	cytosol|plasma membrane	SH3/SH2 adaptor activity			pancreas(1)	1																		---	---	---	---
SKAP2	8935	broad.mit.edu	37	7	26970061	26970061	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26970061delA	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	27508422	27508422	+	IGR	DEL	C	-	-	rs75998598		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27508422delC								EVX1 (222230 upstream) : HIBADH (56641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	27725508	27725509	+	IGR	INS	-	A	A	rs149368944	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27725508_27725509insA								HIBADH (22906 upstream) : TAX1BP1 (53483 downstream)																																			---	---	---	---
TAX1BP1	8887	broad.mit.edu	37	7	27779288	27779288	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27779288delA	uc003szl.2	+						TAX1BP1_uc011jzo.1_Intron|TAX1BP1_uc003szk.2_5'Flank|TAX1BP1_uc011jzp.1_5'Flank	NM_006024	NP_006015			Tax1 (human T-cell leukemia virus type I)						anti-apoptosis|apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production	cytosol	identical protein binding|kinase binding|zinc ion binding			breast(1)	1			GBM - Glioblastoma multiforme(3;0.0823)															---	---	---	---
JAZF1	221895	broad.mit.edu	37	7	27958445	27958445	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27958445delA	uc003szn.2	-						JAZF1_uc003szm.2_Intron	NM_175061	NP_778231			JAZF zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcriptional repressor complex	nucleic acid binding|transcription corepressor activity|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131								T	SUZ12	endometrial stromal tumours								---	---	---	---
JAZF1	221895	broad.mit.edu	37	7	28037363	28037364	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28037363_28037364delTT	uc003szn.2	-							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	28346166	28346167	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28346166_28346167delTT	uc003szo.2	+							NM_182899	NP_878902			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																		---	---	---	---
CREB5	9586	broad.mit.edu	37	7	28655498	28655498	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28655498delC	uc003szq.2	+						CREB5_uc003szo.2_Intron|CREB5_uc003szr.2_Intron	NM_182898	NP_878901			cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2																		---	---	---	---
CREB5	9586	broad.mit.edu	37	7	28858716	28858716	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28858716delT	uc003szq.2	+						CREB5_uc003szo.2_Intron|CREB5_uc003szr.2_Intron|CREB5_uc003szs.2_Intron	NM_182898	NP_878901			cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2																		---	---	---	---
CHN2	1124	broad.mit.edu	37	7	29337029	29337030	+	Intron	INS	-	G	G	rs139936888	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29337029_29337030insG	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	30262040	30262040	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30262040delA								C7orf41 (59659 upstream) : ZNRF2 (61883 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	30266771	30266771	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30266771delT								C7orf41 (64390 upstream) : ZNRF2 (57152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	30297092	30297093	+	IGR	DEL	TT	-	-	rs111477156		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30297092_30297093delTT								C7orf41 (94711 upstream) : ZNRF2 (26830 downstream)																																			---	---	---	---
NOD1	10392	broad.mit.edu	37	7	30508990	30508991	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30508990_30508991delCT	uc003tav.2	-						NOD1_uc010kvs.2_Intron|NOD1_uc003tax.2_Intron|NOD1_uc003tay.2_Intron|NOD1_uc010kvt.2_Intron|NOD1_uc010kvu.2_Intron	NM_006092	NP_006083			nucleotide-binding oligomerization domain						activation of MAPK activity|detection of bacterium|induction of apoptosis|inflammatory response|innate immune response|interleukin-8 biosynthetic process|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of dendritic cell antigen processing and presentation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	basolateral plasma membrane|cytosol	ATP binding|CARD domain binding|caspase activator activity|peptidoglycan binding|protein homodimerization activity			ovary(1)|skin(1)	2																OREG0017938	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM188B	84182	broad.mit.edu	37	7	30921989	30921990	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30921989_30921990insC	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron|AQP1_uc011kac.1_Intron|FAM188B_uc003tbu.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-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31165192delT								ADCYAP1R1 (18881 upstream) : NEUROD6 (211890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	32513049	32513050	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32513049_32513050delTT								PDE1C (174108 upstream) : LSM5 (11895 downstream)																																			---	---	---	---
LSM5	23658	broad.mit.edu	37	7	32526806	32526806	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32526806delA	uc003tct.2	-	5					LSM5_uc003tcu.2_RNA|LSM5_uc011kag.1_3'UTR|LSM5_uc011kah.1_3'UTR	NM_012322	NP_036454			LSM5 homolog, U6 small nuclear RNA associated						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|mRNA processing|RNA splicing	cytosol|nucleus|ribonucleoprotein complex	protein binding|RNA binding				0			GBM - Glioblastoma multiforme(11;0.152)															---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32594260	32594260	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	32706313	32706313	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32706313delA	uc011kai.1	+						uc003tcw.2_Intron	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32838075	32838076	+	Intron	INS	-	CT	CT	rs139791666	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32838075_32838076insCT	uc011kai.1	+							NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	33066270	33066272	+	Intron	DEL	TTT	-	-	rs34317509		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33066270_33066272delTTT	uc011kai.1	+						NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	33076071	33076073	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33076071_33076073delTTT	uc011kai.1	+						NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron|uc003tdl.1_RNA	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
BMPER	168667	broad.mit.edu	37	7	34060471	34060472	+	Intron	INS	-	AC	AC	rs150421476	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34060471_34060472insAC	uc011kap.1	+							NM_133468	NP_597725			BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
BMPER	168667	broad.mit.edu	37	7	34070240	34070240	+	Intron	DEL	T	-	-	rs72361944		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34070240delT	uc011kap.1	+							NM_133468	NP_597725			BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
BMPER	168667	broad.mit.edu	37	7	34118338	34118338	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34118338delT	uc011kap.1	+							NM_133468	NP_597725			BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
DPY19L2P1	554236	broad.mit.edu	37	7	35223145	35223146	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35223145_35223146delAA	uc003teq.1	-											RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	35514773	35514773	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35514773delT								TBX20 (221531 upstream) : HERPUD2 (157499 downstream)																																			---	---	---	---
KIAA0895	23366	broad.mit.edu	37	7	36421280	36421282	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36421280_36421282delAAA	uc003tfd.2	-							NM_001100425	NP_001093895			hypothetical protein LOC23366 isoform 1												0																		---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37128962	37128963	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37128962_37128963insA	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																		---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37444822	37444822	+	Intron	DEL	A	-	-	rs34397484		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37444822delA	uc003tfk.1	-						ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615			engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	37753637	37753637	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37753637delT	uc003tfl.2	+											Homo sapiens, clone IMAGE:3881224, mRNA.																														---	---	---	---
VPS41	27072	broad.mit.edu	37	7	38782964	38782964	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38782964delA	uc003tgy.2	-						VPS41_uc003tgz.2_Intron|VPS41_uc010kxn.2_Intron|VPS41_uc003tgx.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	39125421	39125421	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39125421delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	39967576	39967577	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39967576_39967577delAA								LOC349114 (133355 upstream) : CDK13 (22382 downstream)																																			---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40303503	40303503	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40303503delT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004			dermal papilla derived protein 13								transferase activity			ovary(2)	2																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40627503	40627506	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40627503_40627506delTTTT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004			dermal papilla derived protein 13								transferase activity			ovary(2)	2																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40783248	40783248	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40783248delT	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	40930717	40930717	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40930717delA								C7orf10 (30360 upstream) : INHBA (797886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41081575	41081576	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41081575_41081576insA								C7orf10 (181218 upstream) : INHBA (647027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41416161	41416161	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41416161delT								C7orf10 (515804 upstream) : INHBA (312442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41833308	41833309	+	IGR	INS	-	AG	AG	rs150614671	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41833308_41833309insAG								LOC285954 (14334 upstream) : GLI3 (167241 downstream)																																			---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42194097	42194097	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42194097delT	uc011kbh.1	-						GLI3_uc011kbg.1_5'Flank	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	42337377	42337378	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42337377_42337378delTG								GLI3 (60759 upstream) : C7orf25 (611496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	42863086	42863086	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42863086delT								GLI3 (586468 upstream) : C7orf25 (85788 downstream)																																			---	---	---	---
C7orf25	79020	broad.mit.edu	37	7	42966271	42966271	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42966271delA	uc010kxr.2	-						PSMA2_uc003thy.2_Intron|PSMA2_uc010kxt.2_Intron|PSMA2_uc003thz.1_Intron	NM_001099858	NP_001093328			hypothetical protein LOC79020 a											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	43005509	43005509	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43005509delT								MRPL32 (28058 upstream) : HECW1 (146689 downstream)																																			---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43486768	43486768	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43486768delT	uc003tid.1	+						HECW1_uc011kbi.1_Intron	NM_015052	NP_055867			NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43555856	43555856	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43555856delA	uc003tid.1	+						HECW1_uc011kbi.1_Intron|uc003tig.1_Intron	NM_015052	NP_055867			NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
C7orf44	55744	broad.mit.edu	37	7	43733422	43733423	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43733422_43733423insA	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																		---	---	---	---
POLR2J4	84820	broad.mit.edu	37	7	44059544	44059547	+	5'Flank	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44059544_44059547delTTTT	uc010kxw.2	-						POLR2J4_uc003tjc.2_5'Flank|POLR2J4_uc003tjd.2_5'Flank|POLR2J4_uc003tje.3_5'Flank|POLR2J4_uc003tjh.2_5'Flank					SubName: Full=cDNA FLJ58900, weakly similar to Uroplakin-3B;												0																		---	---	---	---
RASA4P	401331	broad.mit.edu	37	7	44073497	44073500	+	Intron	DEL	AAAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44073497_44073500delAAAG	uc011kbk.1	-						RASA4P_uc003tji.2_RNA|RASA4P_uc010kxx.2_Intron	NM_006989	NP_008920			RAS p21 protein activator 4 isoform 1												0																		---	---	---	---
RASA4P	401331	broad.mit.edu	37	7	44075093	44075094	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44075093_44075094delTT	uc011kbk.1	-						RASA4P_uc003tji.2_Intron|RASA4P_uc010kxx.2_Intron	NM_006989	NP_008920			RAS p21 protein activator 4 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	44140754	44140754	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44140754delT								POLM (18625 upstream) : AEBP1 (3206 downstream)																																			---	---	---	---
MYL7	58498	broad.mit.edu	37	7	44178494	44178494	+	3'UTR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44178494delC	uc003tkg.2	-	7						NM_021223	NP_067046			myosin light chain 2a						actin filament-based movement|smooth muscle contraction	A band|myosin complex	ATPase activity, coupled|calcium ion binding|microfilament motor activity				0																		---	---	---	---
GCK	2645	broad.mit.edu	37	7	44189559	44189559	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44189559delC	uc003tkl.2	-						GCK_uc003tkj.1_Intron|GCK_uc003tkk.1_Intron	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																		---	---	---	---
GCK	2645	broad.mit.edu	37	7	44206135	44206135	+	Intron	DEL	A	-	-	rs75857400		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44206135delA	uc003tkl.2	-							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	44268676	44268676	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44268676delC	uc003tkq.2	-						CAMK2B_uc003tkp.2_Intron|CAMK2B_uc003tkx.2_Intron|CAMK2B_uc010kyd.2_Intron|CAMK2B_uc003tkr.2_Intron|CAMK2B_uc003tks.2_Intron|CAMK2B_uc003tku.2_Intron|CAMK2B_uc003tkv.2_Intron|CAMK2B_uc003tkt.2_Intron|CAMK2B_uc003tkw.2_Intron|CAMK2B_uc010kyc.2_Intron|CAMK2B_uc003tkn.2_Frame_Shift_Del_p.G29fs	NM_001220	NP_001211			calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|synaptic transmission	cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	44634616	44634617	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44634616_44634617delAA								TMED4 (12789 upstream) : OGDH (11554 downstream)																																			---	---	---	---
OGDH	4967	broad.mit.edu	37	7	44747227	44747228	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44747227_44747228insC	uc003tln.2	+	22	2952_2953	c.2843_2844insC	c.(2842-2844)TACfs	p.Y948fs	OGDH_uc011kbx.1_Frame_Shift_Ins_p.Y944fs|OGDH_uc011kby.1_Frame_Shift_Ins_p.Y798fs|OGDH_uc003tlp.2_Frame_Shift_Ins_p.Y959fs|OGDH_uc011kbz.1_Frame_Shift_Ins_p.Y743fs	NM_002541	NP_002532	Q02218	ODO1_HUMAN	oxoglutarate dehydrogenase isoform 1 precursor	948					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)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	44772007	44772007	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44772007delA								OGDH (23339 upstream) : ZMIZ2 (16173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	44823830	44823832	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44823830_44823832delAAA								ZMIZ2 (13097 upstream) : PPIA (12409 downstream)																																			---	---	---	---
CCM2	83605	broad.mit.edu	37	7	45059192	45059192	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45059192delT	uc003tmo.2	+						CCM2_uc003tmn.2_Intron|CCM2_uc003tmp.2_Intron|CCM2_uc003tmq.2_Intron|CCM2_uc003tmr.2_Intron	NM_031443	NP_113631			cerebral cavernous malformation 2 isoform 2						endothelial tube morphogenesis|integrin-mediated signaling pathway|stress-activated MAPK cascade|vasculogenesis	cytoplasm	protein binding				0														Familial_Cerebral_Cavernous_Angioma				---	---	---	---
Unknown	0	broad.mit.edu	37	7	45473392	45473392	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45473392delT								RAMP3 (249545 upstream) : ADCY1 (140347 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	45610265	45610265	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45610265delA								RAMP3 (386418 upstream) : ADCY1 (3474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46108284	46108284	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46108284delT								IGFBP3 (147413 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46150454	46150454	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46150454delA								IGFBP3 (189583 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46984705	46984706	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46984705_46984706delGT								None (None upstream) : TNS3 (330047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	47133640	47133642	+	IGR	DEL	AAA	-	-	rs138442829		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47133640_47133642delAAA								None (None upstream) : TNS3 (181111 downstream)																																			---	---	---	---
TNS3	64759	broad.mit.edu	37	7	47545605	47545605	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47545605delA	uc003tnv.2	-						TNS3_uc003tnw.2_Intron|TNS3_uc010kyo.1_Intron	NM_022748	NP_073585			tensin 3							focal adhesion	protein binding			ovary(4)	4																		---	---	---	---
SUN3	256979	broad.mit.edu	37	7	48045448	48045448	+	Intron	DEL	C	-	-	rs66650652		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48045448delC	uc003tof.2	-						SUN3_uc010kyq.2_Intron|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																		---	---	---	---
SUN3	256979	broad.mit.edu	37	7	48045524	48045524	+	Intron	DEL	T	-	-	rs80067951		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48045524delT	uc003tof.2	-						SUN3_uc010kyq.2_Intron|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																		---	---	---	---
C7orf57	136288	broad.mit.edu	37	7	48076529	48076530	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48076529_48076530delTT	uc003toh.3	+						C7orf57_uc003toi.3_Intron	NM_001100159	NP_001093629			hypothetical protein LOC136288											ovary(1)	1																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48549649	48549650	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48549649_48549650insC	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc010kyt.1_Intron|ABCA13_uc010kyu.1_Intron	NM_152701	NP_689914			ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48571102	48571102	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48571102delT	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc010kyt.1_Intron|ABCA13_uc010kyu.1_Intron	NM_152701	NP_689914			ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	48730675	48730676	+	IGR	INS	-	A	A	rs74960749		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48730675_48730676insA								ABCA13 (43584 upstream) : CDC14C (233481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	48763433	48763433	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48763433delT								ABCA13 (76342 upstream) : CDC14C (200724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	48978208	48978209	+	IGR	DEL	AA	-	-	rs72343823		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48978208_48978209delAA								CDC14C (11159 upstream) : VWC2 (835048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49068826	49068827	+	IGR	INS	-	T	T	rs142725748	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49068826_49068827insT								CDC14C (101777 upstream) : VWC2 (744430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49382159	49382160	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49382159_49382160insG								CDC14C (415110 upstream) : VWC2 (431097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49392097	49392097	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49392097delT								CDC14C (425048 upstream) : VWC2 (421160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49481075	49481075	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49481075delA								CDC14C (514026 upstream) : VWC2 (332182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49537665	49537665	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49537665delT								CDC14C (570616 upstream) : VWC2 (275592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49658961	49658962	+	IGR	INS	-	A	A	rs112400429		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49658961_49658962insA								CDC14C (691912 upstream) : VWC2 (154295 downstream)																																			---	---	---	---
ZPBP	11055	broad.mit.edu	37	7	50118581	50118581	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50118581delA	uc003tou.2	-						ZPBP_uc011kci.1_Intron|ZPBP_uc010kyw.2_Intron	NM_007009	NP_008940			zona pellucida binding protein isoform 1						binding of sperm to zona pellucida	extracellular region					0	Glioma(55;0.08)|all_neural(89;0.245)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	50246730	50246730	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50246730delC								C7orf72 (47372 upstream) : IKZF1 (97648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	51584819	51584819	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51584819delT								COBL (200304 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53536727	53536728	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53536727_53536728insA								POM121L12 (432110 upstream) : HPVC1 (732189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53589321	53589322	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53589321_53589322delAA								POM121L12 (484704 upstream) : HPVC1 (679595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53648167	53648168	+	IGR	DEL	AA	-	-	rs73699155	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53648167_53648168delAA								POM121L12 (543550 upstream) : HPVC1 (620749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53700300	53700301	+	IGR	DEL	GT	-	-	rs35837560		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53700300_53700301delGT								POM121L12 (595683 upstream) : HPVC1 (568616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53779452	53779453	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53779452_53779453delTG								POM121L12 (674835 upstream) : HPVC1 (489464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54739796	54739796	+	IGR	DEL	T	-	-	rs34057564		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54739796delT								VSTM2A (101609 upstream) : SEC61G (80145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54753381	54753381	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54753381delA								VSTM2A (115194 upstream) : SEC61G (66560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54962546	54962547	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54962546_54962547delAA								SEC61G (135607 upstream) : EGFR (124178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	55512962	55512965	+	IGR	DEL	ACAC	-	-	rs71913764		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55512962_55512965delACAC								LANCL2 (11529 upstream) : VOPP1 (25342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	55714741	55714741	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55714741delT								LOC442308 (99 upstream) : FKBP9L (34027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56603689	56603689	+	RNA	DEL	A	-	-	rs35527313		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56603689delA	uc003tsi.1	-	2		c.975delT								Homo sapiens cDNA clone IMAGE:5266012.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	56780676	56780677	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56780676_56780677delAA								DKFZp434L192 (215699 upstream) : ZNF479 (406651 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56959443	56959443	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56959443delT								DKFZp434L192 (394466 upstream) : ZNF479 (227885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56994475	56994475	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56994475delA								DKFZp434L192 (429498 upstream) : ZNF479 (192853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57370756	57370756	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57370756delA								ZNF479 (163185 upstream) : ZNF716 (139127 downstream)																																			---	---	---	---
ZNF716	441234	broad.mit.edu	37	7	57516441	57516441	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57516441delA	uc011kdi.1	+							NM_001159279	NP_001152751			zinc finger protein 716											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	57607440	57607440	+	IGR	DEL	T	-	-	rs148385056		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57607440delT								ZNF716 (74175 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57669993	57669994	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57669993_57669994insG								ZNF716 (136728 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57670485	57670485	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57670485delT								ZNF716 (137220 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57824900	57824900	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57824900delT								ZNF716 (291635 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61064901	61064901	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61064901delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61788480	61788480	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61788480delA								None (None upstream) : LOC643955 (963192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61998089	61998089	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61998089delA								None (None upstream) : LOC643955 (753583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62294150	62294151	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62294150_62294151insA								None (None upstream) : LOC643955 (457521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63189798	63189798	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63189798delT								LOC100287704 (377647 upstream) : ZNF727 (316023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63465979	63465980	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63465979_63465980insT								LOC100287704 (653828 upstream) : ZNF727 (39841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63466581	63466581	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63466581delT								LOC100287704 (654430 upstream) : ZNF727 (39240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63811056	63811057	+	5'Flank	DEL	TT	-	-	rs35939888		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63811056_63811057delTT	uc003tsz.2	+											Homo sapiens cDNA FLJ41146 fis, clone BRACE2036900.																														---	---	---	---
ZNF680	340252	broad.mit.edu	37	7	63988075	63988076	+	Intron	DEL	AA	-	-	rs75049582		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63988075_63988076delAA	uc003tta.2	-						ZNF680_uc010kzr.2_Intron|ZNF680_uc003ttb.2_Intron	NM_178558	NP_848653			zinc finger protein 680 isoform 1						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)																---	---	---	---
INTS4L1	285905	broad.mit.edu	37	7	64643831	64643831	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64643831delT	uc003ttw.2	+							NR_027393				Homo sapiens cDNA FLJ25037 fis, clone CBL03066.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	64906890	64906890	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64906890delT								ZNF92 (40893 upstream) : INTS4L2 (205887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65222951	65222951	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65222951delT	uc003tud.1	-						CCT6P1_uc003tug.2_Intron|CCT6P1_uc003tuh.2_Intron|CCT6P1_uc003tui.2_Intron|uc003tuk.1_5'Flank					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	65226819	65226819	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65226819delA	uc003tud.1	-						CCT6P1_uc003tug.2_Intron|CCT6P1_uc003tuh.2_Intron|CCT6P1_uc003tui.2_Intron					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	65249357	65249357	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65249357delT								CCT6P1 (20696 upstream) : VKORC1L1 (88900 downstream)																																			---	---	---	---
VKORC1L1	154807	broad.mit.edu	37	7	65410252	65410252	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65410252delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	65658566	65658569	+	IGR	DEL	CCTT	-	-	rs72301535		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65658566_65658569delCCTT								CRCP (39015 upstream) : TPST1 (11690 downstream)																																			---	---	---	---
TPST1	8460	broad.mit.edu	37	7	65732626	65732626	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65732626delT	uc003tuw.2	+						TPST1_uc010kzy.2_Intron|TPST1_uc010kzz.2_Intron|TPST1_uc010laa.2_Intron	NM_003596	NP_003587			tyrosylprotein sulfotransferase 1						inflammatory response|peptidyl-tyrosine sulfation	Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	65888988	65888988	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65888988delT								NCRNA00174 (23593 upstream) : LOC493754 (104458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65948360	65948362	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65948360_65948362delAAA								NCRNA00174 (82965 upstream) : LOC493754 (45084 downstream)																																			---	---	---	---
LOC493754	493754	broad.mit.edu	37	7	66006617	66006619	+	Intron	DEL	GGA	-	-	rs10600835		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66006617_66006619delGGA	uc010lac.1	-						LOC493754_uc010lad.2_Intron					Homo sapiens cDNA FLJ14309 fis, clone PLACE3000221.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	66071681	66071681	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66071681delT								LOC493754 (14318 upstream) : RABGEF1 (22209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	66072148	66072149	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66072148_66072149insT								LOC493754 (14785 upstream) : RABGEF1 (21741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	66350658	66350660	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66350658_66350660delTTT								LOC729156 (40845 upstream) : C7orf42 (35543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	66374910	66374910	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66374910delT								LOC729156 (65097 upstream) : C7orf42 (11293 downstream)																																			---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66515897	66515897	+	Intron	DEL	C	-	-	rs78538670		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66515897delC	uc003tvn.2	+						TYW1_uc010lai.2_Intron	NM_018264	NP_060734			radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66645989	66645989	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66645989delT	uc003tvn.2	+						TYW1_uc010lai.2_Intron|TYW1_uc011kef.1_Intron	NM_018264	NP_060734			radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66654389	66654390	+	Intron	INS	-	ATGT	ATGT	rs148656033	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66654389_66654390insATGT	uc003tvn.2	+						TYW1_uc010lai.2_Intron|TYW1_uc011kef.1_Intron	NM_018264	NP_060734			radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	67462704	67462711	+	IGR	DEL	CCTCCCTC	-	-	rs4992376	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67462704_67462711delCCTCCCTC								STAG3L4 (676192 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67546341	67546343	+	IGR	DEL	TTT	-	-	rs111338627		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67546341_67546343delTTT								STAG3L4 (759829 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68268329	68268329	+	IGR	DEL	G	-	-	rs71910280		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68268329delG								None (None upstream) : AUTS2 (795576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68439299	68439299	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68439299delA								None (None upstream) : AUTS2 (624606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68599744	68599744	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68599744delC								None (None upstream) : AUTS2 (464161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68695165	68695165	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68695165delT								None (None upstream) : AUTS2 (368740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68838035	68838036	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68838035_68838036insT								None (None upstream) : AUTS2 (225869 downstream)																																			---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69327537	69327537	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69327537delT	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	69583232	69583239	+	Intron	DEL	AAAAAAAA	-	-	rs11418386		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69583232_69583239delAAAAAAAA	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	69933768	69933768	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69933768delT	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	70053658	70053658	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70053658delT	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	70319664	70319664	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70319664delA								AUTS2 (61780 upstream) : WBSCR17 (278125 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	70335287	70335287	+	IGR	DEL	T	-	-	rs80119664		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70335287delT								AUTS2 (77403 upstream) : WBSCR17 (262502 downstream)																																			---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	70615317	70615317	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70615317delT	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	70743916	70743916	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70743916delT	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	70891912	70891912	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70891912delA	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	71085817	71085817	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71085817delT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	71190374	71190375	+	IGR	INS	-	GTGTGT	GTGTGT	rs149439676	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71190374_71190375insGTGTGT								WBSCR17 (11791 upstream) : CALN1 (54102 downstream)																																			---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71306990	71306990	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71306990delA	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	71390866	71390867	+	Intron	DEL	TC	-	-	rs34885230		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71390866_71390867delTC	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	71691870	71691870	+	Intron	DEL	C	-	-	rs512843	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71691870delC	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	71701955	71701955	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71701955delT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	72790241	72790241	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72790241delG								FKBP6 (17600 upstream) : FZD9 (57868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	72820483	72820483	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72820483delT								FKBP6 (47842 upstream) : FZD9 (27626 downstream)																																			---	---	---	---
BAZ1B	9031	broad.mit.edu	37	7	72879694	72879694	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72879694delA	uc003tyc.2	-							NM_032408	NP_115784			bromodomain adjacent to zinc finger domain, 1B						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	72943848	72943848	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72943848delT								BAZ1B (7240 upstream) : BCL7B (6838 downstream)																																			---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73236159	73236159	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73236159delG	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																		---	---	---	---
WBSCR27	155368	broad.mit.edu	37	7	73254463	73254463	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73254463delG	uc003tzj.2	-						RFC2_uc011kfa.1_Intron|WBSCR27_uc011kfd.1_Intron	NM_152559	NP_689772			Williams-Beuren syndrome chromosome region 27											central_nervous_system(1)	1		Lung NSC(55;0.159)																---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73263099	73263105	+	Intron	DEL	TTTCTTT	-	-	rs72187633		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73263099_73263105delTTTCTTT	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	73291830	73291830	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73291830delT	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	73322569	73322569	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73322569delC	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	73612643	73612643	+	Intron	DEL	T	-	-	rs146566987	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73612643delT	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																		---	---	---	---
CLIP2	7461	broad.mit.edu	37	7	73757365	73757366	+	Intron	DEL	AA	-	-	rs71675497		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73757365_73757366delAA	uc003uam.2	+						CLIP2_uc003uan.2_Intron	NM_003388	NP_003379			CAP-GLY domain containing linker protein 2							microtubule associated complex				skin(3)	3																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73951743	73951744	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73951743_73951744delAA	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73962939	73962939	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73962939delT	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	74004033	74004036	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74004033_74004036delAAAA	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																		---	---	---	---
GTF2IP1	2970	broad.mit.edu	37	7	74776113	74776113	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74776113delA	uc003ubw.2	-						uc003ubz.1_Intron|PMS2L2_uc011kfp.1_Intron|PMS2L2_uc011kfq.1_Intron|uc003ucd.2_Intron|uc010lck.2_Intron					SubName: Full=cDNA FLJ61347, highly similar to General transcription factor II-I;												0																		---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75186655	75186655	+	Intron	DEL	C	-	-	rs75626925		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75186655delC	uc003uds.1	-						HIP1_uc011kfz.1_Intron	NM_005338	NP_005329			huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75270811	75270812	+	Intron	DEL	CT	-	-	rs35405729		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75270811_75270812delCT	uc003uds.1	-							NM_005338	NP_005329			huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
Unknown	0	broad.mit.edu	37	7	75423068	75423069	+	IGR	DEL	AG	-	-	rs112477016		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75423068_75423069delAG								CCL26 (4004 upstream) : CCL24 (18047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	75423954	75423955	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75423954_75423955delAA								CCL26 (4890 upstream) : CCL24 (17161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	75476659	75476659	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75476659delT								CCL24 (33626 upstream) : RHBDD2 (31658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	75538929	75538931	+	IGR	DEL	GAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75538929_75538931delGAA								RHBDD2 (20685 upstream) : POR (5489 downstream)																																			---	---	---	---
POR	5447	broad.mit.edu	37	7	75591332	75591332	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75591332delA	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	75593002	75593002	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75593002delC	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)													---	---	---	---
STYXL1	51657	broad.mit.edu	37	7	75652245	75652245	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75652245delA	uc003uej.3	-						STYXL1_uc011kgf.1_Intron|STYXL1_uc011kgg.1_Intron|STYXL1_uc003ueh.2_Intron|STYXL1_uc003uek.3_Intron|STYXL1_uc003uel.2_Intron|STYXL1_uc003uem.2_Intron|STYXL1_uc010ldg.1_Intron|STYXL1_uc010ldh.1_Intron|STYXL1_uc003uen.1_Intron	NM_016086	NP_057170			map kinase phosphatase-like protein MK-STYX						intracellular signal transduction|protein dephosphorylation	intracellular	protein binding|protein tyrosine/serine/threonine phosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	75821651	75821651	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75821651delT								MDH2 (125723 upstream) : SRRM3 (9565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	76737985	76737985	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76737985delT								LOC100132832 (55630 upstream) : CCDC146 (13949 downstream)																																			---	---	---	---
PION	54103	broad.mit.edu	37	7	76940771	76940771	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76940771delA	uc003ugf.2	-						PION_uc011kgo.1_Intron|PION_uc003ugd.2_Intron	NM_017439	NP_059135			pigeon homolog						beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1																		---	---	---	---
PION	54103	broad.mit.edu	37	7	77021542	77021545	+	Intron	DEL	AAAA	-	-	rs78784395		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77021542_77021545delAAAA	uc003ugf.2	-						PION_uc003ugg.1_Intron	NM_017439	NP_059135			pigeon homolog						beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	77278108	77278108	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77278108delA								PTPN12 (8720 upstream) : RSBN1L (47635 downstream)																																			---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	78004164	78004165	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78004164_78004165delTT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.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	78058597	78058598	+	Intron	INS	-	CTTG	CTTG	rs146085895	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78058597_78058598insCTTG	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.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	78753246	78753246	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78753246delT	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	79208681	79208681	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79208681delA								MAGI2 (125791 upstream) : GNAI1 (555459 downstream)																																			---	---	---	---
CD36	948	broad.mit.edu	37	7	80132023	80132023	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80132023delA	uc003uhc.2	+						GNAT3_uc011kgu.1_Intron	NM_001127444	NP_001120916			CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	81112780	81112780	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81112780delC								SEMA3C (561105 upstream) : HGF (218665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	81278338	81278339	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81278338_81278339delAA	uc003uhk.1	-											Homo sapiens mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	81564984	81564985	+	IGR	INS	-	T	T	rs112692394		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81564984_81564985insT								HGF (165532 upstream) : CACNA2D1 (14433 downstream)																																			---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	81814953	81814955	+	Intron	DEL	TTC	-	-	rs146855692		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81814953_81814955delTTC	uc003uhr.1	-							NM_000722	NP_000713			calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	82219160	82219160	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82219160delT								CACNA2D1 (146129 upstream) : PCLO (164161 downstream)																																			---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82403041	82403042	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82403041_82403042delTT	uc003uhx.2	-							NM_033026	NP_149015			piccolo isoform 1						cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82672209	82672211	+	Intron	DEL	GAT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82672209_82672211delGAT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	82976171	82976172	+	IGR	DEL	TA	-	-	rs138597835		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82976171_82976172delTA								PCLO (183974 upstream) : SEMA3E (17050 downstream)																																			---	---	---	---
SEMA3E	9723	broad.mit.edu	37	7	83119353	83119353	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83119353delA	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	83890729	83890729	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83890729delA								SEMA3A (66512 upstream) : SEMA3D (734145 downstream)																																			---	---	---	---
SEMA3D	223117	broad.mit.edu	37	7	84714447	84714447	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84714447delT	uc003uic.2	-						SEMA3D_uc010led.2_Intron|SEMA3D_uc010lee.1_Intron	NM_152754	NP_689967			semaphorin 3D precursor						cell differentiation|nervous system development	extracellular region|membrane	receptor activity			ovary(3)|large_intestine(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	85754334	85754334	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85754334delT								SEMA3D (938163 upstream) : GRM3 (518896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85932284	85932284	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85932284delT								None (None upstream) : GRM3 (340946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85942304	85942304	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85942304delT								None (None upstream) : GRM3 (330926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	86765009	86765009	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86765009delT								KIAA1324L (75995 upstream) : DMTF1 (16668 downstream)																																			---	---	---	---
DMTF1	9988	broad.mit.edu	37	7	86810923	86810923	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86810923delT	uc003uih.2	+						DMTF1_uc003uii.2_Intron|DMTF1_uc003uij.2_Intron|DMTF1_uc011khb.1_Intron|DMTF1_uc003uik.2_Intron|DMTF1_uc003uil.2_Intron|DMTF1_uc003uin.2_Intron	NM_001142327	NP_001135799			cyclin D binding myb-like transcription factor 1						cell cycle	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(14;0.0058)																	---	---	---	---
RUNDC3B	154661	broad.mit.edu	37	7	87363860	87363860	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87363860delA	uc003ujb.2	+						RUNDC3B_uc011khd.1_Intron|RUNDC3B_uc011khe.1_Intron|RUNDC3B_uc003ujc.2_Intron|RUNDC3B_uc003ujd.2_Intron	NM_138290	NP_612147			RUN domain containing 3B isoform a											skin(1)	1	Esophageal squamous(14;0.00164)																	---	---	---	---
ADAM22	53616	broad.mit.edu	37	7	87739659	87739659	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87739659delT	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)															---	---	---	---
ADAM22	53616	broad.mit.edu	37	7	87758008	87758008	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87758008delT	uc003ujn.2	+						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	87904915	87904916	+	IGR	INS	-	GTGT	GTGT	rs145162316	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87904915_87904916insGTGT								SRI (48607 upstream) : STEAP4 (834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	88141302	88141302	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88141302delT								STEAP4 (205093 upstream) : ZNF804B (247451 downstream)																																			---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88430618	88430620	+	Intron	DEL	AAA	-	-	rs73198671	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88430618_88430620delAAA	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	88776178	88776178	+	Intron	DEL	A	-	-	rs113430975		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88776178delA	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)			---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90504844	90504844	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90504844delT	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90734327	90734327	+	Intron	DEL	A	-	-	rs144806516	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90734327delA	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	91029438	91029438	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91029438delT								FZD1 (131307 upstream) : MTERF (402022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	91082896	91082897	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91082896_91082897insT								FZD1 (184765 upstream) : MTERF (348563 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	91262037	91262038	+	IGR	INS	-	ACAC	ACAC	rs113263767		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91262037_91262038insACAC								FZD1 (363906 upstream) : MTERF (169422 downstream)																																			---	---	---	---
ANKIB1	54467	broad.mit.edu	37	7	91961109	91961110	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91961109_91961110insA	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	91980172	91980172	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91980172delA	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)															---	---	---	---
PEX1	5189	broad.mit.edu	37	7	92118782	92118782	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92118782delA	uc003uly.2	-						PEX1_uc011khr.1_Intron|PEX1_uc010ley.2_Intron|PEX1_uc011khs.1_Intron	NM_000466	NP_000457			peroxin1						microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)															---	---	---	---
C7orf64	84060	broad.mit.edu	37	7	92166147	92166148	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92166147_92166148delTT	uc003ulz.2	+						C7orf64_uc003uma.2_3'UTR|MGC16142_uc011khv.1_5'Flank	NM_032120	NP_115496			hypothetical protein LOC84060								nucleotide binding			ovary(2)	2																		---	---	---	---
CCDC132	55610	broad.mit.edu	37	7	92883251	92883251	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
GNGT1	2792	broad.mit.edu	37	7	93284806	93284806	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93284806delT	uc003umx.1	+											Homo sapiens guanine nucleotide binding protein gamma 1 (GNG1) mRNA, complete cds.						G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|signal transducer activity				0	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)															---	---	---	---
BET1	10282	broad.mit.edu	37	7	93634322	93634323	+	5'Flank	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93634322_93634323delTT	uc003unf.1	-						BET1_uc003une.3_5'Flank	NM_005868	NP_005859			blocked early in transport 1						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein binding				0	all_cancers(62;2.22e-10)|all_epithelial(64;1.38e-09)|Lung NSC(181;0.218)	Breast(660;0.000162)|Ovarian(593;0.000626)	STAD - Stomach adenocarcinoma(171;0.000967)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	93941805	93941805	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93941805delA								BET1 (308115 upstream) : COL1A2 (82068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	94378490	94378491	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94378490_94378491delAA								PEG10 (79486 upstream) : PPP1R9A (158458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	94431809	94431809	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94431809delT								PEG10 (132805 upstream) : PPP1R9A (105140 downstream)																																			---	---	---	---
PPP1R9A	55607	broad.mit.edu	37	7	94573758	94573758	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94573758delC	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)			---	---	---	---
PPP1R9A	55607	broad.mit.edu	37	7	94736116	94736116	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94736116delT	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)			---	---	---	---
PPP1R9A	55607	broad.mit.edu	37	7	94773723	94773723	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94773723delT	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)			---	---	---	---
PON1	5444	broad.mit.edu	37	7	95020105	95020105	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95020105delT	uc011kih.1	-						PON3_uc003unt.2_Intron|PON3_uc011kii.1_Intron					SubName: Full=cDNA FLJ57644, highly similar to Serum paraoxonase/arylesterase 1 (EC 3.1.1.2);						aromatic compound catabolic process|carboxylic acid catabolic process|organophosphate catabolic process|phosphatidylcholine metabolic process|positive regulation of binding|positive regulation of cholesterol efflux|positive regulation of transporter activity|response to external stimulus	spherical high-density lipoprotein particle	aryldialkylphosphatase activity|arylesterase activity|calcium ion binding|phospholipid binding|protein homodimerization activity			pancreas(1)	1	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Atorvastatin(DB01076)|Cefazolin(DB01327)													---	---	---	---
PON2	5445	broad.mit.edu	37	7	95053909	95053909	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95053909delA	uc003unv.2	-						PON2_uc003unu.2_Intron|PON2_uc010lfk.2_Intron|PON2_uc003unw.2_Intron	NM_000305	NP_000296			paraoxonase 2 isoform 1						aromatic compound catabolic process	extracellular region|plasma membrane	arylesterase activity|identical protein binding|metal ion binding				0	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	95086653	95086653	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95086653delT								PON2 (22269 upstream) : ASB4 (28631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	95325865	95325866	+	IGR	DEL	AA	-	-	rs66509722		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95325865_95325866delAA								PDK4 (99940 upstream) : DYNC1I1 (75952 downstream)																																			---	---	---	---
DYNC1I1	1780	broad.mit.edu	37	7	95448667	95448667	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95448667delT	uc003uoc.3	+						DYNC1I1_uc003uod.3_Intron|DYNC1I1_uc003uob.2_Intron|DYNC1I1_uc003uoe.3_Intron|DYNC1I1_uc010lfl.2_Intron	NM_004411	NP_004402			dynein, cytoplasmic 1, intermediate chain 1						vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole|vesicle	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)															---	---	---	---
DYNC1I1	1780	broad.mit.edu	37	7	95598135	95598138	+	Intron	DEL	TCTG	-	-	rs1548398		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95598135_95598138delTCTG	uc003uoc.3	+						DYNC1I1_uc003uod.3_Intron|DYNC1I1_uc003uob.2_Intron|DYNC1I1_uc003uoe.3_Intron|DYNC1I1_uc010lfl.2_Intron	NM_004411	NP_004402			dynein, cytoplasmic 1, intermediate chain 1						vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole|vesicle	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)															---	---	---	---
SLC25A13	10165	broad.mit.edu	37	7	95775777	95775777	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95775777delA	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	96115478	96115478	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96115478delT	uc003uoh.1	-						uc011kil.1_Intron					RecName: Full=Putative uncharacterized protein FLJ42280;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	96163214	96163214	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96163214delA								SLC25A13 (211755 upstream) : SHFM1 (139023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96377127	96377130	+	IGR	DEL	CTTT	-	-	rs113243068		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96377127_96377130delCTTT								SHFM1 (37924 upstream) : DLX6AS (220698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96408610	96408610	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96408610delA								SHFM1 (69407 upstream) : DLX6AS (189218 downstream)																																			---	---	---	---
MGC72080	389538	broad.mit.edu	37	7	97512527	97512527	+	Intron	DEL	A	-	-	rs80094303		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97512527delA	uc010lfp.1	-											Homo sapiens cDNA, FLJ99734.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	97669865	97669866	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97669865_97669866delAG								OCM2 (50449 upstream) : LMTK2 (66331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97688258	97688258	+	IGR	DEL	A	-	-	rs72062607		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97688258delA								OCM2 (68842 upstream) : LMTK2 (47939 downstream)																																			---	---	---	---
LMTK2	22853	broad.mit.edu	37	7	97746848	97746848	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97746848delT	uc003upd.1	+							NM_014916	NP_055731			lemur tyrosine kinase 2 precursor						early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)																	---	---	---	---
TECPR1	25851	broad.mit.edu	37	7	97867391	97867391	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97867391delT	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	98013469	98013471	+	Intron	DEL	AAA	-	-	rs75133787		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98013469_98013471delAAA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	98043569	98043569	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98043569delT								BAIAP2L1 (13142 upstream) : NPTX2 (203028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98119332	98119332	+	IGR	DEL	A	-	-	rs35612519		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98119332delA								BAIAP2L1 (88905 upstream) : NPTX2 (127265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98154373	98154374	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98154373_98154374delAA								BAIAP2L1 (123946 upstream) : NPTX2 (92223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98338482	98338483	+	IGR	INS	-	AAT	AAT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98338482_98338483insAAT								NPTX2 (79301 upstream) : TMEM130 (105629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98393243	98393244	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98393243_98393244insT								NPTX2 (134062 upstream) : TMEM130 (50868 downstream)																																			---	---	---	---
TMEM130	222865	broad.mit.edu	37	7	98457692	98457692	+	Intron	DEL	A	-	-	rs67317732		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98457692delA	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)															---	---	---	---
KPNA7	402569	broad.mit.edu	37	7	98799286	98799286	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98799286delA	uc010lft.2	-							NM_001145715	NP_001139187			karyopherin 7						protein import into nucleus	cytoplasm|nuclear pore	binding|protein transporter activity			kidney(1)|skin(1)	2																		---	---	---	---
ARPC1A	10552	broad.mit.edu	37	7	98927687	98927688	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98927687_98927688delAA	uc003upx.1	+						ARPC1A_uc010lfu.1_Intron|ARPC1A_uc003upy.1_Intron|ARPC1A_uc011kit.1_Intron	NM_006409	NP_006400			actin related protein 2/3 complex subunit 1A						actin cytoskeleton organization|regulation of actin filament polymerization	actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ARPC1A	10552	broad.mit.edu	37	7	98949004	98949004	+	Intron	DEL	T	-	-	rs79633436		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98949004delT	uc003upx.1	+						ARPC1A_uc010lfu.1_Intron|ARPC1A_uc003upy.1_Intron|ARPC1A_uc011kit.1_Intron	NM_006409	NP_006400			actin related protein 2/3 complex subunit 1A						actin cytoskeleton organization|regulation of actin filament polymerization	actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
PTCD1	26024	broad.mit.edu	37	7	99032218	99032220	+	Intron	DEL	AAA	-	-	rs80240572		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99032218_99032220delAAA	uc003uqh.2	-						PTCD1_uc011kiw.1_Intron	NM_015545	NP_056360			pentatricopeptide repeat domain 1											ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
PTCD1	26024	broad.mit.edu	37	7	99062897	99062897	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99062897delA	uc011kiw.1	-						ATP5J2_uc003uql.2_Intron|ATP5J2_uc003uqm.2_Intron|ATP5J2_uc003uqn.2_Intron|ATP5J2_uc003uqo.2_Intron	NM_015545	NP_056360			pentatricopeptide repeat domain 1											ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	99201822	99201822	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99201822delT								ZNF655 (27748 upstream) : ZNF498 (12749 downstream)																																			---	---	---	---
CYP3A43	64816	broad.mit.edu	37	7	99463426	99463426	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99463426delA	uc003urx.1	+						CYP3A43_uc003ury.1_Intron|CYP3A43_uc003urz.1_Intron|CYP3A43_uc003usa.1_Intron|CYP3A43_uc010lgi.1_Intron|CYP3A43_uc003usb.1_Intron	NM_057095	NP_476436			cytochrome P450, family 3, subfamily A,						xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)|skin(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Cetirizine(DB00341)|Doxycycline(DB00254)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	99483732	99483733	+	IGR	DEL	TT	-	-	rs139000883		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99483732_99483733delTT								OR2AE1 (9076 upstream) : TRIM4 (4304 downstream)																																			---	---	---	---
ZKSCAN1	7586	broad.mit.edu	37	7	99621024	99621024	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99621024delT	uc003usk.1	+						ZKSCAN1_uc003usj.2_Intron|ZKSCAN1_uc003usl.1_Intron|ZKSCAN1_uc003usm.1_Intron	NM_003439	NP_003430			zinc finger protein 36						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)															---	---	---	---
ZSCAN21	7589	broad.mit.edu	37	7	99661218	99661218	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99661218delA	uc003uso.2	+						ZSCAN21_uc003usn.1_Intron	NM_145914	NP_666019			zinc finger protein 38						positive regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|protein 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)															---	---	---	---
GAL3ST4	79690	broad.mit.edu	37	7	99757343	99757343	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99757343delA	uc003utt.2	-	3					C7orf43_uc010lgp.2_5'Flank|C7orf43_uc011kjj.1_5'Flank|C7orf43_uc003utr.2_5'Flank|C7orf43_uc003uts.2_5'Flank|GAL3ST4_uc003utu.2_3'UTR|GAL3ST4_uc010lgq.2_3'UTR	NM_024637	NP_078913			galactose-3-O-sulfotransferase 4						cell-cell signaling|oligosaccharide metabolic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi cisterna membrane|integral to membrane|membrane fraction	3'-phosphoadenosine 5'-phosphosulfate binding|galactosylceramide sulfotransferase activity|proteoglycan sulfotransferase activity			ovary(3)	3	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
STAG3	10734	broad.mit.edu	37	7	99780152	99780152	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99780152delT	uc003utx.1	+						STAG3_uc010lgs.1_Intron|STAG3_uc011kjk.1_Intron	NM_012447	NP_036579			stromal antigen 3						chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	99892231	99892231	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99892231delT								GATS (22376 upstream) : SPDYE3 (19833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	99897286	99897286	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99897286delA								GATS (27431 upstream) : SPDYE3 (14778 downstream)																																			---	---	---	---
PILRB	29990	broad.mit.edu	37	7	99936693	99936694	+	Intron	DEL	TT	-	-	rs78792568		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99936693_99936694delTT	uc003uuk.2	+						PMS2L1_uc003uuh.2_5'Flank|PMS2L1_uc003uui.2_5'Flank|PMS2L1_uc010lgv.1_5'Flank|PILRB_uc003uul.2_Intron	NM_013440	NP_038468			paired immunoglobulin-like type 2 receptor beta						activation of transmembrane receptor protein tyrosine kinase activity	integral to plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
PILRA	29992	broad.mit.edu	37	7	99994611	99994611	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99994611delT	uc003uuo.1	+						PILRA_uc011kjo.1_Intron|PILRA_uc003uup.1_Intron|PILRA_uc003uuq.1_Intron	NM_013439	NP_038467			paired immunoglobulin-like type 2 receptor alpha						interspecies interaction between organisms	extracellular region|integral to membrane|plasma membrane	protein binding|receptor activity			skin(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
MEPCE	56257	broad.mit.edu	37	7	100028068	100028068	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100028068delG	uc003uuw.2	+	1	540	c.427delG	c.(427-429)GGGfs	p.G143fs	ZCWPW1_uc003uut.2_5'Flank|ZCWPW1_uc011kjr.1_5'Flank|ZCWPW1_uc003uuu.1_5'Flank|ZCWPW1_uc011kjt.1_5'Flank|ZCWPW1_uc011kju.1_5'Flank|MEPCE_uc003uuv.2_Intron	NM_019606	NP_062552	Q7L2J0	MEPCE_HUMAN	bin3, bicoid-interacting 3	143	Gly-rich.						methyltransferase activity			upper_aerodigestive_tract(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100118998	100118998	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100118998delT								C7orf51 (26576 upstream) : AGFG2 (17836 downstream)																																			---	---	---	---
LRCH4	4034	broad.mit.edu	37	7	100174054	100174054	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100174054delT	uc003uvj.2	-						uc003uvh.2_5'Flank|LRCH4_uc010lgz.2_Intron|LRCH4_uc003uvi.2_Intron|LRCH4_uc011kjw.1_Intron	NM_002319	NP_002310			leucine-rich repeats and calponin homology (CH)						nervous system development	PML body	protein binding			large_intestine(1)|ovary(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100367078	100367079	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100367078_100367079insT	uc003uwj.2	+						ZAN_uc003uwk.2_Intron|ZAN_uc003uwl.2_Intron|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_Intron|ZAN_uc011kkd.1_Intron	NM_003386	NP_003377			zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)															---	---	---	---
SRRT	51593	broad.mit.edu	37	7	100473604	100473604	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100473604delT	uc003uwy.2	+						SRRT_uc010lhl.1_Intron|SRRT_uc003uxa.2_Intron|SRRT_uc003uwz.2_Intron	NM_015908	NP_056992			arsenate resistance protein 2 isoform a						cell proliferation|primary miRNA processing|response to arsenic-containing substance	cytoplasm|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100688249	100688250	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100688249_100688250insT	uc003uxp.1	+						MUC17_uc010lho.1_Intron	NM_001040105	NP_001035194			mucin 17 precursor							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	100726031	100726031	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100726031delT	uc003uxq.2	+						TRIM56_uc003uxr.2_5'Flank	NM_030961	NP_112223			tripartite motif-containing 56						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)																	---	---	---	---
FIS1	51024	broad.mit.edu	37	7	100885220	100885220	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100885220delA	uc003uyj.3	-						FIS1_uc010lht.2_Intron|FIS1_uc010lhu.2_Intron	NM_016068	NP_057152			tetratricopeptide repeat domain 11						apoptosis|mitochondrial fission|peroxisome fission	integral to mitochondrial outer membrane|integral to peroxisomal membrane	protein binding				0	Lung NSC(181;0.168)|all_lung(186;0.215)																	---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101042621	101042622	+	Intron	INS	-	CTTT	CTTT	rs143309560	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101042621_101042622insCTTT	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101134363	101134363	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101134363delA	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101148089	101148090	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101148089_101148090delTG	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101839857	101839857	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101839857delT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530			cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101908637	101908637	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101908637delA	uc003uyt.2	+						CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_001913	NP_001904			cut-like homeobox 1 isoform b						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	101923231	101923231	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101923231delT	uc003uyt.2	+						CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron|CUX1_uc003uyz.2_Intron	NM_001913	NP_001904			cut-like homeobox 1 isoform b						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	101926088	101926088	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101926088delC	uc003uyt.2	+						CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron|CUX1_uc003uyz.2_Intron|SH2B2_uc011kko.1_5'Flank	NM_001913	NP_001904			cut-like homeobox 1 isoform b						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	102030045	102030045	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102030045delT	uc003uzd.1	+						uc003uze.1_Intron|PRKRIP1_uc003uzf.2_Intron|PRKRIP1_uc003uzg.2_Intron|PRKRIP1_uc011kkq.1_Intron	NM_001003686	NP_001003686			SubName: Full=Putative uncharacterized protein PMS2L3;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	102032172	102032172	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102032172delA	uc003uzd.1	+						uc003uze.1_Intron|PRKRIP1_uc003uzf.2_Intron|PRKRIP1_uc003uzg.2_Intron|PRKRIP1_uc011kkq.1_Intron	NM_001003686	NP_001003686			SubName: Full=Putative uncharacterized protein PMS2L3;																														---	---	---	---
RASA4	10156	broad.mit.edu	37	7	102243412	102243412	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102243412delT	uc003vae.2	-						UPK3BL_uc003uzy.2_Intron|RASA4_uc011kla.1_Intron|RASA4_uc010lig.2_Intron|RASA4_uc003vaf.2_Intron|RASA4_uc011klb.1_Intron|RASA4_uc010lih.2_Intron|RASA4_uc011kld.1_Intron|uc003vag.1_Intron	NM_006989	NP_008920			RAS p21 protein activator 4 isoform 1						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytosol|intrinsic to internal side of plasma membrane	metal ion binding|Ras GTPase activator activity				0																		---	---	---	---
RASA4	10156	broad.mit.edu	37	7	102331240	102331241	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102331240_102331241insC	uc011kld.1	-											Homo sapiens mRNA for KIAA0538 protein, partial cds.						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytosol|intrinsic to internal side of plasma membrane	metal ion binding|Ras GTPase activator activity				0																		---	---	---	---
FBXL13	222235	broad.mit.edu	37	7	102512001	102512001	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102512001delT	uc003vaq.2	-						FBXL13_uc010liq.1_Intron|FBXL13_uc010lir.1_Intron|FBXL13_uc003var.2_Intron|FBXL13_uc003vas.2_Intron	NM_145032	NP_659469			F-box and leucine-rich repeat protein 13 isoform												0																		---	---	---	---
FBXL13	222235	broad.mit.edu	37	7	102631106	102631107	+	Intron	INS	-	GA	GA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102631106_102631107insGA	uc003vaq.2	-						FBXL13_uc010liq.1_Intron|FBXL13_uc010lir.1_Intron|FBXL13_uc003var.2_Intron|FBXL13_uc003vas.2_Intron|FBXL13_uc003vav.2_Intron	NM_145032	NP_659469			F-box and leucine-rich repeat protein 13 isoform												0																		---	---	---	---
NAPEPLD	222236	broad.mit.edu	37	7	102781686	102781687	+	Intron	DEL	TG	-	-	rs139564898	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102781686_102781687delTG	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	103361696	103361697	+	Intron	DEL	TC	-	-	rs10540402		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103361696_103361697delTC	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	103483656	103483656	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103483656delT	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	103668232	103668232	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103668232delT								RELN (38269 upstream) : ORC5L (98558 downstream)																																			---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	104153190	104153190	+	Intron	DEL	A	-	-	rs78850794		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104153190delA	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	104206121	104206121	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104206121delT	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	104284498	104284498	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104284498delA	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	104436424	104436425	+	Intron	INS	-	A	A	rs144118847	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104436424_104436425insA	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	104555626	104555626	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104555626delA	uc003vch.1	-							NR_027374				Homo sapiens, clone IMAGE:5754998, mRNA.												0																		---	---	---	---
SRPK2	6733	broad.mit.edu	37	7	104889372	104889373	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104889372_104889373insA	uc003vct.2	-						SRPK2_uc003vcu.2_Intron|SRPK2_uc003vcv.2_Intron|SRPK2_uc003vcw.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	105081835	105081835	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105081835delT								SRPK2 (42037 upstream) : PUS7 (15127 downstream)																																			---	---	---	---
CDHR3	222256	broad.mit.edu	37	7	105672824	105672824	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105672824delT	uc003vdl.3	+						CDHR3_uc003vdk.2_Intron|CDHR3_uc003vdm.3_Intron|CDHR3_uc011klt.1_Intron|CDHR3_uc003vdn.2_Intron	NM_152750	NP_689963			hypothetical protein LOC222256 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	105813684	105813684	+	IGR	DEL	C	-	-	rs34236272		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105813684delC								SYPL1 (60627 upstream) : NAMPT (75050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	106217378	106217378	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106217378delT	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	106376486	106376487	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106376486_106376487delTT	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	106488291	106488291	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106488291delT								FLJ36031 (186700 upstream) : PIK3CG (17432 downstream)																																			---	---	---	---
PRKAR2B	5577	broad.mit.edu	37	7	106772576	106772577	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106772576_106772577insA	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	107082938	107082939	+	Intron	DEL	TT	-	-	rs138317611		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107082938_107082939delTT	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	107162387	107162387	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107162387delA	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	107165683	107165684	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107165683_107165684insT	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	107338764	107338766	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107338764_107338766delTTT	uc003vep.2	+						SLC26A4_uc011kmb.1_Intron|SLC26A4_uc011kmc.1_Intron|SLC26A4_uc011kmd.1_Intron	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				---	---	---	---
DLD	1738	broad.mit.edu	37	7	107533533	107533535	+	Intron	DEL	TAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107533533_107533535delTAA	uc003vet.2	+						DLD_uc010ljm.1_Intron|DLD_uc011kmg.1_Intron|DLD_uc011kmh.1_Intron|DLD_uc011kmi.1_Intron	NM_000108	NP_000099			dihydrolipoamide dehydrogenase precursor						branched chain family amino acid catabolic process|cell redox homeostasis|lysine catabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|tricarboxylic acid cycle	mitochondrial matrix	dihydrolipoyl dehydrogenase activity			central_nervous_system(1)	1					NADH(DB00157)													---	---	---	---
LAMB4	22798	broad.mit.edu	37	7	107698419	107698419	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108536207	108536207	+	IGR	DEL	A	-	-	rs74944127	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108536207delA								C7orf66 (11570 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	109498879	109498879	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109498879delA								C7orf66 (974242 upstream) : EIF3IP1 (100405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	109890347	109890347	+	IGR	DEL	A	-	-	rs35848909		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109890347delA								EIF3IP1 (290077 upstream) : IMMP2L (412763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	110080071	110080072	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110080071_110080072insA								EIF3IP1 (479801 upstream) : IMMP2L (223038 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	110294443	110294444	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110294443_110294444delAA								EIF3IP1 (694173 upstream) : IMMP2L (8666 downstream)																																			---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	110685771	110685772	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110685771_110685772insG	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938			IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)														---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	111114566	111114567	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111114566_111114567delTT	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938			IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)														---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111531004	111531004	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111531004delT	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)																---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111575538	111575538	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111575538delA	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron|DOCK4_uc010ljt.1_Frame_Shift_Del_p.C375fs	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	111848652	111848652	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111848652delT	uc003vge.2	+						DOCK4_uc003vfx.2_5'Flank|DOCK4_uc003vfy.2_5'Flank|DOCK4_uc003vga.1_5'Flank|DOCK4_uc010ljt.1_5'Flank|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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	113702747	113702747	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113702747delA								PPP1R3A (143665 upstream) : FOXP2 (23635 downstream)																																			---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	113810398	113810398	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113810398delA	uc003vgu.2	+						FOXP2_uc003vgt.1_Intron					Homo sapiens full length insert cDNA clone YX52E07.						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	114368923	114368924	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114368923_114368924delTT								FOXP2 (37831 upstream) : MDFIC (193285 downstream)																																			---	---	---	---
CAV1	857	broad.mit.edu	37	7	116195658	116195659	+	Intron	INS	-	AA	AA	rs10672081		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116195658_116195659insAA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	116238288	116238288	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116238288delA								CAV1 (37058 upstream) : MET (74171 downstream)																																			---	---	---	---
ST7	7982	broad.mit.edu	37	7	116658539	116658539	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116658539delT	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_5'Flank|ST7_uc003vir.2_5'Flank	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	116772155	116772156	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116772155_116772156insT	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	117351404	117351404	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117351404delA	uc003vjf.2	-	23						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)														---	---	---	---
CTTNBP2	83992	broad.mit.edu	37	7	117431604	117431604	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117431604delT	uc003vjf.2	-	4	1738	c.1646delA	c.(1645-1647)AAGfs	p.K549fs		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	549	Pro-rich.									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)														---	---	---	---
CTTNBP2	83992	broad.mit.edu	37	7	117481471	117481471	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117481471delT	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)														---	---	---	---
CTTNBP2	83992	broad.mit.edu	37	7	117502111	117502112	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117502111_117502112delAC	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	117913814	117913814	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117913814delT								ANKRD7 (31032 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118275698	118275698	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118275698delT								ANKRD7 (392916 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118372348	118372349	+	IGR	INS	-	AGA	AGA	rs5886920		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118372348_118372349insAGA								ANKRD7 (489566 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118714510	118714510	+	IGR	DEL	C	-	-	rs77946579		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118714510delC								ANKRD7 (831728 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118819290	118819291	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118819290_118819291delTG								ANKRD7 (936508 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118834613	118834614	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118834613_118834614insT								ANKRD7 (951831 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	119399486	119399488	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119399486_119399488delTTT								None (None upstream) : KCND2 (514234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	119872298	119872299	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119872298_119872299delAA								None (None upstream) : KCND2 (41423 downstream)																																			---	---	---	---
KCND2	3751	broad.mit.edu	37	7	120001454	120001455	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120001454_120001455delTT	uc003vjj.1	+							NM_012281	NP_036413			potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
KCND2	3751	broad.mit.edu	37	7	120112616	120112617	+	Intron	INS	-	AC	AC	rs140976059	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120112616_120112617insAC	uc003vjj.1	+							NM_012281	NP_036413			potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
C7orf58	79974	broad.mit.edu	37	7	120670209	120670210	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120670209_120670210delAC	uc003vjq.3	+						C7orf58_uc003vjr.1_Intron|C7orf58_uc003vjs.3_Intron	NM_024913	NP_079189			hypothetical protein LOC79974 isoform 1							endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)																	---	---	---	---
FAM3C	10447	broad.mit.edu	37	7	121023197	121023199	+	Intron	DEL	AAA	-	-	rs35702337		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121023197_121023199delAAA	uc003vjx.2	-						FAM3C_uc010lkm.2_Intron	NM_014888	NP_055703			family with sequence similarity 3, member C						multicellular organismal development	cytoplasmic membrane-bounded vesicle|extracellular region	cytokine activity				0	all_neural(327;0.117)																	---	---	---	---
PTPRZ1	5803	broad.mit.edu	37	7	121588815	121588817	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121588815_121588817delTTT	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																		---	---	---	---
PTPRZ1	5803	broad.mit.edu	37	7	121597015	121597015	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121597015delA	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																		---	---	---	---
AASS	10157	broad.mit.edu	37	7	121738966	121738966	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121738966delA	uc003vka.2	-						AASS_uc011knu.1_Intron|AASS_uc011knv.1_Intron|AASS_uc003vkb.2_Intron|AASS_uc011knw.1_Intron	NM_005763	NP_005754			aminoadipate-semialdehyde synthase precursor						protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	121805716	121805716	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121805716delT								AASS (21372 upstream) : FEZF1 (135733 downstream)																																			---	---	---	---
CADPS2	93664	broad.mit.edu	37	7	122250487	122250487	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122250487delA	uc010lkp.2	-						CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424			Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	122647970	122647971	+	IGR	INS	-	GA	GA	rs143581666	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122647970_122647971insGA								TAS2R16 (12216 upstream) : SLC13A1 (105618 downstream)																																			---	---	---	---
ASB15	142685	broad.mit.edu	37	7	123277059	123277059	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123277059delA	uc003vku.1	+	12					ASB15_uc003vkw.1_3'UTR	NM_080928	NP_563616			ankyrin repeat and SOCS box-containing 15						intracellular signal transduction					skin(2)|lung(1)	3																		---	---	---	---
WASL	8976	broad.mit.edu	37	7	123357246	123357246	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123357246delA	uc003vkz.2	-							NM_003941	NP_003932			Wiskott-Aldrich syndrome gene-like protein						actin polymerization or depolymerization|axon guidance|cellular component movement|nitric oxide metabolic process|protein complex assembly|regulation of nitric-oxide synthase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|cytosol|nucleolus|plasma membrane	actin binding|small GTPase regulator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	123409876	123409879	+	IGR	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123409876_123409879delAAAA								WASL (20760 upstream) : HYALP1 (44314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	124155876	124155876	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124155876delA								TMEM229A (482353 upstream) : GPR37 (230240 downstream)																																			---	---	---	---
GPR37	2861	broad.mit.edu	37	7	124402537	124402537	+	Intron	DEL	A	-	-	rs72280985		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124402537delA	uc003vli.2	-							NM_005302	NP_005293			G protein-coupled receptor 37 precursor							endoplasmic reticulum membrane|integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|lung(1)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	124592598	124592599	+	Intron	INS	-	T	T	rs150472518	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124592598_124592599insT	uc010lkx.1	+						uc003vlp.2_Intron|uc003vlq.1_Intron					Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																														---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126240988	126240988	+	Intron	DEL	T	-	-	rs34047308		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126240988delT	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)			---	---	---	---
ZNF800	168850	broad.mit.edu	37	7	127031357	127031357	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127031357delT	uc003vlx.1	-						ZNF800_uc003vly.1_Intron|ZNF800_uc010lla.2_Intron	NM_176814	NP_789784			zinc finger protein 800						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	127141498	127141498	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127141498delA								ZNF800 (108731 upstream) : GCC1 (79185 downstream)																																			---	---	---	---
SND1	27044	broad.mit.edu	37	7	127309055	127309055	+	Intron	DEL	T	-	-	rs72181011		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127309055delT	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	127391200	127391201	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127391200_127391201delGT	uc003vmi.2	+						SND1_uc010lle.2_Intron	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	127471961	127471961	+	Intron	DEL	C	-	-	rs34084538		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127471961delC	uc003vmi.2	+						SND1_uc010lle.2_Intron	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	127481742	127481743	+	Intron	INS	-	T	T	rs150591180	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127481742_127481743insT	uc003vmi.2	+						SND1_uc010lle.2_Intron	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																		---	---	---	---
C7orf68	29923	broad.mit.edu	37	7	128097963	128097964	+	3'UTR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128097963_128097964insA	uc003vne.3	+	2					C7orf68_uc010lli.2_3'UTR|C7orf68_uc010llj.1_RNA	NM_013332	NP_037464			hypoxia-inducible protein 2						autocrine signaling|positive regulation of cell proliferation|response to stress	cell surface|extracellular space|integral to membrane|stored secretory granule	receptor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	128258651	128258652	+	IGR	INS	-	T	T	rs35746900		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128258651_128258652insT								METTL2B (115674 upstream) : FLJ45340 (22643 downstream)																																			---	---	---	---
KCP	375616	broad.mit.edu	37	7	128548304	128548305	+	Intron	INS	-	A	A	rs150184172	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128548304_128548305insA	uc011kor.1	-						KCP_uc011kos.1_Intron	NM_001135914	NP_001129386			cysteine rich BMP regulator 2 isoform 1							extracellular region				central_nervous_system(1)	1																		---	---	---	---
AHCYL2	23382	broad.mit.edu	37	7	129009392	129009396	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129009392_129009396delTTTTT	uc011kov.1	+						AHCYL2_uc003vot.2_Intron|AHCYL2_uc003vov.2_Intron|AHCYL2_uc011kow.1_Intron	NM_015328	NP_056143			S-adenosylhomocysteine hydrolase-like 2 isoform						one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2																		---	---	---	---
AHCYL2	23382	broad.mit.edu	37	7	129045661	129045661	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129045661delT	uc011kov.1	+						AHCYL2_uc003vot.2_Intron|AHCYL2_uc003vov.2_Intron|AHCYL2_uc011kow.1_Intron|AHCYL2_uc011kox.1_Intron	NM_015328	NP_056143			S-adenosylhomocysteine hydrolase-like 2 isoform						one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	129428145	129428145	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129428145delT								MIR183 (13291 upstream) : UBE2H (44850 downstream)																																			---	---	---	---
UBE2H	7328	broad.mit.edu	37	7	129544126	129544126	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129544126delT	uc003vpf.1	-						UBE2H_uc003vpg.1_Intron	NM_003344	NP_003335			ubiquitin-conjugating enzyme E2H isoform 1						protein K11-linked ubiquitination|protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|ubiquitin-protein ligase activity			skin(1)	1	Melanoma(18;0.0435)																	---	---	---	---
ZC3HC1	51530	broad.mit.edu	37	7	129677291	129677292	+	Intron	INS	-	AAAC	AAAC	rs150885654	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129677291_129677292insAAAC	uc003vpi.2	-						ZC3HC1_uc003vph.2_Intron|ZC3HC1_uc010lma.2_Intron	NM_016478	NP_057562			zinc finger, C3HC type 1						cell division|mitosis	nucleus	protein kinase binding|zinc ion binding				0	Melanoma(18;0.0435)																	---	---	---	---
MEST	4232	broad.mit.edu	37	7	130139661	130139662	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130139661_130139662delAA	uc003vqg.2	+						MEST_uc003vqc.2_Intron|MEST_uc003vqd.2_Intron|MEST_uc003vqf.2_Intron|MEST_uc011kph.1_Intron|MEST_uc010lmg.2_Intron	NM_002402	NP_002393			mesoderm specific transcript isoform a						mesoderm development	endoplasmic reticulum membrane|integral to membrane	hydrolase activity|protein binding			ovary(2)	2	Melanoma(18;0.0435)																	---	---	---	---
MKLN1	4289	broad.mit.edu	37	7	130869290	130869290	+	Intron	DEL	T	-	-	rs111728654		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130869290delT	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	131009803	131009803	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131009803delT	uc011kpm.1	+						MKLN1_uc011kpl.1_Intron|MKLN1_uc010lmh.2_5'Flank|MKLN1_uc003vqs.2_5'Flank|uc003vqr.1_Intron	NM_013255	NP_037387			muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
PODXL	5420	broad.mit.edu	37	7	131219552	131219552	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131219552delA	uc003vqw.3	-						PODXL_uc003vqx.3_Intron	NM_001018111	NP_001018121			podocalyxin-like isoform 1 precursor						cell adhesion|epithelial tube formation|negative regulation of cell-cell adhesion|positive regulation of cell migration|positive regulation of cell-cell adhesion mediated by integrin|regulation of microvillus assembly	actin cytoskeleton|apical plasma membrane|centrosome|filopodium|integral to plasma membrane|lamellipodium|membrane raft|microvillus membrane|nucleolus|ruffle				breast(2)|pancreas(1)	3	Melanoma(18;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	131271576	131271577	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131271576_131271577delTG								PODXL (30200 upstream) : PLXNA4 (536515 downstream)																																			---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	132011929	132011929	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
CHCHD3	54927	broad.mit.edu	37	7	132553767	132553767	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132553767delA	uc003vre.2	-						CHCHD3_uc010lmi.2_Intron|CHCHD3_uc003vrf.2_Intron|CHCHD3_uc010lmj.2_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																		---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133330808	133330809	+	Intron	INS	-	CCA	CCA	rs75123744	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133330808_133330809insCCA	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron	NM_021807	NP_068579			SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)																---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133335253	133335253	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133335253delA	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)																---	---	---	---
AKR1B15	441282	broad.mit.edu	37	7	134247585	134247604	+	Intron	DEL	TCTTTCTTTCTTTCTTTCTT	-	-	rs7786450	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134247585_134247604delTCTTTCTTTCTTTCTTTCTT	uc011kpr.1	+						AKR1B15_uc003vrt.2_5'Flank|AKR1B15_uc011kps.1_5'Flank	NM_001080538	NP_001074007			aldo-keto reductase family 1, member B15								oxidoreductase activity			ovary(1)	1																		---	---	---	---
AKR1B15	441282	broad.mit.edu	37	7	134252866	134252866	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134252866delA	uc011kpr.1	+						AKR1B15_uc003vrt.2_Intron|AKR1B15_uc011kps.1_Intron	NM_001080538	NP_001074007			aldo-keto reductase family 1, member B15								oxidoreductase activity			ovary(1)	1																		---	---	---	---
WDR91	29062	broad.mit.edu	37	7	134880706	134880707	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134880706_134880707delAA	uc003vsp.2	-						WDR91_uc010lmq.2_Intron|WDR91_uc010lmr.2_Intron	NM_014149	NP_054868			WD repeat domain 91											breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
WDR91	29062	broad.mit.edu	37	7	134894606	134894606	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	135211797	135211797	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135211797delA								CNOT4 (16946 upstream) : NUP205 (30865 downstream)																																			---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135301910	135301911	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135301910_135301911insT	uc003vsw.2	+	26	3636_3637	c.3605_3606insT	c.(3604-3606)GATfs	p.D1202fs	NUP205_uc003vsx.2_5'Flank	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1202					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																		---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137300278	137300279	+	Intron	DEL	TG	-	-	rs5887846		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137300278_137300279delTG	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708			diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
AKR1D1	6718	broad.mit.edu	37	7	137761111	137761111	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137761111delA	uc003vtz.2	+						AKR1D1_uc011kqb.1_Intron|AKR1D1_uc011kqc.1_Intron|AKR1D1_uc011kqd.1_Intron|AKR1D1_uc011kqe.1_5'Flank|AKR1D1_uc011kqf.1_5'Flank	NM_005989	NP_005980			aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	137969096	137969099	+	IGR	DEL	CTCA	-	-	rs71728502		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137969096_137969099delCTCA								AKR1D1 (166046 upstream) : TRIM24 (175980 downstream)																																			---	---	---	---
TRIM24	8805	broad.mit.edu	37	7	138184552	138184553	+	Intron	DEL	TT	-	-	rs79579005		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138184552_138184553delTT	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																		---	---	---	---
TRIM24	8805	broad.mit.edu	37	7	138214086	138214086	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138214086delT	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	138539290	138539290	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138539290delT	uc011kql.1	-						KIAA1549_uc011kqi.1_Intron|KIAA1549_uc003vuk.3_Intron|KIAA1549_uc011kqj.1_Intron|KIAA1549_uc011kqk.1_Intron	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								---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138588559	138588600	+	Intron	DEL	GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGC	-	-	rs10235011		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138588559_138588600delGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGC	uc011kql.1	-						KIAA1549_uc003vuk.3_Intron|KIAA1549_uc011kqj.1_Intron	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								---	---	---	---
ZC3HAV1	56829	broad.mit.edu	37	7	138765167	138765167	+	Intron	DEL	T	-	-	rs79353564	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138765167delT	uc003vun.2	-						ZC3HAV1_uc003vuo.2_5'Flank|ZC3HAV1_uc003vup.2_Intron	NM_020119	NP_064504			zinc finger antiviral protein isoform 1						response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
HIPK2	28996	broad.mit.edu	37	7	139345209	139345209	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139345209delA	uc003vvf.3	-						HIPK2_uc003vvd.3_Intron	NM_022740	NP_073577			homeodomain interacting protein kinase 2 isoform						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)																	---	---	---	---
JHDM1D	80853	broad.mit.edu	37	7	139820179	139820179	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																	---	---	---	---
JHDM1D	80853	broad.mit.edu	37	7	139878082	139878089	+	5'Flank	DEL	TCCCTCCC	-	-	rs142303955		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139878082_139878089delTCCCTCCC	uc003vvm.2	-						LOC100134229_uc011kqy.1_RNA	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	139951314	139951314	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139951314delT								LOC100134229 (71875 upstream) : SLC37A3 (82240 downstream)																																			---	---	---	---
SLC37A3	84255	broad.mit.edu	37	7	140038280	140038280	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140038280delT	uc003vvo.2	-						SLC37A3_uc003vvn.2_Intron|SLC37A3_uc003vvp.2_Intron|SLC37A3_uc010lnh.2_Intron	NM_207113	NP_996996			solute carrier family 37 (glycerol-3-phosphate						carbohydrate transport|transmembrane transport	integral to membrane				ovary(3)	3	Melanoma(164;0.0142)																	---	---	---	---
ADCK2	90956	broad.mit.edu	37	7	140387849	140387850	+	Intron	DEL	TT	-	-	rs76614491		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140387849_140387850delTT	uc003vvy.1	+						ADCK2_uc003vvz.2_Intron	NM_052853	NP_443085			aarF domain containing kinase 2							integral to membrane	ATP binding|protein serine/threonine kinase activity				0	Melanoma(164;0.00956)																	---	---	---	---
BRAF	673	broad.mit.edu	37	7	140476994	140476994	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140476994delT	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	140539364	140539365	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140539364_140539365insA	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				---	---	---	---
AGK	55750	broad.mit.edu	37	7	141252809	141252809	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141252809delA	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)																	---	---	---	---
KIAA1147	57189	broad.mit.edu	37	7	141403342	141403343	+	5'Flank	INS	-	TGTGTGTGTGTGTG	TGTGTGTGTGTGTG	rs150720419	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141403342_141403343insTGTGTGTGTGTGTG	uc003vwk.2	-							NM_001080392	NP_001073861			hypothetical protein LOC57189											ovary(1)	1	Melanoma(164;0.0171)																	---	---	---	---
MGAM	8972	broad.mit.edu	37	7	141720753	141720754	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141720753_141720754insT	uc003vwy.2	+							NM_004668	NP_004659			maltase-glucoamylase						polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	142108777	142108778	+	Intron	INS	-	TA	TA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142108777_142108778insTA	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
TRPV6	55503	broad.mit.edu	37	7	142585287	142585288	+	5'Flank	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142585287_142585288delTG	uc003wbx.1	-							NM_018646	NP_061116			transient receptor potential cation channel,						regulation of calcium ion-dependent exocytosis	integral to plasma membrane	calcium channel activity|calmodulin binding			ovary(2)	2	Melanoma(164;0.059)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	142595829	142595829	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142595829delG								TRPV6 (12352 upstream) : TRPV5 (9819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	142777279	142777279	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142777279delA								OR6W1P (16397 upstream) : PIP (51895 downstream)																																			---	---	---	---
CLCN1	1180	broad.mit.edu	37	7	143015297	143015297	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143015297delT	uc003wcr.1	+						CLCN1_uc011ktc.1_Intron	NM_000083	NP_000074			chloride channel 1, skeletal muscle						muscle contraction	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Melanoma(164;0.205)																	---	---	---	---
EPHA1	2041	broad.mit.edu	37	7	143104604	143104604	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143104604delT	uc003wcz.2	-						uc003wda.2_5'Flank	NM_005232	NP_005223			ephrin receptor EphA1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(3)|lung(1)|breast(1)	5	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	143612120	143612120	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143612120delT								FAM115A (12901 upstream) : OR2F2 (20206 downstream)																																			---	---	---	---
TPK1	27010	broad.mit.edu	37	7	144388380	144388381	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144388380_144388381delAA	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-4292-01	TCGA-BR-4292-01									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)													---	---	---	---
TPK1	27010	broad.mit.edu	37	7	144532719	144532719	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144532719delA	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)													---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146936436	146936436	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146936436delA	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	147189014	147189014	+	Intron	DEL	T	-	-	rs2888489	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147189014delT	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	147629206	147629206	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147629206delG	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	147871512	147871512	+	Intron	DEL	G	-	-	rs67002110		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147871512delG	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	147891064	147891065	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147891064_147891065delTT	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	147997192	147997192	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147997192delG	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	148174714	148174715	+	IGR	INS	-	T	T	rs112565995		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148174714_148174715insT								CNTNAP2 (56628 upstream) : C7orf33 (112942 downstream)																																			---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148454288	148454288	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148454288delT	uc010lpg.2	+						CUL1_uc003wey.2_Intron|CUL1_uc003wez.2_Intron	NM_003592	NP_003583			cullin 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)															---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148457382	148457382	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148457382delA	uc010lpg.2	+						CUL1_uc003wey.2_Intron|CUL1_uc003wez.2_Intron	NM_003592	NP_003583			cullin 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	148677872	148677873	+	IGR	INS	-	C	C	rs137871824	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148677872_148677873insC								MIR1975 (39218 upstream) : PDIA4 (22281 downstream)																																			---	---	---	---
PDIA4	9601	broad.mit.edu	37	7	148702830	148702830	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148702830delA	uc003wff.2	-							NM_004911	NP_004902			protein disulfide isomerase A4 precursor						cell redox homeostasis|glycerol ether metabolic process|protein secretion	endoplasmic reticulum lumen|melanosome	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			lung(5)|ovary(1)	6	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)													OREG0018420	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	149077606	149077606	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149077606delT								ZNF212 (124925 upstream) : ZNF777 (50855 downstream)																																			---	---	---	---
ZNF767	79970	broad.mit.edu	37	7	149318362	149318362	+	RNA	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149318362delC	uc003wfy.3	-	2		c.538delG			ZNF767_uc003wfx.2_RNA|ZNF767_uc011kuq.1_RNA	NR_027789				Homo sapiens cDNA FLJ12700 fis, clone NT2RP1000721.											central_nervous_system(1)	1	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00434)															---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149501110	149501110	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149501110delG	uc010lpk.2	+	57	8246	c.8246delG	c.(8245-8247)TGGfs	p.W2749fs		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	2749	TSP type-1 6.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
GIMAP8	155038	broad.mit.edu	37	7	150155230	150155231	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150155230_150155231delGT	uc003whj.2	+							NM_175571	NP_783161			GTPase, IMAP family member 8							endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	150302510	150302510	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150302510delT								GIMAP4 (31470 upstream) : GIMAP6 (19956 downstream)																																			---	---	---	---
AGAP3	116988	broad.mit.edu	37	7	150786252	150786252	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150786252delA	uc003wjg.1	+						AGAP3_uc003wje.1_Intron|AGAP3_uc003wjf.1_Intron|AGAP3_uc010lpy.1_Intron	NM_031946	NP_114152			centaurin, gamma 3 isoform a						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
WDR86	349136	broad.mit.edu	37	7	151101315	151101315	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151101315delA	uc003wkb.2	-						WDR86_uc003wka.2_Intron|WDR86_uc011kvk.1_Intron|WDR86_uc003wkc.2_Intron	NM_198285	NP_938026			WD repeat domain 86												0			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
PRKAG2	51422	broad.mit.edu	37	7	151334477	151334477	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151334477delT	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)														---	---	---	---
GALNT11	63917	broad.mit.edu	37	7	151800158	151800158	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151800158delT	uc010lqg.1	+						GALNT11_uc011kvm.1_Intron|GALNT11_uc003wku.2_Intron|GALNT11_uc003wkv.1_Intron|GALNT11_uc011kvn.1_Intron	NM_022087	NP_071370			N-acetylgalactosaminyltransferase 11							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151851246	151851246	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151851246delA	uc003wla.2	-						MLL3_uc003wkz.2_Intron|MLL3_uc003wkx.2_Intron|MLL3_uc003wky.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	151936095	151936096	+	Intron	DEL	TT	-	-	rs3056723		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151936095_151936096delTT	uc003wla.2	-						MLL3_uc003wkz.2_5'Flank	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	151982393	151982394	+	Intron	INS	-	T	T	rs111983046		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151982393_151982394insT	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								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151987126	151987126	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151987126delA	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	152177685	152177714	+	IGR	DEL	ATAACATAACATAACATAACATAACATAAC	-	-	rs72167655		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152177685_152177714delATAACATAACATAACATAACATAACATAAC								LOC100128822 (15057 upstream) : XRCC2 (165875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	152192633	152192633	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152192633delA								LOC100128822 (30005 upstream) : XRCC2 (150956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	152228171	152228171	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152228171delT								LOC100128822 (65543 upstream) : XRCC2 (115418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	153184780	153184780	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153184780delT								ACTR3B (632317 upstream) : DPP6 (399639 downstream)																																			---	---	---	---
DPP6	1804	broad.mit.edu	37	7	153674630	153674630	+	Intron	DEL	C	-	-	rs4726363	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153674630delC	uc003wli.2	+							NM_001039350	NP_001034439			dipeptidyl-peptidase 6 isoform 3						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154420736	154420736	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154420736delA	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	154676021	154676024	+	Intron	DEL	CACA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154676021_154676024delCACA	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)															---	---	---	---
HTR5A	3361	broad.mit.edu	37	7	154876817	154876818	+	3'UTR	DEL	AC	-	-	rs34932101		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154876817_154876818delAC	uc003wlu.1	+	2						NM_024012	NP_076917			5-hydroxytryptamine receptor 5A							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	154924736	154924736	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154924736delT								HTR5A (47277 upstream) : INSIG1 (164750 downstream)																																			---	---	---	---
RBM33	155435	broad.mit.edu	37	7	155440133	155440133	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155440133delT	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)														---	---	---	---
RBM33	155435	broad.mit.edu	37	7	155473256	155473258	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155473256_155473258delTTT	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	155627938	155627938	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155627938delT								SHH (22971 upstream) : C7orf4 (705247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155888561	155888561	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155888561delT								SHH (283594 upstream) : C7orf4 (444624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	156375768	156375768	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156375768delT								C7orf4 (41973 upstream) : C7orf13 (55294 downstream)																																			---	---	---	---
LMBR1	64327	broad.mit.edu	37	7	156561784	156561784	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156561784delA	uc003wmw.3	-						LMBR1_uc003wmv.3_Intron|LMBR1_uc003wmx.3_Intron|LMBR1_uc010lqn.2_Intron|LMBR1_uc011kvx.1_Intron	NM_022458	NP_071903			limb region 1 protein							integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	157226046	157226047	+	IGR	DEL	GC	-	-	rs34744657		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157226046_157226047delGC								DNAJB6 (15914 upstream) : PTPRN2 (105704 downstream)																																			---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157338027	157338027	+	Intron	DEL	T	-	-	rs113095456	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157338027delT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron|PTPRN2_uc003wnn.2_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	157564651	157564652	+	Intron	INS	-	AC	AC	rs147022846	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157564651_157564652insAC	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	157849892	157849892	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157849892delT	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	158055056	158055057	+	Intron	INS	-	CA	CA	rs139362555	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158055056_158055057insCA	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	158065820	158065821	+	Intron	INS	-	C	C	rs60371479		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158065820_158065821insC	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	158280557	158280558	+	Intron	DEL	AA	-	-	rs79616932		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158280557_158280558delAA	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	158305253	158305254	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158305253_158305254delCA	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	158387856	158387858	+	IGR	DEL	ATA	-	-	rs141952618		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158387856_158387858delATA								PTPRN2 (7374 upstream) : NCAPG2 (36145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	158415857	158415857	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158415857delT								PTPRN2 (35375 upstream) : NCAPG2 (8146 downstream)																																			---	---	---	---
NCAPG2	54892	broad.mit.edu	37	7	158457529	158457529	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158457529delA	uc003wnv.1	-						NCAPG2_uc010lqu.1_Intron|NCAPG2_uc003wnw.1_Intron|NCAPG2_uc003wnx.1_Intron|NCAPG2_uc011kwe.1_Intron|NCAPG2_uc011kwc.1_Intron|NCAPG2_uc011kwd.1_5'Flank	NM_017760	NP_060230			leucine zipper protein 5						cell division|chromosome condensation|mitosis	nucleus	methylated histone residue binding			ovary(1)|breast(1)|kidney(1)	3	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)														---	---	---	---
ESYT2	57488	broad.mit.edu	37	7	158574528	158574529	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158574528_158574529delGT	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																		---	---	---	---
WDR60	55112	broad.mit.edu	37	7	158706914	158706914	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158706914delT	uc003woe.3	+						WDR60_uc010lqv.2_Intron|WDR60_uc010lqw.2_Intron	NM_018051	NP_060521			WD repeat domain 60											ovary(2)|breast(1)|central_nervous_system(1)	4	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	158781182	158781185	+	IGR	DEL	CATG	-	-	rs58504012		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158781182_158781185delCATG								WDR60 (42300 upstream) : LOC154822 (19860 downstream)																																			---	---	---	---
VIPR2	7434	broad.mit.edu	37	7	158866405	158866405	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158866405delT	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	159029715	159029716	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:159029715_159029716insC								VIPR2 (92066 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	25964	25964	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25964delA								None (None upstream) : OR4F21 (90124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	303783	303784	+	IGR	INS	-	T	T	rs149835304	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:303783_303784insT								ZNF596 (106451 upstream) : FBXO25 (53024 downstream)																																			---	---	---	---
FBXO25	26260	broad.mit.edu	37	8	375404	375404	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:375404delT	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	1061388	1061389	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1061388_1061389insT	uc003wpj.1	+											Homo sapiens cDNA clone IMAGE:4824304.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1175326	1175326	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1175326delA								ERICH1 (494100 upstream) : DLGAP2 (274243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1363474	1363475	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1363474_1363475insT								ERICH1 (682248 upstream) : DLGAP2 (86094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1382651	1382651	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1382651delT								ERICH1 (701425 upstream) : DLGAP2 (66918 downstream)																																			---	---	---	---
DLGAP2	9228	broad.mit.edu	37	8	1463665	1463666	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1463665_1463666delCA	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	1605260	1605260	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1605260delT	uc003wpl.2	+						DLGAP2_uc003wpm.2_Intron	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	1633901	1633902	+	Intron	DEL	AA	-	-	rs113424052		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1633901_1633902delAA	uc003wpl.2	+						DLGAP2_uc003wpm.2_Intron	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)														---	---	---	---
CLN8	2055	broad.mit.edu	37	8	1716116	1716116	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1716116delT	uc003wpo.3	+							NM_018941	NP_061764			ceroid-lipofuscinosis, neuronal 8						cell death|ceramide biosynthetic process|cholesterol metabolic process|lipid transport|negative regulation of proteolysis|phospholipid metabolic process	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)														---	---	---	---
KBTBD11	9920	broad.mit.edu	37	8	1946962	1946963	+	Intron	INS	-	CAT	CAT	rs146212167	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1946962_1946963insCAT	uc003wpw.3	+							NM_014867	NP_055682			kelch repeat and BTB (POZ) domain containing 11											pancreas(1)	1		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.72e-05)|READ - Rectum adenocarcinoma(644;0.0929)|COAD - Colon adenocarcinoma(149;0.134)														---	---	---	---
MYOM2	9172	broad.mit.edu	37	8	2031537	2031538	+	Intron	INS	-	GCATCTCACGTGTGCTTAGCA	GCATCTCACGTGTGCTTAGCA	rs141981227	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2031537_2031538insGCATCTCACGTGTGCTTAGCA	uc003wpx.3	+						MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961			myomesin 2						muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)														---	---	---	---
MYOM2	9172	broad.mit.edu	37	8	2085552	2085553	+	Intron	DEL	TG	-	-	rs113254399		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2085552_2085553delTG	uc003wpx.3	+						MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961			myomesin 2						muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	2119152	2119152	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2119152delT								MYOM2 (25773 upstream) : CSMD1 (673724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2309392	2309392	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2309392delT								MYOM2 (216013 upstream) : CSMD1 (483484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2441635	2441635	+	IGR	DEL	T	-	-	rs140010878	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2441635delT								MYOM2 (348256 upstream) : CSMD1 (351241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2613996	2613996	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2613996delT								MYOM2 (520617 upstream) : CSMD1 (178880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2674766	2674766	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2674766delA								MYOM2 (581387 upstream) : CSMD1 (118110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2731918	2731919	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2731918_2731919insA								MYOM2 (638539 upstream) : CSMD1 (60957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2735156	2735156	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2735156delA								MYOM2 (641777 upstream) : CSMD1 (57720 downstream)																																			---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2799865	2799867	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2799865_2799867delAAA	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	2870092	2870092	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2870092delA	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	2937332	2937332	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2937332delT	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	3064193	3064194	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3064193_3064194delTG	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-4292-01	TCGA-BR-4292-01									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	3209834	3209834	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3209834delA	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	3343795	3343796	+	Intron	INS	-	T	T	rs147016948	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3343795_3343796insT	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	3473284	3473285	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3473284_3473285insT	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	3627529	3627529	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3627529delT	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	3656776	3656776	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3656776delT	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	4304459	4304461	+	Intron	DEL	AAA	-	-	rs72007340		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4304459_4304461delAAA	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	4416235	4416235	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4416235delA	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	4586282	4586282	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4586282delA	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	4593907	4593908	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4593907_4593908delGA	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	4736009	4736010	+	Intron	INS	-	ATG	ATG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4736009_4736010insATG	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	5062038	5062039	+	IGR	DEL	AC	-	-	rs145754292		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5062038_5062039delAC								CSMD1 (209710 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5144842	5144842	+	IGR	DEL	T	-	-	rs34949158		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5144842delT								CSMD1 (292514 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5632013	5632014	+	IGR	INS	-	GTTT	GTTT	rs144069938	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5632013_5632014insGTTT								CSMD1 (779685 upstream) : MCPH1 (632107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5876599	5876599	+	IGR	DEL	A	-	-	rs34369173		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5876599delA								None (None upstream) : MCPH1 (387522 downstream)																																			---	---	---	---
MCPH1	79648	broad.mit.edu	37	8	6287050	6287050	+	Intron	DEL	T	-	-	rs112056239		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6287050delT	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	6380518	6380518	+	Intron	DEL	T	-	-	rs73199051	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6380518delT	uc003wqi.2	+						ANGPT2_uc003wqj.3_Intron|ANGPT2_uc003wqk.3_Intron|ANGPT2_uc010lri.2_Intron|ANGPT2_uc003wql.3_Intron	NM_024596	NP_078872			microcephalin							microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)														---	---	---	---
MCPH1	79648	broad.mit.edu	37	8	6443654	6443654	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6443654delT	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	6495290	6495290	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6495290delT	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	6552559	6552559	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6552559delA								MCPH1 (46534 upstream) : AGPAT5 (13319 downstream)																																			---	---	---	---
AGPAT5	55326	broad.mit.edu	37	8	6582189	6582195	+	Intron	DEL	ACCGTTA	-	-	rs141544613		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6582189_6582195delACCGTTA	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	6622143	6622144	+	IGR	DEL	AT	-	-	rs61046814		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6622143_6622144delAT								AGPAT5 (3124 upstream) : XKR5 (43899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6954470	6954471	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6954470_6954471insG								DEFA5 (40211 upstream) : LOC349196 (163671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6964631	6964650	+	IGR	DEL	CATCCATCCATGCATCCATC	-	-	rs59555794	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6964631_6964650delCATCCATCCATGCATCCATC								DEFA5 (50372 upstream) : LOC349196 (153492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6981415	6981415	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6981415delA								DEFA5 (67156 upstream) : LOC349196 (136727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8387721	8387722	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8387721_8387722delTT								SGK223 (148464 upstream) : CLDN23 (171944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8457100	8457100	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8457100delA								SGK223 (217843 upstream) : CLDN23 (102566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8508085	8508087	+	IGR	DEL	AAA	-	-	rs144908448		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8508085_8508087delAAA								SGK223 (268828 upstream) : CLDN23 (51579 downstream)																																			---	---	---	---
MFHAS1	9258	broad.mit.edu	37	8	8738195	8738198	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8738195_8738198delTTTT	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	8769015	8769015	+	IGR	DEL	A	-	-	rs78742641		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8769015delA								MFHAS1 (17884 upstream) : ERI1 (91299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8909168	8909169	+	IGR	DEL	AA	-	-	rs67347090		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8909168_8909169delAA								ERI1 (18319 upstream) : PPP1R3B (84605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9286359	9286361	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9286359_9286361delAAA								PPP1R3B (277275 upstream) : TNKS (127084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9287303	9287304	+	IGR	INS	-	T	T	rs73185279	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9287303_9287304insT								PPP1R3B (278219 upstream) : TNKS (126141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9341806	9341807	+	IGR	DEL	AA	-	-	rs34908864		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9341806_9341807delAA								PPP1R3B (332722 upstream) : TNKS (71638 downstream)																																			---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9610303	9610303	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9610303delA	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-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9722437delT								TNKS (82582 upstream) : LOC157627 (35137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9792019	9792019	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9792019delA								MIR124-1 (31037 upstream) : MSRA (119811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9844712	9844715	+	IGR	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9844712_9844715delAAAA								MIR124-1 (83730 upstream) : MSRA (67115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9887171	9887171	+	IGR	DEL	G	-	-	rs10100074	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9887171delG								MIR124-1 (126189 upstream) : MSRA (24659 downstream)																																			---	---	---	---
MSRA	4482	broad.mit.edu	37	8	9959441	9959442	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9959441_9959442insT	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	10039470	10039471	+	Intron	DEL	AT	-	-	rs11249972	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10039470_10039471delAT	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	10109372	10109372	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10109372delG	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	10271682	10271682	+	Intron	DEL	A	-	-	rs75083845		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10271682delA	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	10322772	10322772	+	IGR	DEL	C	-	-	rs74998236		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10322772delC								MSRA (36373 upstream) : PRSS55 (60309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	10458930	10458930	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10458930delG								PRSS55 (56223 upstream) : RP1L1 (4932 downstream)																																			---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10471308	10471309	+	Intron	INS	-	A	A	rs149973392	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10471308_10471309insA	uc003wtc.2	-							NM_178857	NP_849188			retinitis pigmentosa 1-like 1						intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10472228	10472228	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10472228delA	uc003wtc.2	-							NM_178857	NP_849188			retinitis pigmentosa 1-like 1						intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	10773018	10773018	+	Intron	DEL	T	-	-	rs113163728		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10773018delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	11071776	11071776	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11071776delA								XKR6 (12901 upstream) : MTMR9 (70224 downstream)																																			---	---	---	---
AMAC1L2	83650	broad.mit.edu	37	8	11185853	11185854	+	5'Flank	INS	-	GT	GT	rs151066674	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11185853_11185854insGT	uc003wtp.1	+						uc003wto.1_5'Flank	NM_054028	NP_473369			acyl-malonyl condensing enzyme							integral to membrane					0			STAD - Stomach adenocarcinoma(15;0.00676)	COAD - Colon adenocarcinoma(149;0.0563)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	11189696	11189696	+	IGR	DEL	A	-	-	rs78909439		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11189696delA								AMAC1L2 (1 upstream) : TDH (7450 downstream)																																			---	---	---	---
C8orf12	83656	broad.mit.edu	37	8	11239943	11239943	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11239943delT	uc003wtu.2	+							NR_026814				Homo sapiens mRNA for hypothetical protein (C8orf12 gene).												0																		---	---	---	---
FAM167A	83648	broad.mit.edu	37	8	11303331	11303331	+	5'Flank	DEL	A	-	-	rs35523033		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11303331delA	uc010lry.1	-						FAM167A_uc003wtw.2_Intron	NM_053279	NP_444509			hypothetical protein LOC83648												0																		---	---	---	---
GATA4	2626	broad.mit.edu	37	8	11570562	11570562	+	Intron	DEL	T	-	-	rs35874748		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11570562delT	uc003wuc.2	+						GATA4_uc003wub.1_Intron|GATA4_uc011kxc.1_Intron	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)														---	---	---	---
CTSB	1508	broad.mit.edu	37	8	11722412	11722413	+	Intron	INS	-	CT	CT	rs139427177	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11722412_11722413insCT	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	11733261	11733261	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11733261delA								CTSB (7615 upstream) : DEFB136 (98187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	11810490	11810492	+	IGR	DEL	AAA	-	-	rs35728022		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11810490_11810492delAAA								CTSB (84844 upstream) : DEFB136 (20956 downstream)																																			---	---	---	---
FAM66D	100132923	broad.mit.edu	37	8	12242476	12242476	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12242476delT	uc011kxp.1	+						uc003wvm.1_Intron|FAM66A_uc010lsi.2_Intron|FAM66A_uc010lsj.1_5'Flank					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	12429908	12429911	+	Intron	DEL	AAAC	-	-	rs59822526	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12429908_12429911delAAAC	uc003wvy.3	-						uc003wwa.2_5'Flank					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	12504039	12504039	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12504039delA	uc003wvy.3	-						uc003wwc.3_Intron					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	12554282	12554282	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12554282delA								FAM66D (129928 upstream) : LONRF1 (25124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	12578019	12578019	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12578019delA								FAM66D (153665 upstream) : LONRF1 (1387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	12770446	12770446	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12770446delT								LOC340357 (101536 upstream) : C8orf79 (32705 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	12788696	12788696	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12788696delA								LOC340357 (119786 upstream) : C8orf79 (14455 downstream)																																			---	---	---	---
C8orf79	57604	broad.mit.edu	37	8	12832531	12832534	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12832531_12832534delTTTT	uc010lsq.2	+						C8orf79_uc011kxw.1_Intron	NM_020844	NP_065895			hypothetical protein LOC57604 isoform 1								methyltransferase activity				0																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	12945765	12945765	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12945765delT	uc003wwm.2	-						DLC1_uc003wwk.1_Intron|DLC1_uc003wwl.1_Intron|DLC1_uc011kxx.1_Intron	NM_182643	NP_872584			deleted in liver cancer 1 isoform 1						actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	13147012	13147012	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13147012delT	uc003wwm.2	-						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	13150143	13150143	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13150143delA	uc003wwm.2	-						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	13368489	13368489	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13368489delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	13433100	13433100	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13433100delA								C8orf48 (7304 upstream) : SGCZ (514274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	13513504	13513505	+	IGR	INS	-	A	A	rs142155822	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13513504_13513505insA								C8orf48 (87708 upstream) : SGCZ (433869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	13727978	13727978	+	IGR	DEL	A	-	-	rs4831500	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13727978delA								C8orf48 (302182 upstream) : SGCZ (219396 downstream)																																			---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14412470	14412470	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14412470delA	uc003wwq.2	-						SGCZ_uc010lss.2_5'Flank	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	14533855	14533856	+	Intron	INS	-	TG	TG	rs145238741	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14533855_14533856insTG	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	14614567	14614567	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14614567delT	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	14640943	14640944	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14640943_14640944delAA	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	14968456	14968456	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14968456delA	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	15229230	15229232	+	IGR	DEL	TCC	-	-	rs150772760		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15229230_15229232delTCC								SGCZ (133438 upstream) : TUSC3 (168498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15710556	15710557	+	IGR	INS	-	CCTCTT	CCTCTT	rs149468924	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15710556_15710557insCCTCTT								TUSC3 (88563 upstream) : MSR1 (254831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15752892	15752893	+	IGR	DEL	TT	-	-	rs148786516	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15752892_15752893delTT								TUSC3 (130899 upstream) : MSR1 (212495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15960561	15960562	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15960561_15960562delTG								TUSC3 (338568 upstream) : MSR1 (4826 downstream)																																			---	---	---	---
MSR1	4481	broad.mit.edu	37	8	15978126	15978138	+	Intron	DEL	AAAAAAAAAAAAA	-	-	rs71814384		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15978126_15978138delAAAAAAAAAAAAA	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_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	16346439	16346440	+	IGR	DEL	TG	-	-	rs138858670		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16346439_16346440delTG								MSR1 (296139 upstream) : FGF20 (503894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16566444	16566444	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16566444delA								MSR1 (516144 upstream) : FGF20 (283890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16603785	16603807	+	IGR	DEL	ACATGGCCAATTTCAAGCTCCCG	-	-	rs146612305		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16603785_16603807delACATGGCCAATTTCAAGCTCCCG								MSR1 (553485 upstream) : FGF20 (246527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16638029	16638030	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16638029_16638030insA								MSR1 (587729 upstream) : FGF20 (212304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16705487	16705489	+	IGR	DEL	AGA	-	-	rs10560681		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16705487_16705489delAGA								MSR1 (655187 upstream) : FGF20 (144845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16775835	16775835	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16775835delG								MSR1 (725535 upstream) : FGF20 (74499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16793151	16793152	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16793151_16793152delAC								MSR1 (742851 upstream) : FGF20 (57182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16875550	16875550	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16875550delT								FGF20 (15876 upstream) : EFHA2 (9197 downstream)																																			---	---	---	---
EFHA2	286097	broad.mit.edu	37	8	16921329	16921329	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16921329delA	uc003wxd.2	+							NM_181723	NP_859074			EF-hand domain family, member A2							integral to membrane	calcium ion binding			skin(1)	1				Colorectal(111;0.0686)|COAD - Colon adenocarcinoma(73;0.239)														---	---	---	---
ZDHHC2	51201	broad.mit.edu	37	8	17031606	17031606	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17031606delT	uc003wxe.2	+							NM_016353	NP_057437			zinc finger, DHHC-type containing 2							integral to membrane	acyltransferase activity|zinc ion binding				0				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)														---	---	---	---
VPS37A	137492	broad.mit.edu	37	8	17145187	17145187	+	Intron	DEL	A	-	-	rs74353301		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17145187delA	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	17205893	17205893	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17205893delA	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	17227638	17227639	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17227638_17227639delTT	uc003wxm.2	-							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	17237286	17237286	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17237286delT	uc003wxm.2	-							NM_004686	NP_004677			myotubularin related protein 7								protein tyrosine phosphatase activity			skin(1)	1				Colorectal(111;0.112)														---	---	---	---
PDGFRL	5157	broad.mit.edu	37	8	17478915	17478916	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17478915_17478916delTT	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	17542727	17542727	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17542727delT	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	17641031	17641031	+	Intron	DEL	T	-	-	rs79875542		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17641031delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	17719403	17719403	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17719403delT								MTUS1 (60977 upstream) : FGL1 (2499 downstream)																																			---	---	---	---
FGL1	2267	broad.mit.edu	37	8	17735632	17735632	+	Intron	DEL	T	-	-	rs75625628		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17735632delT	uc003wxx.2	-						FGL1_uc003wxy.2_Intron|FGL1_uc003wxz.2_Intron|FGL1_uc003wya.2_Intron|FGL1_uc003wyb.2_Intron|FGL1_uc003wyc.2_Intron|FGL1_uc003wyd.2_Intron|FGL1_uc003wye.2_Intron|FGL1_uc003wyf.2_Intron	NM_201553	NP_963847			fibrinogen-like 1 precursor						signal transduction	fibrinogen complex	receptor binding				0				Colorectal(111;0.0573)|COAD - Colon adenocarcinoma(73;0.215)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	17891350	17891350	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17891350delA								PCM1 (3895 upstream) : ASAH1 (22575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	17947398	17947399	+	Intron	DEL	TT	-	-	rs146025812		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17947398_17947399delTT	uc003wyp.1	+											full-length cDNA clone CS0DL011YP14 of B cells (Ramos cell line) Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	17994397	17994397	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17994397delT								ASAH1 (51890 upstream) : NAT1 (33574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	18370726	18370727	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18370726_18370727insC								NAT2 (112003 upstream) : PSD3 (14087 downstream)																																			---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18558218	18558218	+	Intron	DEL	T	-	-	rs113197065		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18558218delT	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)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18591238	18591238	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18591238delA	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)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18659343	18659343	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18659343delA	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)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18681289	18681290	+	Intron	DEL	CT	-	-	rs72207091		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18681289_18681290delCT	uc003wza.2	-							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	18736558	18736561	+	Intron	DEL	ACAA	-	-	rs72402831		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18736558_18736561delACAA	uc003wza.2	-							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	18796536	18796537	+	Intron	INS	-	A	A	rs143899713	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18796536_18796537insA	uc003wza.2	-							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	19255818	19255818	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19255818delA								SH2D4A (2504 upstream) : CSGALNACT1 (5855 downstream)																																			---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19411413	19411414	+	Intron	INS	-	AC	AC	rs144561439	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19411413_19411414insAC	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	19413896	19413899	+	Intron	DEL	AAAA	-	-	rs35965072		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19413896_19413899delAAAA	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	19464666	19464668	+	Intron	DEL	AAA	-	-	rs113783252		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19464666_19464668delAAA	uc011kyo.1	-						CSGALNACT1_uc003wzg.2_Intron|CSGALNACT1_uc011kyp.1_Intron	NM_018371	NP_060841			chondroitin sulfate						anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)														---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19482188	19482190	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19482188_19482190delTTT	uc011kyo.1	-						CSGALNACT1_uc003wzg.2_Intron|CSGALNACT1_uc011kyp.1_Intron	NM_018371	NP_060841			chondroitin sulfate						anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)														---	---	---	---
INTS10	55174	broad.mit.edu	37	8	19707655	19707656	+	Intron	DEL	AG	-	-	rs56868715		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19707655_19707656delAG	uc003wzj.2	+							NM_018142	NP_060612			integrator complex subunit 10						snRNA processing	integrator complex	protein binding			ovary(1)	1				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	19838387	19838388	+	IGR	INS	-	A	A	rs138345533	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19838387_19838388insA								LPL (13618 upstream) : SLC18A1 (163979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20243247	20243248	+	IGR	INS	-	CAAC	CAAC	rs78992414	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20243247_20243248insCAAC								LZTS1 (130444 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20379081	20379082	+	IGR	INS	-	ACAC	ACAC	rs138722695	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20379081_20379082insACAC								LZTS1 (266278 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20436515	20436515	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20436515delA								LZTS1 (323712 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20586025	20586025	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20586025delA								LZTS1 (473222 upstream) : GFRA2 (963505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20881432	20881432	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20881432delA								LZTS1 (768629 upstream) : GFRA2 (668098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21017630	21017631	+	IGR	INS	-	TCAC	TCAC	rs145846879	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21017630_21017631insTCAC								LZTS1 (904827 upstream) : GFRA2 (531899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21300255	21300256	+	IGR	DEL	AA	-	-	rs35818786		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21300255_21300256delAA								None (None upstream) : GFRA2 (249274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21344591	21344591	+	IGR	DEL	A	-	-	rs139376874		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21344591delA								None (None upstream) : GFRA2 (204939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21351554	21351559	+	IGR	DEL	TGTGTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21351554_21351559delTGTGTG								None (None upstream) : GFRA2 (197971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21387021	21387022	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21387021_21387022delGT								None (None upstream) : GFRA2 (162508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21496883	21496883	+	IGR	DEL	A	-	-	rs78408402		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21496883delA								None (None upstream) : GFRA2 (52647 downstream)																																			---	---	---	---
GFRA2	2675	broad.mit.edu	37	8	21550684	21550684	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21550684delT	uc003wzu.1	-	9					GFRA2_uc003wzv.1_3'UTR|GFRA2_uc003wzw.1_3'UTR	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)														---	---	---	---
GFRA2	2675	broad.mit.edu	37	8	21578508	21578508	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	21691091	21691091	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21691091delA	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	21828317	21828317	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21828317delA	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)														---	---	---	---
XPO7	23039	broad.mit.edu	37	8	21829688	21829688	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21829688delT	uc003xaa.3	+						XPO7_uc010lti.2_Intron|XPO7_uc010ltj.1_Intron|XPO7_uc010ltk.2_Intron	NM_015024	NP_055839			exportin 7 isoform b						mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)														---	---	---	---
FAM160B2	64760	broad.mit.edu	37	8	21947664	21947665	+	Intron	INS	-	G	G	rs147230760	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21947664_21947665insG	uc011kyx.1	+						FAM160B2_uc011kyw.1_Intron|FAM160B2_uc011kyy.1_Intron	NM_022749	NP_073586			retinoic acid induced 16												0																		---	---	---	---
BMP1	649	broad.mit.edu	37	8	22028439	22028439	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22028439delA	uc003xbg.2	+						BMP1_uc011kzb.1_Intron|BMP1_uc003xba.2_Intron|BMP1_uc003xbb.2_Intron|BMP1_uc003xbe.2_Intron|BMP1_uc003xbc.2_Intron|BMP1_uc003xbd.2_Intron|BMP1_uc003xbf.2_Intron|BMP1_uc011kzc.1_Intron|BMP1_uc003xbh.2_Intron|BMP1_uc003xbi.2_Intron	NM_006129	NP_006120			bone morphogenetic protein 1 isoform 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)														---	---	---	---
BMP1	649	broad.mit.edu	37	8	22036111	22036111	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22036111delT	uc003xbg.2	+						BMP1_uc003xba.2_Intron|BMP1_uc003xbb.2_Intron|BMP1_uc003xbe.2_Intron|BMP1_uc003xbc.2_Intron|BMP1_uc003xbd.2_Intron|BMP1_uc003xbf.2_Intron|BMP1_uc011kzc.1_Intron|BMP1_uc003xbh.2_Intron|BMP1_uc003xbi.2_Intron	NM_006129	NP_006120			bone morphogenetic protein 1 isoform 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)														---	---	---	---
BMP1	649	broad.mit.edu	37	8	22067960	22067963	+	Intron	DEL	CTCT	-	-	rs35296515		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22067960_22067963delCTCT	uc003xbg.2	+						BMP1_uc011kzc.1_Intron|BMP1_uc003xbh.2_Intron|BMP1_uc003xbi.2_Intron	NM_006129	NP_006120			bone morphogenetic protein 1 isoform 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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	22124341	22124342	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22124341_22124342delTT								POLR3D (15662 upstream) : PIWIL2 (8468 downstream)																																			---	---	---	---
SLC39A14	23516	broad.mit.edu	37	8	22275411	22275411	+	Intron	DEL	T	-	-	rs140021415	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22275411delT	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)														---	---	---	---
SLC39A14	23516	broad.mit.edu	37	8	22276057	22276057	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22276057delT	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	22382671	22382671	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22382671delA	uc003xbs.2	+						PPP3CC_uc011kzi.1_Intron|PPP3CC_uc003xbt.2_Intron|PPP3CC_uc011kzj.1_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	22397223	22397223	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22397223delT	uc003xbs.2	+						PPP3CC_uc011kzi.1_Intron|PPP3CC_uc003xbt.2_Intron|PPP3CC_uc011kzj.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	22565500	22565501	+	IGR	DEL	TG	-	-	rs67450163		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22565500_22565501delTG								EGR3 (14685 upstream) : PEBP4 (5264 downstream)																																			---	---	---	---
PEBP4	157310	broad.mit.edu	37	8	22609144	22609147	+	Intron	DEL	TGTG	-	-	rs144655400		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22609144_22609147delTGTG	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	22776442	22776443	+	Intron	INS	-	CACATGTGCA	CACATGTGCA	rs141376967	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22776442_22776443insCACATGTGCA	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)												OREG0018626	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	22834307	22834308	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22834307_22834308delTT								PEBP4 (48886 upstream) : RHOBTB2 (10622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	22841255	22841255	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22841255delT								PEBP4 (55834 upstream) : RHOBTB2 (3675 downstream)																																			---	---	---	---
TNFRSF10B	8795	broad.mit.edu	37	8	22902747	22902747	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22902747delA	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	22914164	22914164	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22914164delA	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)														---	---	---	---
TNFRSF10D	8793	broad.mit.edu	37	8	23008862	23008862	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23008862delA	uc003xcz.1	-							NM_003840	NP_003831			tumor necrosis factor receptor superfamily,						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	23366935	23366936	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23366935_23366936insG								ENTPD4 (51691 upstream) : SLC25A37 (19427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23474259	23474259	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23474259delA								SLC25A37 (44198 upstream) : NKX3-1 (61948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23559917	23559918	+	IGR	INS	-	G	G	rs146685693	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23559917_23559918insG								NKX3-1 (19467 upstream) : NKX2-6 (47 downstream)																																			---	---	---	---
NKX2-6	137814	broad.mit.edu	37	8	23564973	23564973	+	5'Flank	DEL	G	-	-	rs114388350		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23564973delG	uc011kzy.1	-							NM_001136271	NP_001129743			NK2 transcription factor related, locus 6							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	23595062	23595063	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23595062_23595063delAA								NKX2-6 (31140 upstream) : STC1 (104371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23717467	23717467	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23717467delT								STC1 (5147 upstream) : ADAM28 (434113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23764140	23764140	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23764140delA								STC1 (51820 upstream) : ADAM28 (387440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23885679	23885679	+	IGR	DEL	A	-	-	rs78898405		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23885679delA								STC1 (173359 upstream) : ADAM28 (265901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23890133	23890133	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23890133delT								STC1 (177813 upstream) : ADAM28 (261447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24014870	24014871	+	IGR	DEL	TT	-	-	rs145566354		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24014870_24014871delTT								STC1 (302550 upstream) : ADAM28 (136709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24038052	24038052	+	IGR	DEL	G	-	-	rs148480612		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24038052delG								STC1 (325732 upstream) : ADAM28 (113528 downstream)																																			---	---	---	---
ADAM28	10863	broad.mit.edu	37	8	24164642	24164642	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24164642delG	uc003xdy.2	+						ADAM28_uc003xdx.2_Intron|ADAM28_uc011kzz.1_Intron|ADAM28_uc011laa.1_Intron	NM_014265	NP_055080			ADAM metallopeptidase domain 28 isoform 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	24566934	24566935	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24566934_24566935insA								ADAM7 (182453 upstream) : NEFM (204339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24568129	24568129	+	IGR	DEL	T	-	-	rs71652058		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24568129delT								ADAM7 (183648 upstream) : NEFM (203145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24581187	24581189	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24581187_24581189delAAA								ADAM7 (196706 upstream) : NEFM (190085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24705665	24705665	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24705665delT								ADAM7 (321184 upstream) : NEFM (65609 downstream)																																			---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25077223	25077224	+	Intron	DEL	TT	-	-	rs71925728		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25077223_25077224delTT	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	25088582	25088582	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25088582delT	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	25099670	25099670	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25099670delA	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-4292-01	TCGA-BR-4292-01									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	25240127	25240127	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25240127delT	uc003xeg.2	+						PPP2R2A_uc003xek.2_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	25424746	25424746	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25424746delA	uc003xek.2	+							NM_002717	NP_002708			alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25594943	25594943	+	Intron	DEL	A	-	-	rs66579653		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25594943delA	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	25599682	25599682	+	Intron	DEL	C	-	-	rs60979120	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25599682delC	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	25813287	25813288	+	Intron	INS	-	AAAGTCTC	AAAGTCTC	rs150757509	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25813287_25813288insAAAGTCTC	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	26149253	26149253	+	5'UTR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26149253delC	uc003xeu.2	+	1					PPP2R2A_uc003xek.2_Intron|PPP2R2A_uc011laf.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	26163689	26163689	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26163689delA	uc003xeu.2	+						PPP2R2A_uc003xek.2_Intron|PPP2R2A_uc011laf.1_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	26329095	26329096	+	IGR	DEL	AA	-	-	rs66940440		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26329095_26329096delAA								BNIP3L (58451 upstream) : PNMA2 (33100 downstream)																																			---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26439709	26439709	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26439709delT	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	26454999	26454999	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26454999delT	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	26560187	26560187	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26560187delT								DPYSL2 (44494 upstream) : ADRA1A (45480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	26582854	26582854	+	IGR	DEL	T	-	-	rs113151307		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26582854delT								DPYSL2 (67161 upstream) : ADRA1A (22813 downstream)																																			---	---	---	---
ADRA1A	148	broad.mit.edu	37	8	26632581	26632582	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26632581_26632582insG	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)													---	---	---	---
ADRA1A	148	broad.mit.edu	37	8	26665091	26665092	+	Intron	INS	-	AT	AT	rs140880199	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26665091_26665092insAT	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	27123552	27123567	+	IGR	DEL	TCTCTCTCTCCCTCTT	-	-	rs34731970	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27123552_27123567delTCTCTCTCTCCCTCTT								STMN4 (7649 upstream) : TRIM35 (18837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	27135046	27135048	+	IGR	DEL	TTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27135046_27135048delTTC								STMN4 (19143 upstream) : TRIM35 (7356 downstream)																																			---	---	---	---
TRIM35	23087	broad.mit.edu	37	8	27153488	27153489	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27153488_27153489insA	uc003xfl.1	-						TRIM35_uc010lup.1_Intron|TRIM35_uc003xfm.1_Intron	NM_171982	NP_741983			tripartite motif-containing 35 isoform 2						apoptosis|induction of apoptosis|negative regulation of mitotic cell cycle	cytoplasm|nucleus	zinc ion binding				0		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|Epithelial(17;9.34e-10)|Colorectal(74;0.141)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	27438324	27438324	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27438324delT								EPHX2 (35840 upstream) : CLU (16127 downstream)																																			---	---	---	---
CLU	1191	broad.mit.edu	37	8	27463390	27463390	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27463390delA	uc003xfw.1	-						CLU_uc010lux.1_Intron|CLU_uc003xfx.1_Intron|CLU_uc003xfy.1_Intron|CLU_uc003xfz.1_Intron	NM_203339	NP_976084			clusterin isoform 2						chaperone-mediated protein folding|complement activation, classical pathway|innate immune response|lipid metabolic process|negative regulation of apoptosis|negative regulation of protein homooligomerization|platelet activation|platelet degranulation|positive regulation of NF-kappaB transcription factor activity|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|response to misfolded protein|response to virus|reverse cholesterol transport	chromaffin granule|cytosol|endoplasmic reticulum|microsome|mitochondrial membrane|nucleus|perinuclear region of cytoplasm|platelet alpha granule lumen|spherical high-density lipoprotein particle	misfolded protein binding|ubiquitin protein ligase binding			ovary(2)	2		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)														---	---	---	---
SCARA3	51435	broad.mit.edu	37	8	27499010	27499010	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27499010delC	uc003xga.1	+						SCARA3_uc003xgb.1_Intron	NM_016240	NP_057324			scavenger receptor class A, member 3 isoform 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	27574561	27574561	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27574561delA								SCARA3 (40275 upstream) : CCDC25 (16274 downstream)																																			---	---	---	---
PBK	55872	broad.mit.edu	37	8	27690542	27690542	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27690542delA	uc003xgi.2	-						PBK_uc011lap.1_Intron	NM_018492	NP_060962			PDZ binding kinase						mitosis		ATP binding|protein binding|protein serine/threonine kinase activity				0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)														---	---	---	---
C8orf80	389643	broad.mit.edu	37	8	27927265	27927265	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27927265delA	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	28148757	28148758	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28148757_28148758insA								ELP3 (100090 upstream) : PNOC (25891 downstream)																																			---	---	---	---
ZNF395	55893	broad.mit.edu	37	8	28253300	28253300	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28253300delA	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)														---	---	---	---
FZD3	7976	broad.mit.edu	37	8	28359543	28359543	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28359543delT	uc003xgx.2	+						FZD3_uc010lvb.2_Intron	NM_017412	NP_059108			frizzled 3 precursor						canonical Wnt receptor signaling pathway|cell proliferation in midbrain|commissural neuron axon guidance|establishment of planar polarity|facial nucleus development|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|neural tube closure|vasculature development	apical part of cell|axon|cytoplasm|dendrite|integral to membrane|neuron projection membrane|neuronal cell body|presynaptic active zone	G-protein coupled receptor activity|PDZ domain binding|Wnt-protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)														---	---	---	---
INTS9	55756	broad.mit.edu	37	8	28701250	28701250	+	Intron	DEL	T	-	-	rs77839220		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28701250delT	uc003xha.2	-						INTS9_uc011lav.1_Intron|INTS9_uc011law.1_Intron|INTS9_uc011lax.1_Intron|INTS9_uc010lvc.2_Intron|INTS9_uc003xhb.2_Intron	NM_018250	NP_060720			integrator complex subunit 9 isoform 1						snRNA processing	integrator complex	protein binding			central_nervous_system(1)|pancreas(1)	2		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	29230744	29230744	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29230744delC								DUSP4 (22559 upstream) : C8orf75 (348034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29303256	29303256	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29303256delT								DUSP4 (95071 upstream) : C8orf75 (275522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29319254	29319255	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29319254_29319255delAA								DUSP4 (111069 upstream) : C8orf75 (259523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29522470	29522470	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29522470delA								DUSP4 (314285 upstream) : C8orf75 (56308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29556505	29556505	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29556505delA								DUSP4 (348320 upstream) : C8orf75 (22273 downstream)																																			---	---	---	---
C8orf75	619351	broad.mit.edu	37	8	29581562	29581562	+	Intron	DEL	A	-	-	rs33974115		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29581562delA	uc003xhn.2	-							NR_026765				Homo sapiens chromosome 8 open reading frame 75, mRNA (cDNA clone IMAGE:3607242), partial cds.												0																		---	---	---	---
C8orf75	619351	broad.mit.edu	37	8	29584819	29584819	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29584819delT	uc003xhn.2	-							NR_026765				Homo sapiens chromosome 8 open reading frame 75, mRNA (cDNA clone IMAGE:3607242), partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	29661257	29661257	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29661257delT								C8orf75 (55632 upstream) : LOC286135 (117772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29678652	29678652	+	IGR	DEL	G	-	-	rs36163399	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29678652delG								C8orf75 (73027 upstream) : LOC286135 (100377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29828774	29828774	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29828774delT								LOC286135 (17653 upstream) : TMEM66 (91858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29870796	29870796	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29870796delT								LOC286135 (59675 upstream) : TMEM66 (49836 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29916291	29916291	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29916291delA								LOC286135 (105170 upstream) : TMEM66 (4341 downstream)																																			---	---	---	---
TMEM66	51669	broad.mit.edu	37	8	29927925	29927925	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29927925delA	uc003xhs.2	-						TMEM66_uc003xht.2_Intron|TMEM66_uc003xhu.2_Intron|TMEM66_uc003xhv.2_Intron	NM_016127	NP_057211			transmembrane protein 66 precursor							integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(542;0.0993)|Kidney(114;0.119)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	29948673	29948674	+	IGR	INS	-	TTG	TTG	rs151223723	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29948673_29948674insTTG								TMEM66 (8024 upstream) : LEPROTL1 (4248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30106987	30106988	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30106987_30106988delAA								DCTN6 (65928 upstream) : RBPMS (134956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30200431	30200431	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30200431delT								DCTN6 (159372 upstream) : RBPMS (41513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30234464	30234464	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30234464delT								DCTN6 (193405 upstream) : RBPMS (7480 downstream)																																			---	---	---	---
RBPMS	11030	broad.mit.edu	37	8	30288692	30288692	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30288692delG	uc003xic.1	+						RBPMS_uc003xid.1_Intron|RBPMS_uc003xie.1_Intron|RBPMS_uc011lba.1_Intron|RBPMS_uc003xib.2_Intron	NM_006867	NP_006858			RNA-binding protein with multiple splicing						positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)														---	---	---	---
GTF2E2	2961	broad.mit.edu	37	8	30472065	30472065	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30472065delA	uc003xig.2	-							NM_002095	NP_002086			general transcription factor IIE, polypeptide 2,						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	30520764	30520764	+	IGR	DEL	A	-	-	rs78554939		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30520764delA								GTF2E2 (5026 upstream) : GSR (15671 downstream)																																			---	---	---	---
GSR	2936	broad.mit.edu	37	8	30556809	30556809	+	Intron	DEL	A	-	-	rs4628224	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30556809delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	30639568	30639569	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30639568_30639569delTT								UBXN8 (15050 upstream) : PPP2CB (3558 downstream)																																			---	---	---	---
PPP2CB	5516	broad.mit.edu	37	8	30660706	30660706	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30660706delT	uc003xik.2	-							NM_004156	NP_004147			protein phosphatase 2, catalytic subunit, beta						protein dephosphorylation	chromosome, centromeric region|cytoplasm|nucleus|protein phosphatase type 2A complex|spindle pole	metal ion binding				0				KIRC - Kidney renal clear cell carcinoma(542;0.095)|Kidney(114;0.114)	Vitamin E(DB00163)													---	---	---	---
TEX15	56154	broad.mit.edu	37	8	30718437	30718437	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30718437delT	uc011lbc.1	-											Homo sapiens testis expressed 15, mRNA (cDNA clone IMAGE:8860305), partial cds.											ovary(3)|upper_aerodigestive_tract(2)|skin(2)	7				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	30790644	30790644	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30790644delT								TEX15 (44422 upstream) : PURG (62677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30824227	30824227	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30824227delT								TEX15 (78005 upstream) : PURG (29094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30834555	30834555	+	IGR	DEL	A	-	-	rs72018292		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30834555delA								TEX15 (88333 upstream) : PURG (18766 downstream)																																			---	---	---	---
WRN	7486	broad.mit.edu	37	8	30917758	30917758	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30917758delA	uc003xio.3	+							NM_000553	NP_000544			Werner syndrome protein						base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)				Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				---	---	---	---
WRN	7486	broad.mit.edu	37	8	30966158	30966159	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30966158_30966159delAA	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	30994352	30994353	+	Intron	INS	-	GAAT	GAAT	rs146117888	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30994352_30994353insGAAT	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	31029656	31029657	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31029656_31029657delTG	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	31065595	31065595	+	IGR	DEL	G	-	-	rs113611981		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31065595delG								WRN (34319 upstream) : NRG1 (431673 downstream)																																			---	---	---	---
NRG1	3084	broad.mit.edu	37	8	31509301	31509301	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31509301delT	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	31665462	31665463	+	Intron	DEL	CG	-	-	rs3050861		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31665462_31665463delCG	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	31749388	31749388	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31749388delA	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	31860041	31860041	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31860041delT	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	31938281	31938290	+	Intron	DEL	GTGTGTGTGT	-	-	rs72098629	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31938281_31938290delGTGTGTGTGT	uc003xip.2	+						uc003xiq.2_Intron	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	32079551	32079552	+	Intron	DEL	AC	-	-	rs60839450		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32079551_32079552delAC	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	32109417	32109418	+	Intron	INS	-	G	G	rs146669361	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32109417_32109418insG	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	32133357	32133357	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32133357delC	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	32255724	32255724	+	Intron	DEL	A	-	-	rs34669986		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32255724delA	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	32279998	32279998	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32279998delT	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	32419941	32419942	+	Intron	INS	-	A	A	rs35673547	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32419941_32419942insA	uc003xiv.2	+						NRG1_uc003xip.2_Intron|NRG1_uc003xir.2_Intron|NRG1_uc010lvl.2_Intron|NRG1_uc010lvm.2_Intron|NRG1_uc010lvn.2_Intron|NRG1_uc003xis.2_Intron|NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron	NM_013964	NP_039258			neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32522098	32522099	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32522098_32522099insA	uc003xiv.2	+						NRG1_uc003xip.2_Intron|NRG1_uc003xir.2_Intron|NRG1_uc010lvl.2_Intron|NRG1_uc010lvm.2_Intron|NRG1_uc010lvn.2_Intron|NRG1_uc003xis.2_Intron|NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc003xix.2_Intron|NRG1_uc003xiy.2_Intron|NRG1_uc010lvt.2_Intron	NM_013964	NP_039258			neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32604980	32604980	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32604980delA	uc003xiv.2	+						NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc011lbg.1_Intron|NRG1_uc011lbh.1_Intron|NRG1_uc003xiz.1_Intron|NRG1_uc003xja.2_Intron	NM_013964	NP_039258			neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32612095	32612095	+	Intron	DEL	A	-	-	rs76017751		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32612095delA	uc003xiv.2	+						NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc011lbg.1_Intron|NRG1_uc011lbh.1_Intron|NRG1_uc003xja.2_Intron	NM_013964	NP_039258			neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	32632695	32632695	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32632695delT								NRG1 (10137 upstream) : FUT10 (595651 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	32798954	32798954	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32798954delA	uc003xjb.2	+											Homo sapiens cDNA clone IMAGE:4837650.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	32883715	32883715	+	Intron	DEL	T	-	-	rs112794036		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32883715delT	uc003xjb.2	+											Homo sapiens cDNA clone IMAGE:4837650.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	32887830	32887832	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32887830_32887832delAAA	uc003xjb.2	+											Homo sapiens cDNA clone IMAGE:4837650.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	32942092	32942092	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32942092delT								NRG1 (319534 upstream) : FUT10 (286254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33039121	33039122	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33039121_33039122insA								NRG1 (416563 upstream) : FUT10 (189224 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33095667	33095667	+	IGR	DEL	T	-	-	rs75646885		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33095667delT								NRG1 (473109 upstream) : FUT10 (132679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33190007	33190010	+	IGR	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33190007_33190010delAAAA								NRG1 (567449 upstream) : FUT10 (38336 downstream)																																			---	---	---	---
FUT10	84750	broad.mit.edu	37	8	33285647	33285647	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33285647delA	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)														---	---	---	---
C8orf41	80185	broad.mit.edu	37	8	33339874	33339874	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33339874delT	uc010lvu.1	-						MAK16_uc003xjj.2_5'Flank					Homo sapiens cDNA: FLJ23263 fis, clone COL06129.								binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)														---	---	---	---
MAK16	84549	broad.mit.edu	37	8	33343022	33343028	+	Intron	DEL	GCTGTCA	-	-	rs72058969		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33343022_33343028delGCTGTCA	uc003xjj.2	+						C8orf41_uc010lvu.1_Intron	NM_032509	NP_115898			MAK16 homolog							nucleolus				ovary(1)	1																		---	---	---	---
MAK16	84549	broad.mit.edu	37	8	33354873	33354873	+	Intron	DEL	C	-	-	rs68152666		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33354873delC	uc003xjj.2	+						C8orf41_uc010lvu.1_Intron	NM_032509	NP_115898			MAK16 homolog							nucleolus				ovary(1)	1																		---	---	---	---
C8orf41	80185	broad.mit.edu	37	8	33363014	33363015	+	Intron	INS	-	T	T	rs67360483		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33363014_33363015insT	uc003xjl.3	-						C8orf41_uc003xjk.3_Intron|C8orf41_uc010lvv.2_Intron|C8orf41_uc003xjm.3_Intron|C8orf41_uc003xjn.1_Intron	NM_025115	NP_079391			hypothetical protein LOC80185								binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)														---	---	---	---
RNF122	79845	broad.mit.edu	37	8	33406740	33406740	+	Intron	DEL	A	-	-	rs71899502		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33406740delA	uc003xjo.1	-							NM_024787	NP_079063			ring finger protein 122							endoplasmic reticulum|Golgi apparatus|integral to membrane	zinc ion binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0966)|Kidney(114;0.116)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	33445941	33445942	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33445941_33445942delTT								RNF122 (21298 upstream) : DUSP26 (2914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33522752	33522752	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33522752delT								DUSP26 (65313 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33808662	33808663	+	IGR	DEL	CC	-	-	rs76940638		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33808662_33808663delCC								DUSP26 (351223 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33809828	33809828	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33809828delT								DUSP26 (352389 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34147270	34147270	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34147270delA								DUSP26 (689831 upstream) : UNC5D (945705 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34195664	34195664	+	IGR	DEL	T	-	-	rs34925073		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34195664delT								DUSP26 (738225 upstream) : UNC5D (897311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34311926	34311928	+	IGR	DEL	AAA	-	-	rs72203000		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34311926_34311928delAAA								DUSP26 (854487 upstream) : UNC5D (781047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34381330	34381330	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34381330delA								DUSP26 (923891 upstream) : UNC5D (711645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34549874	34549874	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34549874delA								None (None upstream) : UNC5D (543101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34678029	34678029	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34678029delT								None (None upstream) : UNC5D (414946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34792688	34792689	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34792688_34792689delGA								None (None upstream) : UNC5D (300286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	35018708	35018709	+	IGR	INS	-	ACAC	ACAC	rs71910000		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35018708_35018709insACAC								None (None upstream) : UNC5D (74266 downstream)																																			---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35202856	35202856	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35202856delA	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	35503046	35503047	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35503046_35503047delTG	uc003xjr.1	+						UNC5D_uc003xjs.1_Intron	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	35545762	35545763	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35545762_35545763delAA	uc003xjr.1	+						UNC5D_uc003xjs.1_Intron|UNC5D_uc003xjt.1_Intron	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	35610789	35610789	+	Intron	DEL	T	-	-	rs113878768		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35610789delT	uc003xjr.1	+						UNC5D_uc003xjs.1_Intron|UNC5D_uc003xju.1_Intron	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	35633123	35633123	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35633123delT	uc003xjr.1	+						UNC5D_uc003xjs.1_Intron|UNC5D_uc003xju.1_Intron	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	35706272	35706273	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35706272_35706273insA								UNC5D (54092 upstream) : KCNU1 (935569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	35740564	35740564	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35740564delA								UNC5D (88384 upstream) : KCNU1 (901278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	35820955	35820956	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35820955_35820956delGT								UNC5D (168775 upstream) : KCNU1 (820886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36097702	36097703	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36097702_36097703insT								UNC5D (445522 upstream) : KCNU1 (544139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36185278	36185278	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36185278delT								UNC5D (533098 upstream) : KCNU1 (456564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36435206	36435206	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36435206delT								UNC5D (783026 upstream) : KCNU1 (206636 downstream)																																			---	---	---	---
KCNU1	157855	broad.mit.edu	37	8	36779849	36779849	+	Intron	DEL	A	-	-	rs68098747		TCGA-BR-4292-01	TCGA-BR-4292-01									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	36887251	36887251	+	IGR	DEL	T	-	-	rs71996981		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36887251delT								KCNU1 (93610 upstream) : ZNF703 (666050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37024910	37024910	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37024910delA								KCNU1 (231269 upstream) : ZNF703 (528391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37269496	37269496	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37269496delA								KCNU1 (475855 upstream) : ZNF703 (283805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37369862	37369862	+	IGR	DEL	A	-	-	rs112653156		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37369862delA								KCNU1 (576221 upstream) : ZNF703 (183439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37560849	37560849	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37560849delT								ZNF703 (4453 upstream) : ERLIN2 (33248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37593487	37593487	+	Frame_Shift_Del	DEL	A	-	-	rs112819064		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37593487delA	uc003xkb.1	-	2	878	c.529delT	c.(529-531)TCTfs	p.S177fs	ERLIN2_uc003xkc.3_5'Flank|ERLIN2_uc003xkd.2_5'Flank|ERLIN2_uc003xke.3_5'Flank|ERLIN2_uc003xkf.3_5'Flank|ERLIN2_uc003xkg.2_5'Flank					SubName: Full=Putative uncharacterized protein ENSP00000328874;																														---	---	---	---
PROSC	11212	broad.mit.edu	37	8	37630693	37630694	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37630693_37630694insT	uc003xkh.2	+							NM_007198	NP_009129			proline synthetase co-transcribed homolog								pyridoxal phosphate binding			central_nervous_system(1)	1		Lung NSC(58;0.174)	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)		L-Proline(DB00172)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	37644621	37644621	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37644621delA								PROSC (7336 upstream) : GPR124 (9803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37649458	37649458	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37649458delA								PROSC (12173 upstream) : GPR124 (4966 downstream)																																			---	---	---	---
GOT1L1	137362	broad.mit.edu	37	8	37799415	37799416	+	5'Flank	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37799415_37799416insC	uc011lbj.1	-							NM_152413	NP_689626			glutamic-oxaloacetic transaminase 1-like 1						biosynthetic process|cellular amino acid metabolic process	cytoplasm	pyridoxal phosphate binding|transaminase activity			ovary(1)	1	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	37811864	37811864	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37811864delT								GOT1L1 (14217 upstream) : ADRB3 (8652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37836693	37836693	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37836693delA								ADRB3 (12509 upstream) : EIF4EBP1 (51327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37857100	37857101	+	IGR	INS	-	CA	CA	rs141836723	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37857100_37857101insCA								ADRB3 (32916 upstream) : EIF4EBP1 (30919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37865196	37865196	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37865196delT								ADRB3 (41012 upstream) : EIF4EBP1 (22824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37879396	37879399	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37879396_37879399delTTTT								ADRB3 (55212 upstream) : EIF4EBP1 (8621 downstream)																																			---	---	---	---
EIF4EBP1	1978	broad.mit.edu	37	8	37886075	37886076	+	5'Flank	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37886075_37886076insT	uc003xks.2	+							NM_004095	NP_004086			eukaryotic translation initiation factor 4E						G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|positive regulation of mitotic cell cycle|TOR signaling cascade|translation	cytosol					0	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)																---	---	---	---
EIF4EBP1	1978	broad.mit.edu	37	8	37913547	37913548	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37913547_37913548delTT	uc003xks.2	+							NM_004095	NP_004086			eukaryotic translation initiation factor 4E						G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|positive regulation of mitotic cell cycle|TOR signaling cascade|translation	cytosol					0	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	37936969	37936969	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37936969delA								EIF4EBP1 (19087 upstream) : ASH2L (26042 downstream)																																			---	---	---	---
ASH2L	9070	broad.mit.edu	37	8	37969945	37969945	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37969945delT	uc003xkt.3	+						ASH2L_uc011lbk.1_Intron|ASH2L_uc003xku.3_Intron|ASH2L_uc010lwa.2_Intron	NM_004674	NP_004665			ash2-like isoform a						hemopoiesis|histone H3-K4 methylation|positive regulation of cell proliferation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription from RNA polymerase II promoter	Set1C/COMPASS complex	metal ion binding|protein binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)																---	---	---	---
STAR	6770	broad.mit.edu	37	8	38010233	38010233	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38010233delA	uc003xkv.1	-						STAR_uc010lwc.1_5'Flank	NM_001007243	NP_001007244			steroidogenic acute regulatory protein isoform						C21-steroid hormone biosynthetic process	mitochondrial intermembrane space	cholesterol transporter activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.0151)|Lung NSC(58;0.0295)		READ - Rectum adenocarcinoma(644;0.188)														---	---	---	---
DDHD2	23259	broad.mit.edu	37	8	38091446	38091446	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38091446delA	uc003xlb.2	+						DDHD2_uc003xla.2_Intron|DDHD2_uc003xlc.2_Intron|DDHD2_uc011lbl.1_Intron	NM_015214	NP_056029			DDHD domain containing 2 isoform 1						lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)															---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38166665	38166665	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38166665delA	uc003xli.2	-						WHSC1L1_uc011lbm.1_Intron|WHSC1L1_uc010lwe.2_Intron	NM_023034	NP_075447			WHSC1L1 protein isoform long						cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)					T	NUP98	AML								---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38171048	38171048	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38171048delA	uc003xli.2	-						WHSC1L1_uc011lbm.1_Intron|WHSC1L1_uc010lwe.2_Intron	NM_023034	NP_075447			WHSC1L1 protein isoform long						cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)					T	NUP98	AML								---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38241645	38241645	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38241645delT	uc003xli.2	-						WHSC1L1_uc011lbm.1_5'Flank|WHSC1L1_uc010lwe.2_5'Flank|WHSC1L1_uc003xlj.2_5'Flank|LETM2_uc003xlk.2_5'Flank|LETM2_uc011lbn.1_5'Flank|LETM2_uc003xll.1_5'Flank|LETM2_uc003xlm.1_5'Flank|LETM2_uc003xln.1_5'Flank	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	38291846	38291847	+	Intron	DEL	GC	-	-	rs57213852		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38291846_38291847delGC	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	38365580	38365580	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38365580delT								FGFR1 (39228 upstream) : C8orf86 (2772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	38412955	38412955	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38412955delT								C8orf86 (26775 upstream) : RNF5P1 (44740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	38436101	38436101	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38436101delA								C8orf86 (49921 upstream) : RNF5P1 (21594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	38436615	38436616	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38436615_38436616delTT								C8orf86 (50435 upstream) : RNF5P1 (21079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	38487716	38487716	+	IGR	DEL	A	-	-	rs77181026		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38487716delA								RNF5P1 (28941 upstream) : TACC1 (97988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	38545440	38545440	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38545440delA								RNF5P1 (86665 upstream) : TACC1 (40264 downstream)																																			---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38627464	38627465	+	Intron	INS	-	GT	GT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38627464_38627465insGT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	38744506	38744506	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38744506delA								TACC1 (33961 upstream) : PLEKHA2 (14247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	38750780	38750781	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38750780_38750781delAC								TACC1 (40235 upstream) : PLEKHA2 (7972 downstream)																																			---	---	---	---
PLEKHA2	59339	broad.mit.edu	37	8	38793887	38793888	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38793887_38793888insT	uc003xmi.3	+						PLEKHA2_uc011lce.1_Intron	NM_021623	NP_067636			pleckstrin homology domain containing, family A						positive regulation of cell-matrix adhesion	cytoplasm|nucleus|plasma membrane|protein complex	fibronectin binding|laminin binding				0		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
ADAM9	8754	broad.mit.edu	37	8	38880852	38880852	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38880852delT	uc003xmr.2	+						ADAM9_uc011lcf.1_Intron|ADAM9_uc011lcg.1_Intron|ADAM9_uc010lwr.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	38975172	38975172	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38975172delT	uc003xmt.3	+						ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_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)															---	---	---	---
ADAM32	203102	broad.mit.edu	37	8	39119231	39119232	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39119231_39119232insT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	39158955	39158955	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39158955delT								ADAM32 (16520 upstream) : ADAM5P (13227 downstream)																																			---	---	---	---
ADAM5P	255926	broad.mit.edu	37	8	39180475	39180475	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39180475delT	uc003xmw.2	+						ADAM5P_uc003xmx.1_Intron|ADAM5P_uc003xmy.1_Intron|ADAM5P_uc003xmz.1_Intron|ADAM5P_uc010lwt.1_Intron|ADAM5P_uc003xna.2_Intron|ADAM5P_uc003xnb.2_Intron|ADAM5P_uc003xnc.2_Intron|ADAM5P_uc010lws.1_Intron					Homo sapiens mRNA for tMDC II, isoform [a].												0																		---	---	---	---
ADAM3A	1587	broad.mit.edu	37	8	39332896	39332897	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39332896_39332897delAA	uc003xnf.2	-						ADAM3A_uc010lwv.2_Intron|ADAM3A_uc003xne.2_Intron|ADAM3A_uc003xnd.2_Intron|ADAM3A_uc011lci.1_Intron|ADAM3A_uc011lcj.1_Intron	NR_001569				SubName: Full=Putative uncharacterized protein ENSP00000328747;												0																		---	---	---	---
IDO2	169355	broad.mit.edu	37	8	39865257	39865258	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39865257_39865258insA	uc010lwy.1	+						IDO2_uc003xno.1_Intron|IDO2_uc010lwz.1_Intron|IDO2_uc003xnp.1_Intron	NM_194294	NP_919270			indoleamine-pyrrole 2,3 dioxygenase-like 1						tryptophan catabolic process to kynurenine	cytosol	heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	39885424	39885427	+	IGR	DEL	AGAG	-	-	rs147096883		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39885424_39885427delAGAG								IDO2 (11514 upstream) : C8orf4 (125562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	39932327	39932327	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39932327delA								IDO2 (58417 upstream) : C8orf4 (78662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40095912	40095912	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40095912delA								C8orf4 (83091 upstream) : ZMAT4 (292204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40226449	40226449	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40226449delA								C8orf4 (213628 upstream) : ZMAT4 (161667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40238803	40238803	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40238803delC								C8orf4 (225982 upstream) : ZMAT4 (149313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40362251	40362252	+	IGR	INS	-	AGG	AGG	rs139823562	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40362251_40362252insAGG								C8orf4 (349430 upstream) : ZMAT4 (25864 downstream)																																			---	---	---	---
ZMAT4	79698	broad.mit.edu	37	8	40396304	40396304	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40396304delT	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	40436120	40436121	+	Intron	INS	-	CT	CT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40436120_40436121insCT	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	40649926	40649926	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40649926delC	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	40793825	40793826	+	IGR	DEL	AA	-	-	rs113723066		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40793825_40793826delAA								ZMAT4 (38482 upstream) : SFRP1 (325653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40952388	40952388	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40952388delT								ZMAT4 (197045 upstream) : SFRP1 (167091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40978017	40978018	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40978017_40978018insA								ZMAT4 (222674 upstream) : SFRP1 (141461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41043778	41043778	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41043778delT								ZMAT4 (288435 upstream) : SFRP1 (75701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41229633	41229633	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41229633delT								SFRP1 (62653 upstream) : GOLGA7 (118448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41238904	41238907	+	IGR	DEL	ACAA	-	-	rs148482803		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41238904_41238907delACAA								SFRP1 (71924 upstream) : GOLGA7 (109174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41276193	41276194	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41276193_41276194delAA								SFRP1 (109213 upstream) : GOLGA7 (71887 downstream)																																			---	---	---	---
GOLGA7	51125	broad.mit.edu	37	8	41351525	41351525	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41351525delT	uc003xnu.2	+						GOLGA7_uc003xnv.2_Intron|GOLGA7_uc003xnw.2_Intron	NM_016099	NP_057183			golgi autoantigen, golgin subfamily a, 7							Golgi membrane				breast(1)	1	Ovarian(28;0.014)|Colorectal(14;0.0234)|Lung SC(25;0.211)	all_lung(54;0.000771)|Lung NSC(58;0.0031)|Hepatocellular(245;0.014)|Esophageal squamous(32;0.0559)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00596)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)															---	---	---	---
GINS4	84296	broad.mit.edu	37	8	41392258	41392261	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41392258_41392261delTTTT	uc003xnx.2	+						GINS4_uc003xny.2_Intron	NM_032336	NP_115712			GINS complex subunit 4						DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	cytoplasm|nucleoplasm				skin(1)	1	Ovarian(28;0.014)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.00732)|Lung NSC(58;0.0207)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00329)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)															---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41801617	41801617	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41801617delA	uc010lxb.2	-						MYST3_uc010lxc.2_Intron|MYST3_uc003xon.3_Intron|MYST3_uc010lxd.2_Intron	NM_001099412	NP_001092882			MYST histone acetyltransferase (monocytic						histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	41964431	41964432	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41964431_41964432insT								MYST3 (54926 upstream) : AP3M2 (46032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41988072	41988072	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41988072delA								MYST3 (78567 upstream) : AP3M2 (22392 downstream)																																			---	---	---	---
PLAT	5327	broad.mit.edu	37	8	42042793	42042793	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42042793delT	uc003xos.2	-						PLAT_uc010lxf.1_Intron|PLAT_uc010lxg.1_Intron|PLAT_uc003xot.2_Intron|PLAT_uc011lcm.1_Intron|PLAT_uc011lcn.1_Intron	NM_000930	NP_000921			plasminogen activator, tissue isoform 1						blood coagulation|fibrinolysis|negative regulation of proteolysis|protein modification process|proteolysis	cell surface|cytoplasm|extracellular space	protein binding|serine-type endopeptidase activity			breast(1)|skin(1)	2	all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)		Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Iloprost(DB01088)|Reteplase(DB00015)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	42078698	42078700	+	IGR	DEL	AAA	-	-	rs72353017		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42078698_42078700delAAA								PLAT (13504 upstream) : IKBKB (50129 downstream)																																			---	---	---	---
IKBKB	3551	broad.mit.edu	37	8	42155413	42155413	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42155413delA	uc003xow.1	+						IKBKB_uc003xov.2_Intron|IKBKB_uc010lxh.1_Intron|IKBKB_uc011lco.1_Intron|IKBKB_uc010lxj.1_Intron|IKBKB_uc003xox.1_Intron|IKBKB_uc011lcp.1_Intron|IKBKB_uc011lcq.1_Intron|IKBKB_uc010lxi.1_Intron|IKBKB_uc011lcr.1_Intron	NM_001556	NP_001547			inhibitor of nuclear factor kappa B kinase beta						anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)													---	---	---	---
IKBKB	3551	broad.mit.edu	37	8	42176208	42176208	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42176208delT	uc003xow.1	+						IKBKB_uc010lxh.1_Intron|IKBKB_uc011lco.1_Intron|IKBKB_uc010lxj.1_Intron|IKBKB_uc003xox.1_Intron|IKBKB_uc011lcp.1_Intron|IKBKB_uc011lcq.1_Intron|IKBKB_uc010lxi.1_Intron|IKBKB_uc011lcr.1_Intron	NM_001556	NP_001547			inhibitor of nuclear factor kappa B kinase beta						anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)													---	---	---	---
VDAC3	7419	broad.mit.edu	37	8	42257068	42257068	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42257068delT	uc011lct.1	+						VDAC3_uc010lxk.2_Intron|VDAC3_uc003xpc.2_Intron	NM_005662	NP_005653			voltage-dependent anion channel 3 isoform b						adenine transport	mitochondrial outer membrane|pore complex	nucleotide binding|porin activity|protein binding|voltage-gated anion channel activity			upper_aerodigestive_tract(1)	1	all_cancers(6;3.86e-23)|all_lung(13;6.47e-12)|Lung NSC(13;1.08e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00266)|Lung(22;0.00849)|LUSC - Lung squamous cell carcinoma(45;0.024)		Dihydroxyaluminium(DB01375)													---	---	---	---
SLC20A2	6575	broad.mit.edu	37	8	42293634	42293634	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42293634delA	uc010lxl.2	-						SLC20A2_uc010lxm.2_Intron|SLC20A2_uc003xpe.2_Intron|SLC20A2_uc011lcu.1_Intron	NM_006749	NP_006740			solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
SLC20A2	6575	broad.mit.edu	37	8	42297283	42297283	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42297283delA	uc010lxl.2	-						SLC20A2_uc010lxm.2_Intron|SLC20A2_uc003xpe.2_Intron|SLC20A2_uc011lcu.1_Intron	NM_006749	NP_006740			solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
SLC20A2	6575	broad.mit.edu	37	8	42313662	42313662	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42313662delA	uc010lxl.2	-						SLC20A2_uc010lxm.2_Intron|SLC20A2_uc003xpe.2_Intron|SLC20A2_uc011lcu.1_Intron	NM_006749	NP_006740			solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	42477409	42477410	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42477409_42477410delTT								C8orf40 (69270 upstream) : CHRNB3 (75152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42497980	42497981	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42497980_42497981insC								C8orf40 (89841 upstream) : CHRNB3 (54581 downstream)																																			---	---	---	---
CHRNB3	1142	broad.mit.edu	37	8	42557905	42557905	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42557905delA	uc003xpi.1	+							NM_000749	NP_000740			cholinergic receptor, nicotinic, beta						synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	nicotinic acetylcholine-activated cation-selective channel activity|receptor activity			ovary(1)	1	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
RNF170	81790	broad.mit.edu	37	8	42719856	42719857	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42719856_42719857delAA	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)															---	---	---	---
RNF170	81790	broad.mit.edu	37	8	42738210	42738210	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42738210delA	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	42805058	42805059	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42805058_42805059delAA	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								---	---	---	---
FNTA	2339	broad.mit.edu	37	8	42914458	42914458	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42914458delT	uc003xps.2	+						FNTA_uc003xpt.2_Intron|FNTA_uc003xpu.2_Intron|FNTA_uc003xpv.2_Intron	NM_002027	NP_002018			farnesyltransferase, CAAX box, alpha isoform a						cellular component disassembly involved in apoptosis|positive regulation of deacetylase activity|positive regulation of tubulin deacetylation|protein farnesylation|protein geranylgeranylation|transforming growth factor beta receptor signaling pathway	cytosol|microtubule associated complex	alpha-tubulin binding|CAAX-protein geranylgeranyltransferase activity|microtubule binding|protein farnesyltransferase activity			ovary(1)	1	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)															---	---	---	---
SGK196	84197	broad.mit.edu	37	8	42945804	42945804	+	5'Flank	DEL	T	-	-	rs145910017		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42945804delT	uc003xpw.2	+							NM_032237	NP_115613			protein kinase-like protein SgK196							integral to membrane	ATP binding|protein kinase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	43093426	43093427	+	IGR	DEL	CT	-	-	rs113878656		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43093426_43093427delCT								HGSNAT (35457 upstream) : POTEA (54158 downstream)																																			---	---	---	---
POTEA	340441	broad.mit.edu	37	8	43197090	43197090	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43197090delA	uc003xpz.1	+						POTEA_uc003xqa.1_Intron	NM_001005365	NP_001005365			POTE ankyrin domain family, member A isoform 2											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	43224843	43224843	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43224843delT								POTEA (6515 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43433366	43433366	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43433366delA								POTEA (215038 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43541617	43541617	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43541617delT								POTEA (323289 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43665916	43665917	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43665916_43665917insA								POTEA (447588 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43824491	43824492	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43824491_43824492insT								POTEA (606163 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	46912304	46912307	+	IGR	DEL	CTGT	-	-	rs143959621		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46912304_46912307delCTGT								None (None upstream) : BEYLA (840201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	46999747	46999747	+	IGR	DEL	G	-	-	rs111852901		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46999747delG								None (None upstream) : BEYLA (752761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47528223	47528223	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47528223delT								None (None upstream) : BEYLA (224285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47831183	47831183	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47831183delA								BEYLA (63776 upstream) : KIAA0146 (342359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47951247	47951248	+	IGR	INS	-	CTAA	CTAA	rs139838569	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47951247_47951248insCTAA								BEYLA (183840 upstream) : KIAA0146 (222294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	48153907	48153909	+	IGR	DEL	GGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48153907_48153909delGGG								BEYLA (386500 upstream) : KIAA0146 (19633 downstream)																																			---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48276410	48276413	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48276410_48276413delTTTT	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	48396546	48396547	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48396546_48396547delAA	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48577457	48577458	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48577457_48577458delAA	uc003xqd.2	+						KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron|KIAA0146_uc011ldf.1_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48847680	48847680	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48847680delA	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					---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48858291	48858291	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48858291delT	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835			protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)											NHEJ					---	---	---	---
Unknown	0	broad.mit.edu	37	8	48893243	48893245	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48893243_48893245delAAA								MCM4 (3175 upstream) : UBE2V2 (27750 downstream)																																			---	---	---	---
UBE2V2	7336	broad.mit.edu	37	8	48929939	48929939	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48929939delT	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					---	---	---	---
UBE2V2	7336	broad.mit.edu	37	8	48932375	48932376	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48932375_48932376delAA	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					---	---	---	---
UBE2V2	7336	broad.mit.edu	37	8	48964441	48964441	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48964441delC	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					---	---	---	---
UBE2V2	7336	broad.mit.edu	37	8	48967761	48967762	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48967761_48967762delTT	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	48985635	48985636	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48985635_48985636delTC								UBE2V2 (11183 upstream) : EFCAB1 (637715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49037936	49037936	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49037936delT								UBE2V2 (63484 upstream) : EFCAB1 (585415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49083138	49083138	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49083138delT								UBE2V2 (108686 upstream) : EFCAB1 (540213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49226538	49226539	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49226538_49226539delTG								UBE2V2 (252086 upstream) : EFCAB1 (396812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49340833	49340836	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49340833_49340836delTTTT								UBE2V2 (366381 upstream) : EFCAB1 (282515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49345721	49345721	+	IGR	DEL	T	-	-	rs80189077		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49345721delT								UBE2V2 (371269 upstream) : EFCAB1 (277630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49365152	49365152	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49365152delA								UBE2V2 (390700 upstream) : EFCAB1 (258199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49462816	49462817	+	IGR	INS	-	TG	TG	rs146776597	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49462816_49462817insTG								UBE2V2 (488364 upstream) : EFCAB1 (160534 downstream)																																			---	---	---	---
EFCAB1	79645	broad.mit.edu	37	8	49641922	49641922	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49641922delA	uc003xqo.2	-						EFCAB1_uc003xqn.3_Intron|EFCAB1_uc011ldj.1_Intron|EFCAB1_uc010lxx.2_Intron|EFCAB1_uc011ldk.1_Intron	NM_024593	NP_078869			EF-hand calcium binding domain 1 isoform a								calcium ion binding				0		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	49800364	49800365	+	IGR	INS	-	TG	TG	rs150061107	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49800364_49800365insTG								EFCAB1 (152494 upstream) : SNAI2 (29874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49821881	49821881	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49821881delA								EFCAB1 (174011 upstream) : SNAI2 (8358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49920658	49920658	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49920658delT								SNAI2 (86670 upstream) : C8orf22 (64245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50394681	50394682	+	IGR	DEL	TT	-	-	rs34910479		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50394681_50394682delTT								C8orf22 (406040 upstream) : SNTG1 (427667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50791511	50791511	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50791511delT								C8orf22 (802870 upstream) : SNTG1 (30838 downstream)																																			---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	50956821	50956821	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50956821delT	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	51396785	51396785	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51396785delT	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	51724025	51724025	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51724025delT								SNTG1 (18598 upstream) : PXDNL (508119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	51759001	51759001	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51759001delG								SNTG1 (53574 upstream) : PXDNL (473143 downstream)																																			---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52415227	52415227	+	Intron	DEL	T	-	-	rs11306659		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52415227delT	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	52433362	52433362	+	Intron	DEL	A	-	-	rs34407076		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52433362delA	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	52508391	52508391	+	Intron	DEL	A	-	-	rs113364773		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52508391delA	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	52595310	52595311	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52595310_52595311delGA	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	52665812	52665812	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52665812delA	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)																---	---	---	---
PCMTD1	115294	broad.mit.edu	37	8	52774911	52774912	+	Intron	INS	-	AC	AC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52774911_52774912insAC	uc003xqx.3	-						PCMTD1_uc003xqw.3_Intron|PCMTD1_uc011ldn.1_Intron|PCMTD1_uc010lya.2_Intron|PCMTD1_uc011ldo.1_5'Flank	NM_052937	NP_443169			protein-L-isoaspartate (D-aspartate)							cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	52859810	52859810	+	5'Flank	DEL	T	-	-	rs79288288		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52859810delT	uc003xqy.1	+											Homo sapiens cDNA FLJ34440 fis, clone HLUNG2001214.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	52870294	52870294	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52870294delA								PCMTD1 (58559 upstream) : ST18 (153098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	52894423	52894423	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52894423delT								PCMTD1 (82688 upstream) : ST18 (128969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	52919891	52919891	+	IGR	DEL	G	-	-	rs67154534		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52919891delG								PCMTD1 (108156 upstream) : ST18 (103501 downstream)																																			---	---	---	---
FAM150A	389658	broad.mit.edu	37	8	53475168	53475168	+	Intron	DEL	C	-	-	rs149064822	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53475168delC	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	53492622	53492623	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53492622_53492623delAA								FAM150A (14601 upstream) : RB1CC1 (42396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53502591	53502591	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53502591delT								FAM150A (24570 upstream) : RB1CC1 (32428 downstream)																																			---	---	---	---
RB1CC1	9821	broad.mit.edu	37	8	53575915	53575916	+	Intron	DEL	TT	-	-	rs111631545		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53575915_53575916delTT	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	53757246	53757246	+	IGR	DEL	G	-	-	rs2009805	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53757246delG								RB1CC1 (130220 upstream) : NPBWR1 (95222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53774946	53774946	+	IGR	DEL	T	-	-	rs79227755		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53774946delT								RB1CC1 (147920 upstream) : NPBWR1 (77522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54008457	54008457	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54008457delA								NPBWR1 (155004 upstream) : OPRK1 (129819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54187272	54187272	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54187272delA								OPRK1 (23078 upstream) : ATP6V1H (440844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54392694	54392696	+	IGR	DEL	TTT	-	-	rs11315627		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54392694_54392696delTTT								OPRK1 (228500 upstream) : ATP6V1H (235420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54403005	54403005	+	IGR	DEL	A	-	-	rs11469984		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54403005delA								OPRK1 (238811 upstream) : ATP6V1H (225111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54512343	54512344	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54512343_54512344insT								OPRK1 (348149 upstream) : ATP6V1H (115772 downstream)																																			---	---	---	---
ATP6V1H	51606	broad.mit.edu	37	8	54736558	54736558	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54736558delA	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	54779828	54779829	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54779828_54779829insA	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)															---	---	---	---
RGS20	8601	broad.mit.edu	37	8	54800539	54800540	+	Intron	DEL	AA	-	-	rs111681980		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54800539_54800540delAA	uc003xrp.2	+						RGS20_uc003xrq.2_Intron|RGS20_uc010lye.2_Intron|RGS20_uc010lyf.2_Intron|RGS20_uc003xrr.2_Intron|RGS20_uc003xrs.2_Intron|RGS20_uc003xrt.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)															---	---	---	---
RGS20	8601	broad.mit.edu	37	8	54871210	54871211	+	3'UTR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54871210_54871211delAA	uc003xrp.2	+	6					RGS20_uc003xrq.2_3'UTR|RGS20_uc010lye.2_3'UTR|RGS20_uc010lyf.2_3'UTR|RGS20_uc003xrs.2_3'UTR|RGS20_uc003xrt.2_3'UTR	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	55041198	55041198	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55041198delT								LYPLA1 (26621 upstream) : MRPL15 (6583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55100647	55100647	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55100647delA								MRPL15 (39573 upstream) : SOX17 (269848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55177446	55177446	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55177446delA								MRPL15 (116372 upstream) : SOX17 (193049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55177659	55177660	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55177659_55177660delTT								MRPL15 (116585 upstream) : SOX17 (192835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55204277	55204278	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55204277_55204278delAA								MRPL15 (143203 upstream) : SOX17 (166217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55279670	55279673	+	IGR	DEL	AAAA	-	-	rs79686360		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55279670_55279673delAAAA								MRPL15 (218596 upstream) : SOX17 (90822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55328130	55328131	+	IGR	INS	-	TT	TT	rs150170439	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55328130_55328131insTT								MRPL15 (267056 upstream) : SOX17 (42364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55747190	55747191	+	IGR	INS	-	AT	AT	rs139801108	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55747190_55747191insAT								RP1 (64659 upstream) : XKR4 (267826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55768528	55768533	+	IGR	DEL	CACACC	-	-	rs145846116	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55768528_55768533delCACACC								RP1 (85997 upstream) : XKR4 (246484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55820083	55820086	+	IGR	DEL	TTTT	-	-	rs112319762		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55820083_55820086delTTTT								RP1 (137552 upstream) : XKR4 (194931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55884651	55884651	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55884651delT								RP1 (202120 upstream) : XKR4 (130366 downstream)																																			---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56049815	56049815	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56049815delA	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	56113630	56113630	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56113630delT	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	56135396	56135396	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56135396delT	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	56139213	56139213	+	Intron	DEL	T	-	-	rs68151515		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56139213delT	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	56205604	56205605	+	Intron	INS	-	T	T	rs142074940	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56205604_56205605insT	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)															---	---	---	---
TGS1	96764	broad.mit.edu	37	8	56714005	56714006	+	Intron	DEL	TT	-	-	rs33910297		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56714005_56714006delTT	uc003xsj.3	+						TGS1_uc010lyh.2_Intron	NM_024831	NP_079107			trimethylguanosine synthase homolog						cellular lipid metabolic process|ncRNA metabolic process|regulation of transcription, DNA-dependent|RNA capping|spliceosomal snRNP assembly|transcription, DNA-dependent	Cajal body|cytosol	RNA trimethylguanosine synthase activity			ovary(1)|lung(1)|breast(1)	3		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	56760679	56760680	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56760679_56760680insG								TGS1 (22676 upstream) : LYN (31706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56773964	56773964	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56773964delT								TGS1 (35961 upstream) : LYN (18422 downstream)																																			---	---	---	---
LYN	4067	broad.mit.edu	37	8	56852022	56852023	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56852022_56852023delAG	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)															---	---	---	---
LYN	4067	broad.mit.edu	37	8	56888886	56888889	+	Intron	DEL	AAAA	-	-	rs35717306		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56888886_56888889delAAAA	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)															---	---	---	---
LYN	4067	broad.mit.edu	37	8	56892782	56892782	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56892782delT	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)															---	---	---	---
LYN	4067	broad.mit.edu	37	8	56915622	56915624	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56915622_56915624delTTT	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	57002442	57002442	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57002442delA								RPS20 (15302 upstream) : MOS (23060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57050461	57050462	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57050461_57050462delTT								MOS (23920 upstream) : PLAG1 (23007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57146712	57146712	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57146712delT								CHCHD7 (15538 upstream) : SDR16C5 (65858 downstream)																																			---	---	---	---
SDR16C5	195814	broad.mit.edu	37	8	57215565	57215565	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57215565delA	uc003xsy.1	-						SDR16C5_uc010lyk.1_Intron|SDR16C5_uc010lyl.1_Intron	NM_138969	NP_620419			epidermal retinal dehydrogenase 2						detection of light stimulus involved in visual perception|keratinocyte proliferation|retinal metabolic process|retinol metabolic process	endoplasmic reticulum membrane|integral to membrane|integral to membrane of membrane fraction	binding|retinol dehydrogenase activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	57314334	57314335	+	IGR	INS	-	AC	AC	rs145311874	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57314334_57314335insAC								SDR16C5 (81093 upstream) : PENK (39178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58045141	58045141	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58045141delT								IMPAD1 (138714 upstream) : C8orf71 (146961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58200344	58200344	+	IGR	DEL	T	-	-	rs79518077		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58200344delT								C8orf71 (3056 upstream) : FAM110B (706769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58291436	58291437	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58291436_58291437delAA								C8orf71 (94148 upstream) : FAM110B (615676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58312165	58312166	+	IGR	INS	-	T	T	rs145912967	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58312165_58312166insT								C8orf71 (114877 upstream) : FAM110B (594947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58574647	58574647	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58574647delA								C8orf71 (377359 upstream) : FAM110B (332466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58773118	58773118	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58773118delA								C8orf71 (575830 upstream) : FAM110B (133995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58819220	58819221	+	IGR	DEL	AA	-	-	rs79267688		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58819220_58819221delAA								C8orf71 (621932 upstream) : FAM110B (87892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58903869	58903869	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58903869delA								C8orf71 (706581 upstream) : FAM110B (3244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59156674	59156674	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59156674delT								FAM110B (94397 upstream) : UBXN2B (167149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59164737	59164738	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59164737_59164738delTG								FAM110B (102460 upstream) : UBXN2B (159085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59246007	59246007	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59246007delA								FAM110B (183730 upstream) : UBXN2B (77816 downstream)																																			---	---	---	---
UBXN2B	137886	broad.mit.edu	37	8	59335639	59335641	+	Intron	DEL	ATC	-	-	rs35213875		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59335639_59335641delATC	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	59432526	59432526	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59432526delA								CYP7A1 (19806 upstream) : SDCBP (33202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59445373	59445374	+	IGR	INS	-	TC	TC	rs139272230	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59445373_59445374insTC								CYP7A1 (32653 upstream) : SDCBP (20354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59593142	59593142	+	IGR	DEL	T	-	-	rs7464451		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59593142delT								NSMAF (20738 upstream) : TOX (124835 downstream)																																			---	---	---	---
TOX	9760	broad.mit.edu	37	8	59870370	59870370	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59870370delT	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)																---	---	---	---
TOX	9760	broad.mit.edu	37	8	59874092	59874093	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59874092_59874093delTT	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)																---	---	---	---
TOX	9760	broad.mit.edu	37	8	59988576	59988579	+	Intron	DEL	AAAG	-	-	rs141759097	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59988576_59988579delAAAG	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	60256644	60256644	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60256644delT								TOX (224877 upstream) : CA8 (844779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60270888	60270888	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60270888delT								TOX (239121 upstream) : CA8 (830535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60412349	60412350	+	IGR	INS	-	A	A	rs150872259	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60412349_60412350insA								TOX (380582 upstream) : CA8 (689073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60442619	60442619	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60442619delA								TOX (410852 upstream) : CA8 (658804 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60594456	60594456	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60594456delA								TOX (562689 upstream) : CA8 (506967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60597635	60597635	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60597635delA								TOX (565868 upstream) : CA8 (503788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60672252	60672252	+	IGR	DEL	A	-	-	rs34318367		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60672252delA								TOX (640485 upstream) : CA8 (429171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60827438	60827438	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60827438delA								TOX (795671 upstream) : CA8 (273985 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	61354522	61354524	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61354522_61354524delTTT								CA8 (160568 upstream) : RAB2A (75035 downstream)																																			---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61435419	61435419	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61435419delA	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	61645633	61645633	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61645633delA	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	61704958	61704959	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61704958_61704959delTT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	61800384	61800384	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61800384delT								CHD7 (20921 upstream) : CLVS1 (400141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	61961402	61961402	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61961402delT								CHD7 (181939 upstream) : CLVS1 (239123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62161482	62161482	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62161482delT								CHD7 (382019 upstream) : CLVS1 (39043 downstream)																																			---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62233935	62233935	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62233935delT	uc003xuh.2	+						CLVS1_uc003xug.2_Intron|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																		---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62264120	62264120	+	Intron	DEL	A	-	-	rs35751660		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62264120delA	uc003xuh.2	+						CLVS1_uc003xug.2_Intron|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																		---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62267848	62267849	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62267848_62267849delTT	uc003xuh.2	+						CLVS1_uc003xug.2_Intron|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																		---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62271914	62271914	+	Intron	DEL	T	-	-	rs111320505		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62271914delT	uc003xuh.2	+						CLVS1_uc003xug.2_Intron|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																		---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62326966	62326967	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62326966_62326967delTT	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																		---	---	---	---
ASPH	444	broad.mit.edu	37	8	62453922	62453922	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62453922delA	uc003xuj.2	-						ASPH_uc011leg.1_Intron	NM_004318	NP_004309			aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)													---	---	---	---
ASPH	444	broad.mit.edu	37	8	62480019	62480019	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62480019delA	uc003xuj.2	-						ASPH_uc011leg.1_Intron|ASPH_uc003xuo.2_Intron	NM_004318	NP_004309			aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)													---	---	---	---
ASPH	444	broad.mit.edu	37	8	62610519	62610520	+	Intron	DEL	AG	-	-	rs7012401	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62610519_62610520delAG	uc003xuj.2	-						ASPH_uc003xuo.2_Intron|ASPH_uc003xun.2_Intron|ASPH_uc011lek.1_Intron|ASPH_uc003xum.2_Intron|ASPH_uc003xur.2_Intron|ASPH_uc003xus.2_Intron	NM_004318	NP_004309			aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)													---	---	---	---
ASPH	444	broad.mit.edu	37	8	62619799	62619799	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62619799delA	uc003xuj.2	-						ASPH_uc003xuo.2_Intron|ASPH_uc003xun.2_Intron|ASPH_uc011lek.1_Intron|ASPH_uc003xum.2_Intron|ASPH_uc003xur.2_Intron|ASPH_uc003xus.2_Intron	NM_004318	NP_004309			aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	62646103	62646103	+	IGR	DEL	A	-	-	rs71853393		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62646103delA								ASPH (18904 upstream) : NKAIN3 (515398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62753120	62753120	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62753120delA								ASPH (125921 upstream) : NKAIN3 (408381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62809566	62809567	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62809566_62809567delTT								ASPH (182367 upstream) : NKAIN3 (351934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62963303	62963303	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62963303delA								ASPH (336104 upstream) : NKAIN3 (198198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62992904	62992905	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62992904_62992905delTT								ASPH (365705 upstream) : NKAIN3 (168596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	63009446	63009448	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63009446_63009448delAAA								ASPH (382247 upstream) : NKAIN3 (152053 downstream)																																			---	---	---	---
NKAIN3	286183	broad.mit.edu	37	8	63313807	63313807	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63313807delT	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	63324877	63324877	+	Intron	DEL	A	-	-	rs149439773		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63324877delA	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	63353262	63353262	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63353262delT	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	63637484	63637484	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63637484delT	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	63781886	63781886	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63781886delC	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)																---	---	---	---
GGH	8836	broad.mit.edu	37	8	63929777	63929777	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63929777delA	uc003xuw.2	-							NM_003878	NP_003869			gamma-glutamyl hydrolase precursor						glutamine metabolic process	extracellular space|lysosome|melanosome	gamma-glutamyl-peptidase activity				0	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|L-Glutamic Acid(DB00142)													---	---	---	---
GGH	8836	broad.mit.edu	37	8	63938642	63938642	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63938642delT	uc003xuw.2	-							NM_003878	NP_003869			gamma-glutamyl hydrolase precursor						glutamine metabolic process	extracellular space|lysosome|melanosome	gamma-glutamyl-peptidase activity				0	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	64002485	64002486	+	IGR	DEL	AA	-	-	rs35464712		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64002485_64002486delAA								TTPA (3873 upstream) : YTHDF3 (78635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64204256	64204257	+	IGR	INS	-	GT	GT	rs138405630	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64204256_64204257insGT								YTHDF3 (78911 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64423778	64423778	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64423778delA								YTHDF3 (298433 upstream) : MIR124-2 (867928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64534207	64534207	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64534207delA								YTHDF3 (408862 upstream) : MIR124-2 (757499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64750459	64750459	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64750459delA								YTHDF3 (625114 upstream) : MIR124-2 (541247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64813731	64813731	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64813731delT								YTHDF3 (688386 upstream) : MIR124-2 (477975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64868144	64868144	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64868144delA								YTHDF3 (742799 upstream) : MIR124-2 (423562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64904327	64904327	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64904327delA								YTHDF3 (778982 upstream) : MIR124-2 (387379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64962656	64962656	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64962656delA								YTHDF3 (837311 upstream) : MIR124-2 (329050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64963167	64963168	+	IGR	INS	-	TCTC	TCTC	rs146927596	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64963167_64963168insTCTC								YTHDF3 (837822 upstream) : MIR124-2 (328538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65058582	65058594	+	IGR	DEL	AAAAAAAAAAAAA	-	-	rs72108247		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65058582_65058594delAAAAAAAAAAAAA								YTHDF3 (933237 upstream) : MIR124-2 (233112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65093175	65093175	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65093175delA								YTHDF3 (967830 upstream) : MIR124-2 (198531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65293805	65293805	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65293805delT	uc003xvd.2	+						uc003xve.2_Intron|uc003xvf.2_RNA					Homo sapiens cDNA FLJ42262 fis, clone TKIDN2013134.																														---	---	---	---
LOC401463	401463	broad.mit.edu	37	8	65496953	65496954	+	5'Flank	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65496953_65496954insG	uc003xvh.2	-											Homo sapiens cDNA FLJ39831 fis, clone SPLEN2012961.												0																		---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65515495	65515495	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65515495delT	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)																---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65583429	65583429	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65583429delT	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)																---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65698228	65698228	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65698228delA	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	65716952	65716953	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65716952_65716953insT								CYP7B1 (5604 upstream) : ARMC1 (798119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65741933	65741933	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65741933delA								CYP7B1 (30585 upstream) : ARMC1 (773139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65795223	65795223	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65795223delT								CYP7B1 (83875 upstream) : ARMC1 (719849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65804570	65804583	+	IGR	DEL	TCCTTCCTTCCTTC	-	-	rs10591068	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65804570_65804583delTCCTTCCTTCCTTC								CYP7B1 (93222 upstream) : ARMC1 (710489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66154180	66154181	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66154180_66154181delAA								CYP7B1 (442832 upstream) : ARMC1 (360891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66183233	66183233	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66183233delT								CYP7B1 (471885 upstream) : ARMC1 (331839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66377605	66377605	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66377605delA								CYP7B1 (666257 upstream) : ARMC1 (137467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66445566	66445566	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66445566delC	uc003xvk.1	-											Homo sapiens cDNA FLJ37641 fis, clone BRHIP2000087.																														---	---	---	---
PDE7A	5150	broad.mit.edu	37	8	66740603	66740603	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66740603delT	uc003xvq.2	-						PDE7A_uc003xvr.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	66785155	66785155	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66785155delT								PDE7A (31400 upstream) : DNAJC5B (148636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66845793	66845793	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66845793delT								PDE7A (92038 upstream) : DNAJC5B (87998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66853826	66853827	+	IGR	DEL	CA	-	-	rs35921841		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66853826_66853827delCA								PDE7A (100071 upstream) : DNAJC5B (79964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	67319372	67319372	+	IGR	DEL	A	-	-	rs72305508		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67319372delA								CRH (228674 upstream) : RRS1 (21891 downstream)																																			---	---	---	---
SGK3	23678	broad.mit.edu	37	8	67740361	67740361	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67740361delA	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)															---	---	---	---
C8orf45	157777	broad.mit.edu	37	8	67819305	67819305	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67819305delT	uc003xwz.3	+						C8orf45_uc011lew.1_Intron|C8orf45_uc011lex.1_Intron	NM_173518	NP_775789			minichromosome maintenance complex						DNA replication		ATP binding|DNA binding			ovary(1)	1	Breast(64;0.186)		Epithelial(68;0.00384)|OV - Ovarian serous cystadenocarcinoma(28;0.00913)|all cancers(69;0.0175)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
COPS5	10987	broad.mit.edu	37	8	67961711	67961711	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67961711delA	uc003xxe.2	-						COPS5_uc003xxd.2_Intron|COPS5_uc003xxf.2_Intron|COPS5_uc010lyu.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)															---	---	---	---
COPS5	10987	broad.mit.edu	37	8	67963608	67963608	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67963608delA	uc003xxe.2	-						COPS5_uc003xxd.2_Intron|COPS5_uc003xxf.2_Intron|COPS5_uc010lyu.1_Intron|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	68011197	68011197	+	Intron	DEL	T	-	-	rs74385209		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68011197delT	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68066152	68066153	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68066152_68066153delTT	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68094553	68094554	+	Intron	DEL	TT	-	-	rs112406408		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68094553_68094554delTT	uc003xxi.2	+						ARFGEF1_uc003xxl.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron|CSPP1_uc010lyw.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68169318	68169319	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68169318_68169319insT	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	68208890	68208890	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68208890delT	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	68282952	68282952	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68282952delT								ARFGEF1 (27040 upstream) : CPA6 (51454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	68319249	68319249	+	IGR	DEL	A	-	-	rs75255829		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68319249delA								ARFGEF1 (63337 upstream) : CPA6 (15157 downstream)																																			---	---	---	---
CPA6	57094	broad.mit.edu	37	8	68338135	68338135	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68338135delT	uc003xxq.3	-						CPA6_uc003xxr.3_Intron	NM_020361	NP_065094			carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)															---	---	---	---
CPA6	57094	broad.mit.edu	37	8	68386154	68386154	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68386154delA	uc003xxq.3	-						CPA6_uc003xxr.3_Intron	NM_020361	NP_065094			carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)															---	---	---	---
CPA6	57094	broad.mit.edu	37	8	68460383	68460384	+	Intron	INS	-	CT	CT	rs145147190	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68460383_68460384insCT	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	68821156	68821156	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68821156delC								CPA6 (162536 upstream) : PREX2 (43192 downstream)																																			---	---	---	---
PREX2	80243	broad.mit.edu	37	8	69011541	69011542	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69011541_69011542insA	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146			DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69431150	69431150	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69431150delA	uc010lyz.2	+						C8orf34_uc010lyy.1_Intron|C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190			hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)															---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69472380	69472382	+	Intron	DEL	TTT	-	-	rs72284022		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69472380_69472382delTTT	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190			hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)															---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69494927	69494927	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69494927delT	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190			hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)															---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69550874	69550874	+	Intron	DEL	T	-	-	rs79803409		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69550874delT	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190			hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)															---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69613749	69613749	+	Intron	DEL	T	-	-	rs11291622		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69613749delT	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190			hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	69959510	69959510	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69959510delA	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																														---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70437038	70437038	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70437038delT	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)															---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70552363	70552364	+	Intron	INS	-	AAGA	AAGA	rs150606573	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70552363_70552364insAAGA	uc010lza.1	+						SULF1_uc003xyd.2_Intron|SULF1_uc003xye.2_Intron|SULF1_uc003xyf.2_Intron|SULF1_uc003xyg.2_Intron|SULF1_uc003xyh.1_Intron|SULF1_uc003xyi.1_Intron|SULF1_uc003xyj.1_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)															---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70552833	70552833	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70552833delT	uc010lza.1	+						SULF1_uc003xyd.2_Intron|SULF1_uc003xye.2_Intron|SULF1_uc003xyf.2_Intron|SULF1_uc003xyg.2_Intron|SULF1_uc003xyh.1_Intron|SULF1_uc003xyi.1_Intron|SULF1_uc003xyj.1_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	70708484	70708485	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70708484_70708485delTT	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)															---	---	---	---
SLCO5A1	81796	broad.mit.edu	37	8	70721969	70721970	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70721969_70721970delGT	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	70804367	70804367	+	IGR	DEL	A	-	-	rs142250291		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70804367delA								SLCO5A1 (57068 upstream) : PRDM14 (159658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	70815930	70815930	+	IGR	DEL	T	-	-	rs35348421		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70815930delT								SLCO5A1 (68631 upstream) : PRDM14 (148095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	70903377	70903377	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70903377delT								SLCO5A1 (156078 upstream) : PRDM14 (60648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	70922196	70922197	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70922196_70922197delAA								SLCO5A1 (174897 upstream) : PRDM14 (41828 downstream)																																			---	---	---	---
PRDM14	63978	broad.mit.edu	37	8	70972329	70972332	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70972329_70972332delAAAA	uc003xym.2	-							NM_024504	NP_078780			PR domain containing 14						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	71008104	71008104	+	IGR	DEL	T	-	-	rs66921279		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71008104delT								PRDM14 (24542 upstream) : NCOA2 (16163 downstream)																																			---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71123689	71123690	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71123689_71123690delAA	uc003xyn.1	-							NM_006540	NP_006531			nuclear receptor coactivator 2						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)					T	RUNXBP2	AML								---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71146732	71146733	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71146732_71146733insT	uc003xyn.1	-							NM_006540	NP_006531			nuclear receptor coactivator 2						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)					T	RUNXBP2	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	8	71450067	71450068	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71450067_71450068delTT								NCOA2 (134047 upstream) : TRAM1 (35605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	71483646	71483646	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71483646delA								NCOA2 (167626 upstream) : TRAM1 (2027 downstream)																																			---	---	---	---
LACTB2	51110	broad.mit.edu	37	8	71580992	71580993	+	Intron	INS	-	G	G	rs141269253		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71580992_71580993insG	uc011lfd.1	-						LACTB2_uc003xyp.2_Intron|XKR9_uc003xyq.2_5'Flank|XKR9_uc010lze.2_5'Flank|XKR9_uc010lzd.2_5'Flank	NM_016027	NP_057111			lactamase, beta 2								hydrolase activity|metal ion binding			ovary(1)	1	Breast(64;0.0716)		Epithelial(68;0.00319)|all cancers(69;0.0175)|OV - Ovarian serous cystadenocarcinoma(28;0.0628)|BRCA - Breast invasive adenocarcinoma(89;0.166)													OREG0018822	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	71697126	71697126	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71697126delT								XKR9 (48950 upstream) : EYA1 (412544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	71722772	71722773	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71722772_71722773insG								XKR9 (74596 upstream) : EYA1 (386897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	71851208	71851211	+	IGR	DEL	TTTT	-	-	rs67595743		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71851208_71851211delTTTT								XKR9 (203032 upstream) : EYA1 (258459 downstream)																																			---	---	---	---
EYA1	2138	broad.mit.edu	37	8	72227225	72227225	+	Intron	DEL	T	-	-	rs66961256		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72227225delT	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	72439384	72439384	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72439384delA	uc003xyw.2	-											Homo sapiens cDNA clone IMAGE:5264099.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	72675478	72675481	+	IGR	DEL	AATC	-	-	rs149947662		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72675478_72675481delAATC								EYA1 (401011 upstream) : MSC (78296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	72703920	72703920	+	IGR	DEL	A	-	-	rs142729565		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72703920delA								EYA1 (429453 upstream) : MSC (49857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	72753457	72753458	+	5'Flank	INS	-	TGTGTG	TGTGTG	rs138422218	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72753457_72753458insTGTGTG	uc011lff.1	+						uc003xyy.2_5'Flank					Homo sapiens cDNA FLJ41321 fis, clone BRAMY2045299.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	72916899	72916900	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72916899_72916900insC	uc011lff.1	+						uc003xyy.2_Intron					Homo sapiens cDNA FLJ41321 fis, clone BRAMY2045299.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	73227676	73227677	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73227676_73227677delTC	uc010lzg.2	-											Homo sapiens cDNA, FLJ99767.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	73390009	73390010	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73390009_73390010delAA	uc010lzg.2	-											Homo sapiens cDNA, FLJ99767.																														---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73821305	73821306	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73821305_73821306insT	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	73877176	73877176	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73877176delA								KCNB2 (26594 upstream) : TERF1 (43921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	73964115	73964115	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73964115delA								TERF1 (4128 upstream) : C8orf84 (12664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	73964793	73964793	+	IGR	DEL	T	-	-	rs67112108		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73964793delT								TERF1 (4806 upstream) : C8orf84 (11986 downstream)																																			---	---	---	---
C8orf84	157869	broad.mit.edu	37	8	73988892	73988892	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73988892delA	uc003xzf.2	-							NM_153225	NP_694957			RPE-spondin precursor						immune response	extracellular region	polysaccharide binding|scavenger receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	74043701	74043701	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74043701delT								C8orf84 (38194 upstream) : RPL7 (159174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	74080379	74080379	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74080379delA								C8orf84 (74872 upstream) : RPL7 (122496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	74260111	74260111	+	Intron	DEL	G	-	-	rs56989865		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74260111delG	uc003xzk.1	-											Homo sapiens cDNA FLJ46349 fis, clone TESTI4047746.																														---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74360534	74360534	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74360534delT	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron	NM_014393	NP_055208			staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)															---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74403118	74403118	+	Intron	DEL	A	-	-	rs35579595		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74403118delA	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron	NM_014393	NP_055208			staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)															---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74421954	74421954	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74421954delA	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron	NM_014393	NP_055208			staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	74685299	74685299	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74685299delA								STAU2 (25356 upstream) : UBE2W (7033 downstream)																																			---	---	---	---
UBE2W	55284	broad.mit.edu	37	8	74742889	74742889	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74742889delT	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	74782628	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74782628delA	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	74796733	74796733	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74796733delA								UBE2W (5623 upstream) : TCEB1 (61901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	74848425	74848426	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74848425_74848426delAC								UBE2W (57315 upstream) : TCEB1 (10208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75028413	75028413	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75028413delA								LY96 (87108 upstream) : JPH1 (118528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75039921	75039921	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75039921delC								LY96 (98616 upstream) : JPH1 (107020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75143108	75143108	+	IGR	DEL	C	-	-	rs80257431		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75143108delC								LY96 (201803 upstream) : JPH1 (3833 downstream)																																			---	---	---	---
JPH1	56704	broad.mit.edu	37	8	75151421	75151422	+	Intron	INS	-	T	T	rs78531442		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75151421_75151422insT	uc003yae.2	-						JPH1_uc003yaf.2_Intron|JPH1_uc003yag.1_Intron	NM_020647	NP_065698			junctophilin 1						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)															---	---	---	---
GDAP1	54332	broad.mit.edu	37	8	75275006	75275007	+	Intron	INS	-	CT	CT	rs140955331	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75275006_75275007insCT	uc003yah.2	+						GDAP1_uc011lfj.1_Intron|GDAP1_uc003yai.2_Intron	NM_018972	NP_061845			ganglioside-induced differentiation-associated							cytoplasm					0	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	75489497	75489497	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75489497delA								GDAP1 (210164 upstream) : MIR2052 (128431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75555588	75555588	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75555588delA	uc003yaj.1	+											Homo sapiens cDNA FLJ39080 fis, clone NT2RP7018197.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	75661636	75661636	+	Intron	DEL	A	-	-	rs72095931		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75661636delA	uc003yaj.1	+											Homo sapiens cDNA FLJ39080 fis, clone NT2RP7018197.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	75673284	75673285	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75673284_75673285delTT								MIR2052 (55302 upstream) : PI15 (63487 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75679184	75679184	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75679184delT								MIR2052 (61202 upstream) : PI15 (57588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75701136	75701136	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75701136delT								MIR2052 (83154 upstream) : PI15 (35636 downstream)																																			---	---	---	---
PI15	51050	broad.mit.edu	37	8	75742524	75742525	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75742524_75742525insA	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	75929747	75929747	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75929747delT	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)															---	---	---	---
HNF4G	3174	broad.mit.edu	37	8	76452404	76452405	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76452404_76452405insT	uc003yaq.2	+						HNF4G_uc003yap.1_Intron|HNF4G_uc003yar.2_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	76844998	76844998	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76844998delA								HNF4G (365939 upstream) : LOC100192378 (678117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77008151	77008151	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77008151delT								HNF4G (529092 upstream) : LOC100192378 (514964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77420554	77420562	+	IGR	DEL	AAAAAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77420554_77420562delAAAAAAAAA								HNF4G (941495 upstream) : LOC100192378 (102553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77834318	77834318	+	IGR	DEL	A	-	-	rs75418884		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77834318delA								ZFHX4 (54798 upstream) : PEX2 (58178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77993227	77993228	+	IGR	DEL	TC	-	-	rs76555085	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77993227_77993228delTC								PEX2 (80703 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78120746	78120746	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78120746delA								PEX2 (208222 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78300264	78300272	+	IGR	DEL	AAAAAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78300264_78300272delAAAAAAAAA								PEX2 (387740 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78501125	78501125	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78501125delA								PEX2 (588601 upstream) : PKIA (927211 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78648771	78648771	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78648771delA								PEX2 (736247 upstream) : PKIA (779565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78847782	78847782	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78847782delT								PEX2 (935258 upstream) : PKIA (580554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78913873	78913880	+	IGR	DEL	AGATAGAG	-	-	rs141563436	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78913873_78913880delAGATAGAG								None (None upstream) : PKIA (514456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78983548	78983549	+	IGR	DEL	AA	-	-	rs34857955		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78983548_78983549delAA								None (None upstream) : PKIA (444787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79367689	79367689	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79367689delA								None (None upstream) : PKIA (60647 downstream)																																			---	---	---	---
PKIA	5569	broad.mit.edu	37	8	79439008	79439009	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79439008_79439009delAA	uc003yba.2	+						PKIA_uc003ybb.2_Intron	NM_006823	NP_006814			cAMP-dependent protein kinase inhibitor alpha								cAMP-dependent protein kinase inhibitor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	79754715	79754716	+	IGR	INS	-	A	A	rs144592403	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79754715_79754716insA								IL7 (36957 upstream) : STMN2 (768664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79828775	79828776	+	IGR	DEL	TG	-	-	rs112128211		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79828775_79828776delTG								IL7 (111017 upstream) : STMN2 (694604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79831665	79831665	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79831665delT								IL7 (113907 upstream) : STMN2 (691715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80135022	80135022	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80135022delT								IL7 (417264 upstream) : STMN2 (388358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80161171	80161172	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80161171_80161172delAA								IL7 (443413 upstream) : STMN2 (362208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80263698	80263698	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80263698delA								IL7 (545940 upstream) : STMN2 (259682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80357940	80357940	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80357940delA								IL7 (640182 upstream) : STMN2 (165440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80388232	80388233	+	IGR	INS	-	CA	CA	rs144844347	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80388232_80388233insCA								IL7 (670474 upstream) : STMN2 (135147 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80401847	80401848	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80401847_80401848delTT								IL7 (684089 upstream) : STMN2 (121532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80496990	80496990	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80496990delA								IL7 (779232 upstream) : STMN2 (26390 downstream)																																			---	---	---	---
STMN2	11075	broad.mit.edu	37	8	80573168	80573168	+	Intron	DEL	A	-	-	rs5892686		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80573168delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	80736204	80736204	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80736204delT	uc003ybn.2	-											Homo sapiens cDNA FLJ30770 fis, clone FEBRA2000734.																														---	---	---	---
TPD52	7163	broad.mit.edu	37	8	81068119	81068119	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81068119delA	uc003ybs.1	-						TPD52_uc010lzs.1_Intron|TPD52_uc003ybt.1_Intron	NM_001025253	NP_001020424			tumor protein D52 isoform 2						anatomical structure morphogenesis|B cell differentiation|secretion	endoplasmic reticulum|perinuclear region of cytoplasm	calcium ion binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	81189717	81189717	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81189717delA								TPD52 (105881 upstream) : ZBTB10 (208137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81199420	81199420	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81199420delA								TPD52 (115584 upstream) : ZBTB10 (198434 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81352109	81352109	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81352109delT								TPD52 (268273 upstream) : ZBTB10 (45745 downstream)																																			---	---	---	---
ZBTB10	65986	broad.mit.edu	37	8	81430890	81430890	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81430890delT	uc003ybx.3	+						ZBTB10_uc003ybv.3_Intron|ZBTB10_uc003ybw.3_Intron|ZBTB10_uc010lzt.2_Intron	NM_001105539	NP_001099009			zinc finger and BTB domain containing 10 isoform						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	81472059	81472059	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81472059delA								ZBTB10 (37451 upstream) : ZNF704 (78710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81540005	81540005	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81540005delA								ZBTB10 (105397 upstream) : ZNF704 (10764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81803840	81803841	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81803840_81803841delGT								ZNF704 (16824 upstream) : PAG1 (76207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82086211	82086211	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82086211delT								PAG1 (61908 upstream) : FABP5 (106574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82102777	82102777	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82102777delT								PAG1 (78474 upstream) : FABP5 (90008 downstream)																																			---	---	---	---
FABP5	2171	broad.mit.edu	37	8	82196888	82196888	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82196888delT	uc003yca.1	+	4						NM_001444	NP_001435			fatty acid binding protein 5						epidermis development	cytoplasm	fatty acid binding|protein binding|transporter activity				0	Lung NSC(7;3.57e-05)|all_lung(9;0.00011)		Epithelial(68;0.102)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	82461464	82461465	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82461464_82461465delAC								FABP12 (17914 upstream) : IMPA1 (107686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82530375	82530375	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82530375delT								FABP12 (86825 upstream) : IMPA1 (38776 downstream)																																			---	---	---	---
SNX16	64089	broad.mit.edu	37	8	82715467	82715467	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82715467delA	uc011lft.1	-						SNX16_uc003ycn.2_Intron|SNX16_uc003yco.2_Intron	NM_022133	NP_071416			sorting nexin 16 isoform a						cell communication|early endosome to late endosome transport|endosome to lysosome transport|protein targeting to lysosome	early endosome membrane|extrinsic to endosome membrane|late endosome membrane|lysosome	identical protein binding|phosphatidylinositol binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	82897319	82897319	+	IGR	DEL	T	-	-	rs112003334		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82897319delT								SNX16 (142798 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82905226	82905227	+	IGR	DEL	AA	-	-	rs112868434		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82905226_82905227delAA								SNX16 (150705 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82948655	82948656	+	IGR	INS	-	AACTTG	AACTTG	rs147257102	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82948655_82948656insAACTTG								SNX16 (194134 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83050432	83050432	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83050432delA								SNX16 (295911 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83525264	83525265	+	IGR	INS	-	T	T	rs66482054		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83525264_83525265insT								SNX16 (770743 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83595653	83595654	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83595653_83595654delCA								SNX16 (841132 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84035167	84035167	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84035167delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84294118	84294118	+	IGR	DEL	A	-	-	rs35332098		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84294118delA								None (None upstream) : RALYL (801335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84389806	84389808	+	IGR	DEL	ATT	-	-	rs138289422		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84389806_84389808delATT								None (None upstream) : RALYL (705645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84456293	84456293	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84456293delT								None (None upstream) : RALYL (639160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84624616	84624617	+	IGR	DEL	TG	-	-	rs71904916		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84624616_84624617delTG								None (None upstream) : RALYL (470836 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84689134	84689134	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84689134delA								None (None upstream) : RALYL (406319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84824664	84824664	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84824664delA								None (None upstream) : RALYL (270789 downstream)																																			---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85215762	85215762	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85215762delT	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	85493104	85493104	+	Intron	DEL	T	-	-	rs35101771		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85493104delT	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	85508384	85508386	+	Intron	DEL	AGA	-	-	rs35385007		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85508384_85508386delAGA	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	85666949	85666950	+	Intron	INS	-	C	C	rs141357915	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85666949_85666950insC	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron|RALYL_uc003ycu.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	85683452	85683453	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85683452_85683453delTC	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron|RALYL_uc003ycu.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	85748085	85748086	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85748085_85748086delTT	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	85887823	85887824	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85887823_85887824insA								RALYL (53752 upstream) : LRRCC1 (131553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	85890298	85890299	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85890298_85890299insA								RALYL (56227 upstream) : LRRCC1 (129078 downstream)																																			---	---	---	---
E2F5	1875	broad.mit.edu	37	8	86120974	86120974	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86120974delA	uc003ycz.3	+						E2F5_uc003yda.3_Intron|E2F5_uc010mab.2_Intron|E2F5_uc003ydb.3_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																		---	---	---	---
CA13	377677	broad.mit.edu	37	8	86309302	86309303	+	Intron	INS	-	GT	GT	rs140311069	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86309302_86309303insGT	uc003ydf.1	+											Homo sapiens cDNA FLJ36434 fis, clone THYMU2012002.						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0																		---	---	---	---
CA2	760	broad.mit.edu	37	8	86382463	86382463	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86382463delT	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	86434702	86434702	+	IGR	DEL	A	-	-	rs78966394		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86434702delA								CA2 (40981 upstream) : REXO1L1 (133862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	86970475	86970475	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86970475delT								REXO1L1 (395207 upstream) : PSKH2 (90218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	87030697	87030697	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87030697delA								REXO1L1 (455429 upstream) : PSKH2 (29996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	87103992	87103995	+	IGR	DEL	GGAA	-	-	rs72136292		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87103992_87103995delGGAA								PSKH2 (22141 upstream) : ATP6V0D2 (7144 downstream)																																			---	---	---	---
ATP6V0D2	245972	broad.mit.edu	37	8	87111504	87111504	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87111504delA	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	87274709	87274710	+	IGR	INS	-	C	C	rs56243139	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87274709_87274710insC								SLC7A13 (32100 upstream) : WWP1 (80284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	87297158	87297158	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87297158delA								SLC7A13 (54549 upstream) : WWP1 (57836 downstream)																																			---	---	---	---
WWP1	11059	broad.mit.edu	37	8	87439393	87439394	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87439393_87439394delAA	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																		---	---	---	---
CPNE3	8895	broad.mit.edu	37	8	87536910	87536912	+	Intron	DEL	TTT	-	-	rs148582959		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87536910_87536912delTTT	uc003ydv.2	+							NM_003909	NP_003900			copine III						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	87624416	87624416	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87624416delA	uc003ydx.2	-						CNGB3_uc010maj.2_Intron	NM_019098	NP_061971			cyclic nucleotide gated channel beta 3						signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3																		---	---	---	---
CNBD1	168975	broad.mit.edu	37	8	87929389	87929392	+	Intron	DEL	TATC	-	-	rs74844211		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87929389_87929392delTATC	uc003ydy.2	+							NM_173538	NP_775809			cyclic nucleotide binding domain containing 1											ovary(3)	3																		---	---	---	---
CNBD1	168975	broad.mit.edu	37	8	87943706	87943707	+	Intron	INS	-	T	T	rs141442926	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87943706_87943707insT	uc003ydy.2	+							NM_173538	NP_775809			cyclic nucleotide binding domain containing 1											ovary(3)	3																		---	---	---	---
CNBD1	168975	broad.mit.edu	37	8	87984846	87984847	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87984846_87984847delAC	uc003ydy.2	+							NM_173538	NP_775809			cyclic nucleotide binding domain containing 1											ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	88476683	88476684	+	IGR	DEL	TT	-	-	rs141882951		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88476683_88476684delTT								CNBD1 (81728 upstream) : DCAF4L2 (406289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88558457	88558469	+	IGR	DEL	ACGAAAATAATGA	-	-	rs80216537		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88558457_88558469delACGAAAATAATGA								CNBD1 (163502 upstream) : DCAF4L2 (324504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88795498	88795498	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88795498delA								CNBD1 (400543 upstream) : DCAF4L2 (87475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88936377	88936377	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88936377delA								DCAF4L2 (50081 upstream) : MMP16 (113085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	89015122	89015123	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89015122_89015123insT								DCAF4L2 (128826 upstream) : MMP16 (34339 downstream)																																			---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89096696	89096696	+	Intron	DEL	A	-	-	rs28991872	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89096696delA	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	89107406	89107406	+	Intron	DEL	T	-	-	rs36060278		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89107406delT	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	89811595	89811596	+	IGR	INS	-	GT	GT	rs143391866	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89811595_89811596insGT								MMP16 (471878 upstream) : RIPK2 (958379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	89877461	89877462	+	IGR	DEL	TC	-	-	rs57828203		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89877461_89877462delTC								MMP16 (537744 upstream) : RIPK2 (892513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90079379	90079379	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90079379delT								MMP16 (739662 upstream) : RIPK2 (690596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90650610	90650610	+	IGR	DEL	T	-	-	rs11332382		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90650610delT								None (None upstream) : RIPK2 (119365 downstream)																																			---	---	---	---
RIPK2	8767	broad.mit.edu	37	8	90786332	90786332	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90786332delA	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)															---	---	---	---
RIPK2	8767	broad.mit.edu	37	8	90798702	90798702	+	Intron	DEL	A	-	-	rs112047259		TCGA-BR-4292-01	TCGA-BR-4292-01									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-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	90940477	90940477	+	IGR	DEL	A	-	-	rs79067075		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90940477delA								OSGIN2 (384 upstream) : NBN (5087 downstream)																																			---	---	---	---
NBN	4683	broad.mit.edu	37	8	90948043	90948043	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90948043delA	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				---	---	---	---
Unknown	0	broad.mit.edu	37	8	91135715	91135715	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91135715delT								CALB1 (28028 upstream) : TMEM64 (498508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91145769	91145769	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91145769delA								CALB1 (38082 upstream) : TMEM64 (488454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91204411	91204423	+	IGR	DEL	AGCATTAATAAAT	-	-	rs140334226		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91204411_91204423delAGCATTAATAAAT								CALB1 (96724 upstream) : TMEM64 (429800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91225478	91225478	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91225478delT								CALB1 (117791 upstream) : TMEM64 (408745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91301900	91301901	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91301900_91301901insA								CALB1 (194213 upstream) : TMEM64 (332322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91536642	91536643	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91536642_91536643delTG								CALB1 (428955 upstream) : TMEM64 (97580 downstream)																																			---	---	---	---
TMEM64	169200	broad.mit.edu	37	8	91674759	91674759	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91674759delT	uc003yeo.2	-							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	91681336	91681336	+	Intron	DEL	T	-	-	rs67806159		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91681336delT	uc003yeo.2	-							NM_001008495	NP_001008495			transmembrane protein 64 isoform 1							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(11;0.0598)															---	---	---	---
SLC26A7	115111	broad.mit.edu	37	8	92247115	92247116	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92247115_92247116delTC	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	92455796	92455797	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92455796_92455797insA								SLC26A7 (45416 upstream) : RUNX1T1 (515355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	92611413	92611413	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92611413delA								SLC26A7 (201033 upstream) : RUNX1T1 (359739 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	92691982	92691982	+	IGR	DEL	A	-	-	rs35200724		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92691982delA								SLC26A7 (281602 upstream) : RUNX1T1 (279170 downstream)																																			---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	93046899	93046900	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93046899_93046900delTG	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	93052384	93052386	+	Intron	DEL	ACA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93052384_93052386delACA	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	93088474	93088475	+	5'Flank	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93088474_93088475insA	uc003yfd.2	-						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	93102419	93102421	+	Intron	DEL	TTT	-	-	rs113019970		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93102419_93102421delTTT	uc011lgi.1	-						RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_Intron|RUNX1T1_uc003yfh.1_Intron	NM_175636	NP_783554			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	93222158	93222159	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93222158_93222159delTT								RUNX1T1 (114452 upstream) : C8orf83 (673706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93262976	93262976	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93262976delT								RUNX1T1 (155270 upstream) : C8orf83 (632889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93335730	93335730	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93335730delA								RUNX1T1 (228024 upstream) : C8orf83 (560135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93665349	93665349	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93665349delT								RUNX1T1 (557643 upstream) : C8orf83 (230516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93676393	93676393	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93676393delA								RUNX1T1 (568687 upstream) : C8orf83 (219472 downstream)																																			---	---	---	---
C8orf83	286144	broad.mit.edu	37	8	93961900	93961903	+	Intron	DEL	GAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93961900_93961903delGAAA	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	94036146	94036146	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94036146delA								C8orf83 (6245 upstream) : FAM92A1 (676627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94045308	94045308	+	IGR	DEL	T	-	-	rs79408077		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94045308delT								C8orf83 (15407 upstream) : FAM92A1 (667465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94072111	94072112	+	IGR	INS	-	A	A	rs146670083	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94072111_94072112insA								C8orf83 (42210 upstream) : FAM92A1 (640661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94102028	94102029	+	IGR	INS	-	G	G	rs141675251	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94102028_94102029insG								C8orf83 (72127 upstream) : FAM92A1 (610744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94262510	94262512	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94262510_94262512delAAA								C8orf83 (232609 upstream) : FAM92A1 (450261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94436425	94436425	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94436425delT								C8orf83 (406524 upstream) : FAM92A1 (276348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	95294742	95294742	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95294742delA								GEM (20185 upstream) : RAD54B (89447 downstream)																																			---	---	---	---
RAD54B	25788	broad.mit.edu	37	8	95460923	95460926	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95460923_95460926delAAAA	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	95507406	95507406	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95507406delT	uc003ygo.1	-						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	95615563	95615563	+	IGR	DEL	A	-	-	rs142361716		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95615563delA								KIAA1429 (49875 upstream) : ESRP1 (37801 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	95642281	95642282	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95642281_95642282delTT								KIAA1429 (76593 upstream) : ESRP1 (11082 downstream)																																			---	---	---	---
ESRP1	54845	broad.mit.edu	37	8	95674081	95674081	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95674081delA	uc003ygq.3	+						ESRP1_uc003ygr.3_Intron|ESRP1_uc003ygs.3_Intron|ESRP1_uc003ygt.3_Intron|ESRP1_uc003ygu.3_Intron|ESRP1_uc003ygv.2_Intron|ESRP1_uc003ygw.2_Intron	NM_017697	NP_060167			RNA binding motif protein 35A isoform 1						mRNA processing|regulation of RNA splicing|RNA splicing	nucleus|plasma membrane	mRNA binding|nucleotide binding		ESRP1/RAF1(4)	prostate(4)	4																		---	---	---	---
DPY19L4	286148	broad.mit.edu	37	8	95781239	95781240	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95781239_95781240delAA	uc003ygx.2	+							NM_181787	NP_861452			dpy-19-like 4							integral to membrane				ovary(2)	2	Breast(36;3.85e-06)																	---	---	---	---
DPY19L4	286148	broad.mit.edu	37	8	95781927	95781927	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95781927delA	uc003ygx.2	+							NM_181787	NP_861452			dpy-19-like 4							integral to membrane				ovary(2)	2	Breast(36;3.85e-06)																	---	---	---	---
DPY19L4	286148	broad.mit.edu	37	8	95792466	95792466	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95792466delT	uc003ygx.2	+							NM_181787	NP_861452			dpy-19-like 4							integral to membrane				ovary(2)	2	Breast(36;3.85e-06)																	---	---	---	---
INTS8	55656	broad.mit.edu	37	8	95864822	95864822	+	Intron	DEL	T	-	-	rs112550808		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95864822delT	uc003yhb.2	+						INTS8_uc003yha.1_Intron|INTS8_uc011lgq.1_Intron|INTS8_uc011lgr.1_Intron|INTS8_uc010mba.2_Intron	NM_017864	NP_060334			integrator complex subunit 8						snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)																	---	---	---	---
C8orf38	137682	broad.mit.edu	37	8	95931411	95931411	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95931411delT	uc003yhf.2	+						C8orf38_uc003yhe.1_Intron					RecName: Full=UPF0551 protein C8orf38, mitochondrial; AltName: Full=Putative phytoene synthase; Flags: Precursor;						biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)																	---	---	---	---
C8orf38	137682	broad.mit.edu	37	8	96011158	96011159	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96011158_96011159delGT	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)																	---	---	---	---
PLEKHF2	79666	broad.mit.edu	37	8	96157377	96157377	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96157377delA	uc003yhn.1	+							NM_024613	NP_078889			phafin 2							transport vesicle	metal ion binding|protein binding			ovary(2)	2	Breast(36;3.18e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	96186566	96186567	+	IGR	DEL	TT	-	-	rs80203229		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96186566_96186567delTT								PLEKHF2 (17655 upstream) : C8orf37 (71668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96297734	96297734	+	IGR	DEL	A	-	-	rs141235942		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96297734delA								C8orf37 (16297 upstream) : GDF6 (856826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96524357	96524357	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96524357delT								C8orf37 (242920 upstream) : GDF6 (630203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96640587	96640588	+	IGR	INS	-	GC	GC	rs151264621	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96640587_96640588insGC								C8orf37 (359150 upstream) : GDF6 (513972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96754435	96754437	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96754435_96754437delTTT								C8orf37 (472998 upstream) : GDF6 (400123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96933728	96933728	+	IGR	DEL	A	-	-	rs113531146		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96933728delA								C8orf37 (652291 upstream) : GDF6 (220832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96977957	96977964	+	IGR	DEL	AGGGAAGG	-	-	rs67336860		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96977957_96977964delAGGGAAGG								C8orf37 (696520 upstream) : GDF6 (176596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96980976	96980976	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96980976delA								C8orf37 (699539 upstream) : GDF6 (173584 downstream)																																			---	---	---	---
GDF6	392255	broad.mit.edu	37	8	97169448	97169448	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97169448delT	uc003yhp.2	-							NM_001001557	NP_001001557			growth differentiation factor 6 precursor						activin receptor signaling pathway|BMP signaling pathway|growth|pathway-restricted SMAD protein phosphorylation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			ovary(1)|breast(1)|pancreas(1)	3	Breast(36;2.67e-05)																	---	---	---	---
MTERFD1	51001	broad.mit.edu	37	8	97253144	97253144	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97253144delA	uc003yhs.1	-						MTERFD1_uc003yhr.1_Intron|MTERFD1_uc010mbd.1_Intron	NM_015942	NP_057026			MTERF domain containing 1 precursor						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion	transcription regulatory region DNA binding			ovary(1)	1	Breast(36;5.16e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	97415881	97415881	+	IGR	DEL	A	-	-	rs147082342		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97415881delA								PTDSS1 (69107 upstream) : SDC2 (90001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	97442285	97442286	+	IGR	INS	-	TTTG	TTTG	rs138498550	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97442285_97442286insTTTG								PTDSS1 (95511 upstream) : SDC2 (63596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	97449362	97449363	+	IGR	DEL	TT	-	-	rs113833888		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97449362_97449363delTT								PTDSS1 (102588 upstream) : SDC2 (56519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	97500960	97500960	+	IGR	DEL	A	-	-	rs112288904		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97500960delA								PTDSS1 (154186 upstream) : SDC2 (4922 downstream)																																			---	---	---	---
SDC2	6383	broad.mit.edu	37	8	97505522	97505522	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97505522delT	uc003yhv.1	+							NM_002998	NP_002989			syndecan 2 precursor							integral to plasma membrane	cytoskeletal protein binding|PDZ domain binding			ovary(2)	2	Breast(36;3.41e-05)				Sargramostim(DB00020)													---	---	---	---
SDC2	6383	broad.mit.edu	37	8	97619347	97619347	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97619347delC	uc003yhv.1	+						SDC2_uc011lgu.1_Intron	NM_002998	NP_002989			syndecan 2 precursor							integral to plasma membrane	cytoskeletal protein binding|PDZ domain binding			ovary(2)	2	Breast(36;3.41e-05)				Sargramostim(DB00020)													---	---	---	---
SDC2	6383	broad.mit.edu	37	8	97620471	97620471	+	Intron	DEL	A	-	-	rs80090550		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97620471delA	uc003yhv.1	+						SDC2_uc011lgu.1_Intron	NM_002998	NP_002989			syndecan 2 precursor							integral to plasma membrane	cytoskeletal protein binding|PDZ domain binding			ovary(2)	2	Breast(36;3.41e-05)				Sargramostim(DB00020)													---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97655514	97655516	+	5'Flank	DEL	AAT	-	-	rs10566222		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97655514_97655516delAAT	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	97727041	97727041	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97727041delT	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	97910280	97910282	+	Intron	DEL	GTT	-	-	rs148092788		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97910280_97910282delGTT	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	98058460	98058460	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98058460delT	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	98299168	98299168	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98299168delT								TSPYL5 (8992 upstream) : MTDH (357239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98318347	98318347	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98318347delA								TSPYL5 (28171 upstream) : MTDH (338060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98319503	98319503	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98319503delA								TSPYL5 (29327 upstream) : MTDH (336904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98459294	98459297	+	IGR	DEL	TTTT	-	-	rs72408932		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98459294_98459297delTTTT								TSPYL5 (169118 upstream) : MTDH (197110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98527717	98527718	+	IGR	DEL	TT	-	-	rs113429772		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98527717_98527718delTT								TSPYL5 (237541 upstream) : MTDH (128689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98599285	98599285	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98599285delA								TSPYL5 (309109 upstream) : MTDH (57122 downstream)																																			---	---	---	---
MTDH	92140	broad.mit.edu	37	8	98680679	98680680	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98680679_98680680insA	uc003yhz.2	+							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	98777481	98777481	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98777481delA								MTDH (34994 upstream) : LAPTM4B (10328 downstream)																																			---	---	---	---
LAPTM4B	55353	broad.mit.edu	37	8	98827797	98827797	+	Intron	DEL	T	-	-	rs111936259		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98827797delT	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	98867259	98867262	+	IGR	DEL	AAAA	-	-	rs77182966		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98867259_98867262delAAAA								LAPTM4B (2430 upstream) : MATN2 (14049 downstream)																																			---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98946678	98946679	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98946678_98946679insA	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	99026526	99026526	+	Intron	DEL	A	-	-	rs34821398		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99026526delA	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)															---	---	---	---
C8orf47	203111	broad.mit.edu	37	8	99102829	99102830	+	Intron	DEL	AA	-	-	rs80153741		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99102829_99102830delAA	uc003yih.1	+							NM_173549	NP_775820			hypothetical protein LOC203111												0	Breast(36;2.31e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	99181218	99181219	+	IGR	DEL	TT	-	-	rs35365950		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99181218_99181219delTT								POP1 (9150 upstream) : NIPAL2 (23168 downstream)																																			---	---	---	---
NIPAL2	79815	broad.mit.edu	37	8	99209310	99209310	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99209310delT	uc003yil.1	-						NIPAL2_uc011lgw.1_Intron|NIPAL2_uc003yim.1_Intron	NM_024759	NP_079035			NIPA-like domain containing 2							integral to membrane					0																		---	---	---	---
STK3	6788	broad.mit.edu	37	8	99502136	99502136	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99502136delA	uc003yip.2	-						STK3_uc003yio.2_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
STK3	6788	broad.mit.edu	37	8	99510366	99510366	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99510366delT	uc003yip.2	-						STK3_uc003yio.2_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
STK3	6788	broad.mit.edu	37	8	99526772	99526773	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99526772_99526773delAA	uc003yip.2	-						STK3_uc003yio.2_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	100016945	100016945	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100016945delT								OSR2 (52621 upstream) : VPS13B (8549 downstream)																																			---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100262158	100262159	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100262158_100262159insA	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	100359211	100359211	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100359211delT	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	100473387	100473387	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100473387delT	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	100690398	100690398	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100690398delT	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	100702260	100702260	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100702260delT	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	100819905	100819906	+	Intron	INS	-	TG	TG	rs144674961	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100819905_100819906insTG	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	100844570	100844579	+	Intron	DEL	TTTTTTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100844570_100844579delTTTTTTTTTT	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	100860836	100860837	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100860836_100860837insT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360			vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	100918458	100918458	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100918458delT								COX6C (12563 upstream) : RGS22 (54818 downstream)																																			---	---	---	---
RGS22	26166	broad.mit.edu	37	8	101056855	101056858	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101056855_101056858delTTTT	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron|RGS22_uc011lgz.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)															---	---	---	---
RNF19A	25897	broad.mit.edu	37	8	101274109	101274109	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101274109delT	uc003yjj.1	-						RNF19A_uc003yjk.1_Intron	NM_015435	NP_056250			ring finger protein 19						microtubule cytoskeleton organization|protein modification process	centrosome|integral to membrane	ligase activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	101376790	101376790	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101376790delT								RNF19A (54463 upstream) : ANKRD46 (145197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101491203	101491205	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101491203_101491205delTTT								RNF19A (168876 upstream) : ANKRD46 (30782 downstream)																																			---	---	---	---
ANKRD46	157567	broad.mit.edu	37	8	101543093	101543093	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101543093delA	uc003yjm.2	-						ANKRD46_uc003yjn.1_Intron|ANKRD46_uc003yjo.1_Intron|ANKRD46_uc003yjp.1_Intron	NM_198401	NP_940683			ankyrin repeat domain 46							integral to membrane					0	all_cancers(14;5.07e-05)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000353)|all_lung(17;0.000998)		Epithelial(11;2.61e-11)|all cancers(13;5.03e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.49e-06)|STAD - Stomach adenocarcinoma(118;0.0957)															---	---	---	---
SNX31	169166	broad.mit.edu	37	8	101624504	101624504	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101624504delA	uc003yjr.2	-						SNX31_uc011lha.1_5'Flank|SNX31_uc011lhb.1_Intron	NM_152628	NP_689841			sorting nexin 31						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	101673878	101673879	+	IGR	INS	-	C	C	rs139270833	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101673878_101673879insC								SNX31 (11985 upstream) : PABPC1 (41265 downstream)																																			---	---	---	---
PABPC1	26986	broad.mit.edu	37	8	101716283	101716290	+	Intron	DEL	AAAAAAAA	-	-	rs34116624		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101716283_101716290delAAAAAAAA	uc003yjs.1	-						PABPC1_uc011lhc.1_Intron|PABPC1_uc011lhd.1_Intron|PABPC1_uc003yjt.1_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	101739299	101739299	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101739299delA								PABPC1 (4984 upstream) : YWHAZ (191505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101781009	101781009	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101781009delA								PABPC1 (46694 upstream) : YWHAZ (149795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101840144	101840145	+	IGR	INS	-	TG	TG	rs71703816		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101840144_101840145insTG								PABPC1 (105829 upstream) : YWHAZ (90659 downstream)																																			---	---	---	---
YWHAZ	7534	broad.mit.edu	37	8	101933024	101933027	+	Intron	DEL	GGGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101933024_101933027delGGGG	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	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)													---	---	---	---
YWHAZ	7534	broad.mit.edu	37	8	101936107	101936107	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101936107delA	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_3'UTR	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	102463905	102463905	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102463905delT								NACAP1 (78970 upstream) : GRHL2 (40763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102485968	102485968	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102485968delT								NACAP1 (101033 upstream) : GRHL2 (18700 downstream)																																			---	---	---	---
GRHL2	79977	broad.mit.edu	37	8	102681190	102681192	+	3'UTR	DEL	ATG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102681190_102681192delATG	uc010mbu.2	+	16						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	102722598	102722598	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102722598delT	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)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103296962	103296962	+	Intron	DEL	A	-	-	rs79929192		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103296962delA	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)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103351758	103351760	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103351758_103351760delAAA	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)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103380664	103380665	+	Intron	DEL	TC	-	-	rs7838700	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103380664_103380665delTC	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	103506141	103506142	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103506141_103506142delAA								UBR5 (81646 upstream) : ODF1 (57706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103534478	103534479	+	IGR	INS	-	A	A	rs143295623	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103534478_103534479insA								UBR5 (109983 upstream) : ODF1 (29369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103733055	103733055	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103733055delA								KLF10 (65072 upstream) : AZIN1 (105482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103942791	103942791	+	IGR	DEL	T	-	-	rs72271681		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103942791delT								AZIN1 (66394 upstream) : ATP6V1C1 (90457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103951830	103951831	+	IGR	DEL	AA	-	-	rs35889968		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103951830_103951831delAA								AZIN1 (75433 upstream) : ATP6V1C1 (81417 downstream)																																			---	---	---	---
ATP6V1C1	528	broad.mit.edu	37	8	104032070	104032070	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
BAALC	79870	broad.mit.edu	37	8	104230787	104230787	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104230787delC	uc003yld.2	+						BAALC_uc003yle.2_Intron|uc003ylf.2_Intron|BAALC_uc003ylg.2_Intron|BAALC_uc010mcc.2_Intron	NM_024812	NP_079088			brain and acute leukemia, cytoplasmic isoform 1							centrosome|membrane|nucleus					0			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)															---	---	---	---
BAALC	79870	broad.mit.edu	37	8	104236916	104236917	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104236916_104236917insA	uc003yld.2	+						BAALC_uc003yle.2_Intron|uc003ylf.2_Intron|BAALC_uc003ylg.2_Intron|BAALC_uc010mcc.2_Intron	NM_024812	NP_079088			brain and acute leukemia, cytoplasmic isoform 1							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	104322666	104322666	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104322666delT	uc003ylh.2	+						FZD6_uc003yli.2_Intron|FZD6_uc003ylj.2_Intron|FZD6_uc011lhn.1_Intron|FZD6_uc011lho.1_Intron|FZD6_uc011lhp.1_Intron	NM_003506	NP_003497			frizzled 6 isoform a precursor						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	104363588	104363589	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104363588_104363589insG								FZD6 (18496 upstream) : CTHRC1 (20197 downstream)																																			---	---	---	---
SLC25A32	81034	broad.mit.edu	37	8	104416858	104416859	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104416858_104416859insA	uc003yll.2	-						SLC25A32_uc011lhr.1_Intron	NM_030780	NP_110407			solute carrier family 25, member 32						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	104439487	104439487	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104439487delT	uc003yln.2	+						DCAF13_uc003ylm.1_Intron|DCAF13_uc003ylo.2_Intron	NM_015420	NP_056235			WD repeats and SOF1 domain containing						rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex				breast(1)	1																		---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104589545	104589546	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104589545_104589546insA	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	104683422	104683422	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104683422delA	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	104781292	104781292	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104781292delA	uc003ylp.2	+							NM_001100117	NP_001093587			regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
DPYS	1807	broad.mit.edu	37	8	105409054	105409057	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105409054_105409057delAAAA	uc003yly.3	-						DPYS_uc010mcf.1_Intron	NM_001385	NP_001376			dihydropyrimidinase						protein homotetramerization|pyrimidine nucleoside catabolic process|thymine catabolic process|uracil catabolic process	cytosol	dihydropyrimidinase activity|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)															---	---	---	---
LRP12	29967	broad.mit.edu	37	8	105578089	105578089	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105578089delA	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	105817736	105817736	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105817736delG								LRP12 (216516 upstream) : ZFPM2 (513411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105912055	105912060	+	IGR	DEL	ATGTGT	-	-	rs71944506		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105912055_105912060delATGTGT								LRP12 (310835 upstream) : ZFPM2 (419087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	106020970	106020970	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106020970delT								LRP12 (419750 upstream) : ZFPM2 (310177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	106082534	106082534	+	IGR	DEL	C	-	-	rs149219963	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106082534delC								LRP12 (481314 upstream) : ZFPM2 (248613 downstream)																																			---	---	---	---
ZFPM2	23414	broad.mit.edu	37	8	106410086	106410086	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106410086delA	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	106726445	106726445	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106726445delG	uc003ymd.2	+						ZFPM2_uc011lhs.1_Intron	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	106801318	106801319	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106801318_106801319delTT	uc003ymd.2	+						ZFPM2_uc011lhs.1_Intron	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	107043007	107043008	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107043007_107043008insC								ZFPM2 (226242 upstream) : OXR1 (239465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107158675	107158675	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107158675delT								ZFPM2 (341910 upstream) : OXR1 (123798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107232858	107232858	+	IGR	DEL	A	-	-	rs71996641		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107232858delA								ZFPM2 (416093 upstream) : OXR1 (49615 downstream)																																			---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107376166	107376166	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107376166delT	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	107600492	107600492	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107600492delT	uc011lht.1	+						OXR1_uc003ymf.2_Intron	NM_018002	NP_060472			oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	107801986	107801986	+	IGR	DEL	G	-	-	rs112939729		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107801986delG								ABRA (19514 upstream) : ANGPT1 (459725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107920115	107920116	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107920115_107920116insT								ABRA (137643 upstream) : ANGPT1 (341595 downstream)																																			---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108292000	108292000	+	Intron	DEL	G	-	-	rs5893835		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108292000delG	uc003ymn.2	-						ANGPT1_uc011lhv.1_Intron|ANGPT1_uc003ymo.2_Intron	NM_001146	NP_001137			angiopoietin 1 precursor						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)															---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108296789	108296789	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108296789delA	uc003ymn.2	-						ANGPT1_uc011lhv.1_Intron|ANGPT1_uc003ymo.2_Intron|ANGPT1_uc003ymp.3_3'UTR	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	108590383	108590384	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108590383_108590384insG								ANGPT1 (80129 upstream) : RSPO2 (321161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108609605	108609605	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108609605delT								ANGPT1 (99351 upstream) : RSPO2 (301940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108750645	108750645	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108750645delT								ANGPT1 (240391 upstream) : RSPO2 (160900 downstream)																																			---	---	---	---
EIF3E	3646	broad.mit.edu	37	8	109218817	109218818	+	Intron	INS	-	TG	TG	rs140964651	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109218817_109218818insTG	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)															---	---	---	---
TTC35	9694	broad.mit.edu	37	8	109462630	109462630	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109462630delT	uc003ymw.1	+							NM_014673	NP_055488			tetratricopeptide repeat domain 35							endoplasmic reticulum|nucleus	binding			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(57;2.34e-10)															---	---	---	---
TMEM74	157753	broad.mit.edu	37	8	109664018	109664018	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109664018delT	uc003ymx.2	-											Homo sapiens cDNA FLJ30668 fis, clone FCBBF1000675.						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)															---	---	---	---
TMEM74	157753	broad.mit.edu	37	8	109712713	109712717	+	Intron	DEL	GAAAA	-	-	rs67337678		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109712713_109712717delGAAAA	uc003ymx.2	-											Homo sapiens cDNA FLJ30668 fis, clone FCBBF1000675.						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)															---	---	---	---
TMEM74	157753	broad.mit.edu	37	8	109745105	109745105	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109745105delA	uc003ymx.2	-											Homo sapiens cDNA FLJ30668 fis, clone FCBBF1000675.						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)															---	---	---	---
TMEM74	157753	broad.mit.edu	37	8	109764273	109764276	+	Intron	DEL	TGAA	-	-	rs112796113		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109764273_109764276delTGAA	uc003ymx.2	-											Homo sapiens cDNA FLJ30668 fis, clone FCBBF1000675.						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	110083906	110083906	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110083906delA								TMEM74 (284136 upstream) : TRHR (15833 downstream)																																			---	---	---	---
NUDCD1	84955	broad.mit.edu	37	8	110343277	110343277	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110343277delA	uc003ynb.3	-						NUDCD1_uc003yna.2_5'Flank|NUDCD1_uc010mcl.2_Intron|NUDCD1_uc010mcm.1_5'Flank	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)															---	---	---	---
EBAG9	9166	broad.mit.edu	37	8	110573290	110573290	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110573290delT	uc003ynf.2	+						EBAG9_uc003yng.2_Intron	NM_198120	NP_936056			estrogen receptor binding site associated						apoptosis|regulation of cell growth	focal adhesion|Golgi membrane|integral to membrane|soluble fraction	apoptotic protease activator activity				0			OV - Ovarian serous cystadenocarcinoma(57;1.39e-14)															---	---	---	---
SYBU	55638	broad.mit.edu	37	8	110664623	110664623	+	Intron	DEL	T	-	-	rs111759751		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110664623delT	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																		---	---	---	---
SYBU	55638	broad.mit.edu	37	8	110700870	110700870	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110700870delT	uc010mcv.2	-						SYBU_uc010mcu.2_Intron|SYBU_uc003ynp.3_Intron	NM_001099744	NP_001093214			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	110782116	110782117	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110782116_110782117delCT								SYBU (78096 upstream) : KCNV1 (197118 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111042928	111042929	+	IGR	DEL	TA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111042928_111042929delTA								KCNV1 (54852 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111055674	111055674	+	IGR	DEL	C	-	-	rs147117812		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111055674delC								KCNV1 (67598 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111102835	111102835	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111102835delT								KCNV1 (114759 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111787336	111787337	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111787336_111787337insT								KCNV1 (799260 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111878810	111878811	+	IGR	INS	-	AA	AA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111878810_111878811insAA								KCNV1 (890734 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112160611	112160611	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112160611delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112383589	112383589	+	IGR	DEL	A	-	-	rs67768211		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112383589delA								None (None upstream) : CSMD3 (851572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112416020	112416020	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112416020delA								None (None upstream) : CSMD3 (819141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112710580	112710580	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112710580delT								None (None upstream) : CSMD3 (524581 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112766390	112766390	+	IGR	DEL	T	-	-	rs72103857		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112766390delT								None (None upstream) : CSMD3 (468771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112955489	112955490	+	IGR	INS	-	A	A	rs143624555	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112955489_112955490insA								None (None upstream) : CSMD3 (279671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112990209	112990209	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112990209delT								None (None upstream) : CSMD3 (244952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	113101682	113101682	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113101682delT								None (None upstream) : CSMD3 (133479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	113180843	113180843	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113180843delT								None (None upstream) : CSMD3 (54318 downstream)																																			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113445590	113445590	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113445590delA	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	113512339	113512339	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113512339delA	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	113710690	113710691	+	Intron	INS	-	G	G	rs149579795	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113710690_113710691insG	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	113854006	113854006	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113854006delA	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	113944857	113944857	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113944857delA	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	114107514	114107514	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114107514delA	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	114142373	114142373	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114142373delA	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	114248779	114248779	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114248779delT	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	114411759	114411759	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114411759delA	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	114713494	114713494	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114713494delT								CSMD3 (264252 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	114784252	114784253	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114784252_114784253insT								CSMD3 (335010 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	114966070	114966070	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114966070delT								CSMD3 (516828 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115149056	115149056	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115149056delT								CSMD3 (699814 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115237371	115237371	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115237371delT								CSMD3 (788129 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115342489	115342490	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115342489_115342490delTT								CSMD3 (893247 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115770366	115770366	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115770366delA								None (None upstream) : TRPS1 (650359 downstream)																																			---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116490031	116490031	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116490031delT	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	116673334	116673334	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116673334delA	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	116681042	116681044	+	5'UTR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116681042_116681044delAAA	uc003ynz.2	-	1					TRPS1_uc011lhy.1_5'Flank|TRPS1_uc003yny.2_5'UTR|TRPS1_uc010mcy.2_5'UTR	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	116747242	116747243	+	IGR	INS	-	TTCTTTCTTTCTTTCTTTCTTTCTTTCT	TTCTTTCTTTCTTTCTTTCTTTCTTTCT	rs11269874		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116747242_116747243insTTCTTTCTTTCTTTCTTTCTTTCTTTCT								TRPS1 (66014 upstream) : EIF3H (909813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117007036	117007036	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117007036delT								TRPS1 (325808 upstream) : EIF3H (650020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117013438	117013438	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117013438delT								TRPS1 (332210 upstream) : EIF3H (643618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117047509	117047509	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117047509delT								TRPS1 (366281 upstream) : EIF3H (609547 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117359848	117359849	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117359848_117359849delAC								TRPS1 (678620 upstream) : EIF3H (297207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117362185	117362185	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117362185delA								TRPS1 (680957 upstream) : EIF3H (294871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117416489	117416494	+	IGR	DEL	TTTTTT	-	-	rs13279999		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117416489_117416494delTTTTTT								TRPS1 (735261 upstream) : EIF3H (240562 downstream)																																			---	---	---	---
EIF3H	8667	broad.mit.edu	37	8	117667147	117667147	+	Intron	DEL	T	-	-	rs67362497		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117667147delT	uc003yoa.2	-						EIF3H_uc003yob.2_Intron	NM_003756	NP_003747			eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			lung(3)	3	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)																	---	---	---	---
EIF3H	8667	broad.mit.edu	37	8	117705927	117705927	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117705927delT	uc003yoa.2	-						EIF3H_uc003yob.2_Intron|EIF3H_uc011lhz.1_Intron	NM_003756	NP_003747			eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			lung(3)	3	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	117810495	117810495	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117810495delT								UTP23 (23576 upstream) : RAD21 (47679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117905127	117905127	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117905127delT								RAD21 (18022 upstream) : C8orf85 (45337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117924953	117924953	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117924953delC								RAD21 (37848 upstream) : C8orf85 (25511 downstream)																																			---	---	---	---
SLC30A8	169026	broad.mit.edu	37	8	118009217	118009218	+	Intron	DEL	TT	-	-	rs76589865		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118009217_118009218delTT	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)															---	---	---	---
SLC30A8	169026	broad.mit.edu	37	8	118078960	118078960	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118078960delT	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)															---	---	---	---
SLC30A8	169026	broad.mit.edu	37	8	118172642	118172643	+	Intron	INS	-	TGTG	TGTG	rs73702979		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118172642_118172643insTGTG	uc003yoh.2	+						SLC30A8_uc010mcz.2_Intron|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	118446163	118446163	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118446163delG								SLC30A8 (257211 upstream) : MED30 (86802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118478271	118478271	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118478271delA								SLC30A8 (289319 upstream) : MED30 (54694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118515583	118515584	+	IGR	INS	-	GAG	GAG	rs140411631		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118515583_118515584insGAG								SLC30A8 (326631 upstream) : MED30 (17381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118574471	118574473	+	IGR	DEL	ATG	-	-	rs75835794		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118574471_118574473delATG								MED30 (21972 upstream) : EXT1 (237129 downstream)																																			---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118903768	118903768	+	Intron	DEL	A	-	-	rs11295136		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118903768delA	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	118946496	118946496	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118946496delA	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	118974685	118974685	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118974685delA	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	119140325	119140325	+	IGR	DEL	A	-	-	rs113105836		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119140325delA								EXT1 (16267 upstream) : SAMD12 (61370 downstream)																																			---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119229253	119229253	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119229253delT	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	119375720	119375720	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119375720delT	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	119498654	119498654	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119498654delA	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	119619479	119619479	+	Intron	DEL	T	-	-	rs71988507		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119619479delT	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	119698767	119698769	+	IGR	DEL	TCA	-	-	rs34681491		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119698767_119698769delTCA								SAMD12 (64533 upstream) : TNFRSF11B (237028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	119713306	119713307	+	IGR	INS	-	T	T	rs148853875	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119713306_119713307insT								SAMD12 (79072 upstream) : TNFRSF11B (222490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	119861985	119861985	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119861985delT								SAMD12 (227751 upstream) : TNFRSF11B (73812 downstream)																																			---	---	---	---
COLEC10	10584	broad.mit.edu	37	8	120077039	120077040	+	5'Flank	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120077039_120077040delTT	uc003yoo.2	+							NM_006438	NP_006429			collectin sub-family member 10 precursor							collagen|cytoplasm	mannose binding			ovary(2)|skin(1)	3	all_cancers(13;4.13e-26)|Lung NSC(37;1.36e-07)|Ovarian(258;0.018)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00113)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	120190790	120190791	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120190790_120190791delGA								COLEC10 (71595 upstream) : MAL2 (29819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120523248	120523248	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120523248delT								NOV (86570 upstream) : ENPP2 (46071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120556629	120556629	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120556629delT								NOV (119951 upstream) : ENPP2 (12690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120706829	120706830	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120706829_120706830insT								ENPP2 (55723 upstream) : TAF2 (36185 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120725202	120725203	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120725202_120725203delTT								ENPP2 (74096 upstream) : TAF2 (17812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120737829	120737830	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120737829_120737830delTT								ENPP2 (86723 upstream) : TAF2 (5185 downstream)																																			---	---	---	---
TAF2	6873	broad.mit.edu	37	8	120745211	120745211	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120745211delT	uc003you.2	-							NM_003184	NP_003175			TBP-associated factor 2						G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	120940984	120940988	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120940984_120940988delTTTTT	uc003yow.3	+						DEPDC6_uc011lid.1_Intron	NM_022783	NP_073620			DEP domain containing 6						intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis	intracellular	protein binding				0	Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121330983	121330983	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121330983delA	uc003yox.2	+						COL14A1_uc003yoz.2_Intron	NM_021110	NP_066933			collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121334969	121334969	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121334969delT	uc003yox.2	+						COL14A1_uc003yoz.2_Intron	NM_021110	NP_066933			collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121373302	121373302	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121373302delT	uc003yox.2	+						COL14A1_uc003yoz.2_Intron	NM_021110	NP_066933			collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
MTBP	27085	broad.mit.edu	37	8	121534750	121534750	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121534750delT	uc003ypc.1	+							NM_022045	NP_071328			Mdm2, transformed 3T3 cell double minute 2, p53						cell cycle arrest					skin(2)|ovary(1)	3	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
SNTB1	6641	broad.mit.edu	37	8	121739208	121739208	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121739208delT	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	122253618	122253618	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122253618delA								SNTB1 (429309 upstream) : HAS2 (371653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122300992	122300993	+	IGR	INS	-	A	A	rs76253211		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122300992_122300993insA								SNTB1 (476683 upstream) : HAS2 (324278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122397343	122397343	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122397343delT								SNTB1 (573034 upstream) : HAS2 (227928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122402131	122402132	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122402131_122402132delTT								SNTB1 (577822 upstream) : HAS2 (223139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122571195	122571196	+	IGR	INS	-	GT	GT	rs142489245	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122571195_122571196insGT								SNTB1 (746886 upstream) : HAS2 (54075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122604780	122604781	+	IGR	INS	-	A	A	rs139613301	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122604780_122604781insA								SNTB1 (780471 upstream) : HAS2 (20490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122615126	122615126	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122615126delA								SNTB1 (790817 upstream) : HAS2 (10145 downstream)																																			---	---	---	---
HAS2	3037	broad.mit.edu	37	8	122634077	122634077	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122634077delT	uc003yph.2	-							NM_005328	NP_005319			hyaluronan synthase 2							integral to plasma membrane	hyaluronan synthase activity		HAS2/PLAG1(10)	soft_tissue(10)|ovary(5)	15	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	122970243	122970243	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122970243delT	uc003ypj.2	-											Homo sapiens, clone IMAGE:5466006, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	123035063	123035064	+	Intron	INS	-	TCCTT	TCCTT	rs142767211	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123035063_123035064insTCCTT	uc003ypj.2	-											Homo sapiens, clone IMAGE:5466006, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	123058957	123058958	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123058957_123058958delAG	uc003ypj.2	-											Homo sapiens, clone IMAGE:5466006, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	123065916	123065916	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123065916delA	uc003ypj.2	-											Homo sapiens, clone IMAGE:5466006, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	123202099	123202100	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123202099_123202100delAA								HAS2AS (545166 upstream) : ZHX2 (591801 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123284229	123284231	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123284229_123284231delAAA								HAS2AS (627296 upstream) : ZHX2 (509670 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123358777	123358777	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123358777delA								HAS2AS (701844 upstream) : ZHX2 (435124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123713816	123713817	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123713816_123713817delTT								None (None upstream) : ZHX2 (80084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123731826	123731826	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123731826delA								None (None upstream) : ZHX2 (62075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123782555	123782555	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123782555delT								None (None upstream) : ZHX2 (11346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123783742	123783742	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123783742delA								None (None upstream) : ZHX2 (10159 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	124022725	124022725	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124022725delG								ZHX2 (35970 upstream) : DERL1 (2843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	124187299	124187299	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124187299delT								WDR67 (22909 upstream) : FAM83A (3988 downstream)																																			---	---	---	---
FAM83A	84985	broad.mit.edu	37	8	124207991	124207991	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124207991delA	uc003ypv.2	+						FAM83A_uc003ypw.2_Intron|FAM83A_uc003ypy.2_Intron|FAM83A_uc003ypx.2_Intron|FAM83A_uc003ypz.2_Intron	NM_032899	NP_116288			hypothetical protein LOC84985 isoform a											ovary(3)|skin(1)	4	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
C8orf76	84933	broad.mit.edu	37	8	124255784	124255785	+	5'Flank	DEL	AA	-	-	rs79915362		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124255784_124255785delAA	uc003yqc.1	-						C8orf76_uc003yqd.2_Intron	NM_032847	NP_116236			hypothetical protein LOC84933								binding			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	124462783	124462783	+	IGR	DEL	C	-	-	rs35711184		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124462783delC								WDYHV1 (8523 upstream) : FBXO32 (52576 downstream)																																			---	---	---	---
FBXO32	114907	broad.mit.edu	37	8	124539101	124539101	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124539101delT	uc003yqr.2	-						FBXO32_uc003yqq.2_Intron|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	124574055	124574055	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124574055delT								FBXO32 (20609 upstream) : KLHL38 (83860 downstream)																																			---	---	---	---
ANXA13	312	broad.mit.edu	37	8	124708147	124708147	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124708147delC	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-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	125092566	125092566	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125092566delT	uc003yqw.2	+						uc003yqy.1_Intron	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	125135061	125135062	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125135061_125135062delTT	uc003yqy.1	-											Homo sapiens cDNA FLJ32770 fis, clone TESTI2001898.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	125182395	125182395	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125182395delA	uc003yqy.1	-											Homo sapiens cDNA FLJ32770 fis, clone TESTI2001898.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	125397806	125397806	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125397806delA								TMEM65 (12866 upstream) : TRMT12 (65242 downstream)																																			---	---	---	---
TATDN1	83940	broad.mit.edu	37	8	125527206	125527206	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125527206delT	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	125701229	125701229	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125701229delA	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	125733540	125733541	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125733540_125733541delAA	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	125795356	125795356	+	IGR	DEL	A	-	-	rs112031998		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125795356delA								MTSS1 (54626 upstream) : LOC157381 (156528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125931621	125931621	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125931621delT								MTSS1 (190891 upstream) : LOC157381 (20263 downstream)																																			---	---	---	---
LOC157381	157381	broad.mit.edu	37	8	125955694	125955694	+	RNA	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125955694delA	uc003yro.1	+	3		c.419delA			LOC157381_uc003yrp.2_RNA|LOC157381_uc003yrq.1_RNA					Homo sapiens cDNA FLJ32337 fis, clone PROST2005880.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	125981594	125981595	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125981594_125981595delAA								LOC157381 (18257 upstream) : ZNF572 (3944 downstream)																																			---	---	---	---
KIAA0196	9897	broad.mit.edu	37	8	126046747	126046747	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126046747delA	uc003yrt.2	-						KIAA0196_uc011lir.1_Intron|KIAA0196_uc003yru.1_Intron	NM_014846	NP_055661			strumpellin						cell death	WASH complex				ovary(2)	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)															---	---	---	---
KIAA0196	9897	broad.mit.edu	37	8	126093479	126093485	+	Intron	DEL	TTTTTTT	-	-	rs141124545		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126093479_126093485delTTTTTTT	uc003yrt.2	-						KIAA0196_uc011lir.1_Intron	NM_014846	NP_055661			strumpellin						cell death	WASH complex				ovary(2)	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)															---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126321966	126321966	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126321966delA	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-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126490902delA								TRIB1 (40260 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126510287	126510289	+	IGR	DEL	TTT	-	-	rs35561817		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126510287_126510289delTTT								TRIB1 (59645 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126518156	126518157	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126518156_126518157insG								TRIB1 (67514 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126531511	126531514	+	IGR	DEL	ACAC	-	-	rs113684950		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126531511_126531514delACAC								TRIB1 (80869 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126564247	126564247	+	IGR	DEL	A	-	-	rs75466096	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126564247delA								TRIB1 (113605 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126564273	126564273	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126564273delA								TRIB1 (113631 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126615706	126615706	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126615706delC								TRIB1 (165064 upstream) : FAM84B (948981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126711430	126711430	+	IGR	DEL	T	-	-	rs72435874		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126711430delT								TRIB1 (260788 upstream) : FAM84B (853257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126861108	126861110	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126861108_126861110delTTT								TRIB1 (410466 upstream) : FAM84B (703577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126885205	126885208	+	IGR	DEL	AAAA	-	-	rs72059488		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126885205_126885208delAAAA								TRIB1 (434563 upstream) : FAM84B (679479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127045202	127045202	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127045202delA								TRIB1 (594560 upstream) : FAM84B (519485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127119631	127119632	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127119631_127119632delTC								TRIB1 (668989 upstream) : FAM84B (445055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127129198	127129198	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127129198delT								TRIB1 (678556 upstream) : FAM84B (435489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127283948	127283948	+	IGR	DEL	A	-	-	rs78870981		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127283948delA								TRIB1 (833306 upstream) : FAM84B (280739 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127366493	127366494	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127366493_127366494insT								TRIB1 (915851 upstream) : FAM84B (198193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127455072	127455072	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127455072delA								None (None upstream) : FAM84B (109615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127592894	127592897	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127592894_127592897delTTTT								FAM84B (22428 upstream) : LOC727677 (709165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127722513	127722514	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127722513_127722514delAA								FAM84B (152047 upstream) : LOC727677 (579548 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127745143	127745145	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127745143_127745145delTTT								FAM84B (174677 upstream) : LOC727677 (556917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127860732	127860734	+	IGR	DEL	AAA	-	-	rs35011340		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127860732_127860734delAAA								FAM84B (290266 upstream) : LOC727677 (441328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128032766	128032766	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128032766delA								FAM84B (462300 upstream) : LOC727677 (269296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128221318	128221319	+	RNA	INS	-	TTG	TTG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128221318_128221319insTTG	uc003ysa.1	-	2		c.923_924insCAA								Homo sapiens cDNA FLJ43320 fis, clone NT2RI2024935.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	128247608	128247608	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128247608delT								FAM84B (677142 upstream) : LOC727677 (54454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128257272	128257272	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128257272delA								FAM84B (686806 upstream) : LOC727677 (44790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128259899	128259899	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128259899delA								FAM84B (689433 upstream) : LOC727677 (42163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128569342	128569343	+	IGR	INS	-	ACAG	ACAG	rs139320135	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128569342_128569343insACAG								LOC727677 (74958 upstream) : MYC (178422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128652308	128652308	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128652308delT								LOC727677 (157924 upstream) : MYC (95457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128700459	128700460	+	RNA	INS	-	A	A	rs142484189	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128700459_128700460insA	uc003ysg.2	-	3		c.1426_1427insT								Homo sapiens, clone IMAGE:5554747, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	128709838	128709838	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128709838delT	uc003ysg.2	-											Homo sapiens, clone IMAGE:5554747, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	128761877	128761879	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128761877_128761879delAAA								MYC (8199 upstream) : PVT1 (44900 downstream)																																			---	---	---	---
PVT1	5820	broad.mit.edu	37	8	129015214	129015215	+	Intron	INS	-	CTTC	CTTC			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	129135016	129135016	+	IGR	DEL	T	-	-	rs34982323		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129135016delT								PVT1 (21518 upstream) : MIR1208 (27346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129303072	129303072	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129303072delT								MIR1208 (140638 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129431618	129431618	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129431618delT	uc003ysn.2	-											Homo sapiens cDNA clone IMAGE:3877235, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	129939221	129939222	+	IGR	INS	-	GTGT	GTGT	rs150163767	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129939221_129939222insGTGT								MIR1208 (776787 upstream) : GSDMC (821221 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130145800	130145801	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130145800_130145801insA								MIR1208 (983366 upstream) : GSDMC (614642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130151661	130151661	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130151661delA								MIR1208 (989227 upstream) : GSDMC (608782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130293434	130293435	+	IGR	DEL	TC	-	-	rs72091074		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130293434_130293435delTC								None (None upstream) : GSDMC (467008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130356500	130356500	+	IGR	DEL	T	-	-	rs11320731		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130356500delT								None (None upstream) : GSDMC (403943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130441632	130441632	+	IGR	DEL	T	-	-	rs115982822	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130441632delT								None (None upstream) : GSDMC (318811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130816410	130816410	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130816410delA								GSDMC (17276 upstream) : FAM49B (37308 downstream)																																			---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131108439	131108439	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131108439delA	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	131123598	131123598	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131123598delA	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	131220793	131220793	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131220793delT	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	131227156	131227156	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131227156delT	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	132238574	132238574	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132238574delT								ADCY8 (185739 upstream) : EFR3A (677785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132397529	132397530	+	IGR	DEL	AA	-	-	rs67728461		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132397529_132397530delAA								ADCY8 (344694 upstream) : EFR3A (518829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132521862	132521862	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132521862delT								ADCY8 (469027 upstream) : EFR3A (394497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132606961	132606961	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132606961delT								ADCY8 (554126 upstream) : EFR3A (309398 downstream)																																			---	---	---	---
EFR3A	23167	broad.mit.edu	37	8	132980467	132980467	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132980467delT	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)															---	---	---	---
EFR3A	23167	broad.mit.edu	37	8	133006333	133006333	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133006333delA	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)															---	---	---	---
HHLA1	10086	broad.mit.edu	37	8	133086577	133086578	+	Intron	DEL	TT	-	-	rs78748313		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133086577_133086578delTT	uc011liy.1	-						HHLA1_uc003yth.2_Intron	NM_001145095	NP_001138567			HERV-H LTR-associating 1							extracellular region					0																		---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133365613	133365613	+	Intron	DEL	A	-	-	rs74633965		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133365613delA	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	133400223	133400228	+	Intron	DEL	GAAGAG	-	-	rs7841255		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133400223_133400228delGAAGAG	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	133429926	133429929	+	Intron	DEL	CATT	-	-	rs58718470	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133429926_133429929delCATT	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)															---	---	---	---
LRRC6	23639	broad.mit.edu	37	8	133684057	133684057	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133684057delA	uc003ytk.2	-						LRRC6_uc003ytl.2_Intron	NM_012472	NP_036604			leucine rich repeat containing 6							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	133823712	133823712	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133823712delT	uc003ytt.2	+						PHF20L1_uc003ytr.2_3'UTR|PHF20L1_uc010mdv.2_3'UTR|PHF20L1_uc003yts.2_Intron|PHF20L1_uc011lja.1_Intron|PHF20L1_uc003ytu.1_Intron|PHF20L1_uc003ytv.2_3'UTR	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)															---	---	---	---
TG	7038	broad.mit.edu	37	8	133897375	133897376	+	Intron	DEL	GG	-	-	rs67142567		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133897375_133897376delGG	uc003ytw.2	+							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	133921745	133921746	+	Intron	DEL	GG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133921745_133921746delGG	uc003ytw.2	+						TG_uc010mdw.2_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	134054733	134054733	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134054733delT	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron|SLA_uc003ytz.2_Intron|SLA_uc011lje.1_Intron|SLA_uc011ljf.1_Intron|SLA_uc011ljg.1_Intron|SLA_uc011ljd.1_Intron	NM_003235	NP_003226			thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)														---	---	---	---
TG	7038	broad.mit.edu	37	8	134118374	134118374	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134118374delG	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.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)														---	---	---	---
WISP1	8840	broad.mit.edu	37	8	134222664	134222665	+	Intron	INS	-	T	T	rs147865384	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134222664_134222665insT	uc003yub.2	+						WISP1_uc003yuc.2_Intron|WISP1_uc010meb.2_Intron|WISP1_uc010mec.2_Intron|WISP1_uc010med.2_Intron|WISP1_uc003yud.2_5'Flank	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)															---	---	---	---
WISP1	8840	broad.mit.edu	37	8	134222866	134222866	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134222866delT	uc003yub.2	+						WISP1_uc003yuc.2_Intron|WISP1_uc010meb.2_Intron|WISP1_uc010mec.2_Intron|WISP1_uc010med.2_Intron|WISP1_uc003yud.2_5'Flank	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)															---	---	---	---
NDRG1	10397	broad.mit.edu	37	8	134284022	134284034	+	Intron	DEL	AAAAAAAAAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134284022_134284034delAAAAAAAAAAAAA	uc003yuh.2	-						NDRG1_uc003yug.2_Intron|NDRG1_uc010mee.2_Intron|NDRG1_uc010mef.2_Intron|NDRG1_uc011ljh.1_Intron|NDRG1_uc011lji.1_Intron	NM_001135242	NP_001128714			N-myc downstream regulated 1						cellular response to hypoxia|response to metal ion	cytoplasm|microtubule cytoskeleton|nucleus|plasma membrane	protein binding			ovary(4)	4	all_epithelial(106;4.26e-24)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	134332565	134332565	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134332565delA								NDRG1 (23018 upstream) : ST3GAL1 (134526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	134334069	134334070	+	IGR	INS	-	A	A	rs145594138	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134334069_134334070insA								NDRG1 (24522 upstream) : ST3GAL1 (133021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	134447665	134447665	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134447665delT								NDRG1 (138118 upstream) : ST3GAL1 (19426 downstream)																																			---	---	---	---
ST3GAL1	6482	broad.mit.edu	37	8	134540426	134540426	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
ST3GAL1	6482	broad.mit.edu	37	8	134559521	134559521	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134559521delT	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)															---	---	---	---
ST3GAL1	6482	broad.mit.edu	37	8	134575021	134575024	+	Intron	DEL	TTTC	-	-	rs6150827		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134575021_134575024delTTTC	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	134643783	134643784	+	IGR	INS	-	C	C	rs72722195	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134643783_134643784insC								ST3GAL1 (59600 upstream) : ZFAT (846249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	134644056	134644057	+	IGR	DEL	TT	-	-	rs150375364		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134644056_134644057delTT								ST3GAL1 (59873 upstream) : ZFAT (845976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	134745039	134745039	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134745039delA								ST3GAL1 (160856 upstream) : ZFAT (744994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135244470	135244470	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135244470delA								ST3GAL1 (660287 upstream) : ZFAT (245563 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135334634	135334634	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135334634delT								ST3GAL1 (750451 upstream) : ZFAT (155399 downstream)																																			---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135595715	135595716	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135595715_135595716insC	uc003yup.2	-						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)															---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135661264	135661264	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135661264delA	uc003yup.2	-						ZFAT_uc003yun.2_Intron|ZFAT_uc003yuo.2_Intron|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron|ZFAT_uc003yur.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)															---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135692336	135692336	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135692336delA	uc003yup.2	-						ZFAT_uc003yun.2_Intron|ZFAT_uc003yuo.2_Intron|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron|ZFAT_uc003yur.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)															---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135698793	135698793	+	Intron	DEL	A	-	-	rs76131775		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135698793delA	uc003yup.2	-						ZFAT_uc003yun.2_Intron|ZFAT_uc003yuo.2_Intron|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron|ZFAT_uc003yur.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	135754100	135754101	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135754100_135754101delAA								ZFAT (28819 upstream) : MIR30B (58662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136199167	136199167	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136199167delT								MIR30D (381979 upstream) : LOC286094 (47207 downstream)																																			---	---	---	---
LOC286094	286094	broad.mit.edu	37	8	136257775	136257776	+	Intron	DEL	TA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136257775_136257776delTA	uc011ljm.1	+							NR_026706				Homo sapiens cDNA clone IMAGE:4837396.												0																		---	---	---	---
LOC286094	286094	broad.mit.edu	37	8	136268297	136268297	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136268297delT	uc011ljm.1	+							NR_026706				Homo sapiens cDNA clone IMAGE:4837396.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	136426591	136426602	+	IGR	DEL	GGGGAGGAGGAA	-	-	rs36216975		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136426591_136426602delGGGGAGGAGGAA								LOC286094 (114632 upstream) : KHDRBS3 (43114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136695730	136695731	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136695730_136695731insTG								KHDRBS3 (35884 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136814937	136814937	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136814937delA								KHDRBS3 (155091 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136931866	136931866	+	IGR	DEL	A	-	-	rs35178981		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136931866delA								KHDRBS3 (272020 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136971880	136971883	+	IGR	DEL	TGTG	-	-	rs113223316		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136971880_136971883delTGTG								KHDRBS3 (312034 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137291624	137291624	+	IGR	DEL	T	-	-	rs11345987		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137291624delT								KHDRBS3 (631778 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137320514	137320514	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137320514delT								KHDRBS3 (660668 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137573052	137573053	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137573052_137573053delAA								KHDRBS3 (913206 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137919166	137919166	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137919166delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137997857	137997880	+	IGR	DEL	GTGTGTGTGTGTGTGTGTGTGTGT	-	-	rs36215727	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137997857_137997880delGTGTGTGTGTGTGTGTGTGTGTGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138064590	138064590	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138064590delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138209604	138209604	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138209604delT								None (None upstream) : FAM135B (932664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138429011	138429012	+	IGR	DEL	TC	-	-	rs150100124		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138429011_138429012delTC								None (None upstream) : FAM135B (713256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138450371	138450371	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138450371delT								None (None upstream) : FAM135B (691897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138517785	138517785	+	IGR	DEL	C	-	-	rs35327013		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138517785delC								None (None upstream) : FAM135B (624483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138548747	138548747	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138548747delA								None (None upstream) : FAM135B (593521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138552053	138552053	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138552053delT								None (None upstream) : FAM135B (590215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138878562	138878562	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138878562delT								None (None upstream) : FAM135B (263706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138931468	138931468	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138931468delA								None (None upstream) : FAM135B (210800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	139005091	139005091	+	IGR	DEL	T	-	-	rs34006145		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139005091delT								None (None upstream) : FAM135B (137177 downstream)																																			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139230996	139230997	+	Intron	INS	-	CACACA	CACACA	rs139117207	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139230996_139230997insCACACA	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	139236286	139236286	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139236286delG	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	139247550	139247551	+	Intron	INS	-	T	T	rs144240707	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139247550_139247551insT	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	139273388	139273388	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139273388delA	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	139313733	139313733	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139313733delT	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	139455713	139455713	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139455713delA	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	139587565	139587566	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139587565_139587566delTT								FAM135B (78500 upstream) : COL22A1 (12913 downstream)																																			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139693235	139693235	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139693235delG	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	139701402	139701402	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139701402delG	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	139727809	139727809	+	Intron	DEL	T	-	-	rs5895555		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139727809delT	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	139775005	139775006	+	Intron	INS	-	TTC	TTC	rs150348962	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139775005_139775006insTTC	uc003yvd.2	-						COL22A1_uc011ljo.1_5'Flank	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	139807337	139807337	+	Intron	DEL	A	-	-	rs35355736		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139807337delA	uc003yvd.2	-							NM_152888	NP_690848			collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)												HNSCC(7;0.00092)			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139928197	139928198	+	5'Flank	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139928197_139928198insA	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	139953420	139953421	+	IGR	INS	-	GT	GT	rs148050780	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139953420_139953421insGT								COL22A1 (27184 upstream) : KCNK9 (659661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	139992029	139992029	+	IGR	DEL	T	-	-	rs77500001		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139992029delT								COL22A1 (65793 upstream) : KCNK9 (621053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140061009	140061009	+	IGR	DEL	A	-	-	rs34275992		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140061009delA								COL22A1 (134773 upstream) : KCNK9 (552073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140304647	140304649	+	IGR	DEL	CTT	-	-	rs143305229		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140304647_140304649delCTT								COL22A1 (378411 upstream) : KCNK9 (308433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140379002	140379004	+	IGR	DEL	AAA	-	-	rs145766899		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140379002_140379004delAAA								COL22A1 (452766 upstream) : KCNK9 (234078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140391332	140391332	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140391332delA								COL22A1 (465096 upstream) : KCNK9 (221750 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140541948	140541948	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140541948delA								COL22A1 (615712 upstream) : KCNK9 (71134 downstream)																																			---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	140809669	140809670	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140809669_140809670insT	uc003yvj.2	-						TRAPPC9_uc003yvh.2_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	140968457	140968458	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140968457_140968458delTT	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	141047684	141047685	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141047684_141047685delAC	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	141167143	141167143	+	Intron	DEL	T	-	-	rs67192772		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141167143delT	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	141318980	141318981	+	Intron	DEL	AA	-	-	rs76677309		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141318980_141318981delAA	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	141358717	141358717	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141358717delA	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	141373701	141373701	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141373701delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	141485427	141485427	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141485427delT								TRAPPC9 (16749 upstream) : CHRAC1 (35974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	141504301	141504301	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141504301delA								TRAPPC9 (35623 upstream) : CHRAC1 (17100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	141506011	141506011	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141506011delT								TRAPPC9 (37333 upstream) : CHRAC1 (15390 downstream)																																			---	---	---	---
EIF2C2	27161	broad.mit.edu	37	8	141543905	141543906	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141543905_141543906delAA	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	141549044	141549044	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141549044delA	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	141730517	141730517	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141730517delA	uc003yvu.2	-						PTK2_uc011ljp.1_5'Flank|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	141785026	141785027	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141785026_141785027delTT	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-4292-01	TCGA-BR-4292-01									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	141898873	141898873	+	Intron	DEL	T	-	-	rs33962881		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141898873delT	uc003yvu.2	-						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	141972878	141972878	+	Intron	DEL	A	-	-	rs80044882		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141972878delA	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	141977561	141977564	+	Intron	DEL	TTTT	-	-	rs11357214		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141977561_141977564delTTTT	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	142064004	142064004	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142064004delA								PTK2 (52672 upstream) : DENND3 (74716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	142115729	142115729	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142115729delA								PTK2 (104397 upstream) : DENND3 (22991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	142285709	142285710	+	IGR	DEL	AA	-	-	rs77350976		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142285709_142285710delAA								SLC45A4 (21484 upstream) : LOC731779 (64938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	142357758	142357767	+	IGR	DEL	ACATACACAT	-	-	rs28690109		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142357758_142357767delACATACACAT								LOC731779 (3039 upstream) : GPR20 (8822 downstream)																																			---	---	---	---
PTP4A3	11156	broad.mit.edu	37	8	142418094	142418094	+	Intron	DEL	A	-	-	rs35572820		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142418094delA	uc010mes.2	+											Homo sapiens cDNA, FLJ18299.							early endosome|plasma membrane	identical protein binding|prenylated protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0	all_cancers(97;2.55e-15)|all_epithelial(106;1.39e-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;0.0474)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	142551266	142551284	+	IGR	DEL	CACACACACACCACACAGA	-	-	rs35734448		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142551266_142551284delCACACACACACCACACAGA								FLJ43860 (33936 upstream) : MIR1302-7 (316319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	142701874	142701874	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142701874delT								FLJ43860 (184544 upstream) : MIR1302-7 (165729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	142724261	142724269	+	IGR	DEL	TGGTGATGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142724261_142724269delTGGTGATGG								FLJ43860 (206931 upstream) : MIR1302-7 (143334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143055671	143055671	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143055671delT								MIR1302-7 (187997 upstream) : NCRNA00051 (224046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143171420	143171420	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143171420delG								MIR1302-7 (303746 upstream) : NCRNA00051 (108297 downstream)																																			---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143312129	143312136	+	Intron	DEL	CCATCCAT	-	-	rs36014631		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143312129_143312136delCCATCCAT	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron	NM_145003	NP_659440			t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143394500	143394501	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143394500_143394501delTG	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron|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)																	---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143449494	143449494	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143449494delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	143513747	143513748	+	IGR	INS	-	CCATCA	CCATCA	rs144949638		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143513747_143513748insCCATCA								TSNARE1 (29204 upstream) : BAI1 (31629 downstream)																																			---	---	---	---
BAI1	575	broad.mit.edu	37	8	143610702	143610703	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	143662295	143662296	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143662295_143662296delTT								BAI1 (35928 upstream) : ARC (30114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	144164161	144164161	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144164161delG								C8orf31 (28441 upstream) : LY6H (75171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	144172672	144172673	+	IGR	INS	-	AACAAC	AACAAC	rs151168732	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144172672_144172673insAACAAC								C8orf31 (36952 upstream) : LY6H (66659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	144321757	144321757	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144321757delT								GPIHBP1 (22714 upstream) : ZFP41 (7234 downstream)																																			---	---	---	---
RHPN1	114822	broad.mit.edu	37	8	144459233	144459234	+	Intron	INS	-	GT	GT	rs142163832	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144459233_144459234insGT	uc003yyb.2	+							NM_052924	NP_443156			rhophilin 1						signal transduction	intracellular				large_intestine(1)	1	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)															---	---	---	---
TSTA3	7264	broad.mit.edu	37	8	144695197	144695197	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144695197delG	uc003yza.2	-						TSTA3_uc003yzb.2_Intron	NM_003313	NP_003304			tissue specific transplantation antigen P35B						'de novo' GDP-L-fucose biosynthetic process|leukocyte cell-cell adhesion		coenzyme binding|electron carrier activity|GDP-4-dehydro-D-rhamnose reductase activity|GDP-L-fucose synthase activity|isomerase activity			pancreas(1)	1	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;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)		NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	144825608	144825608	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144825608delT	uc003yzl.1	+											Homo sapiens cDNA FLJ33892 fis, clone CTONG2007623.																														---	---	---	---
SCRIB	23513	broad.mit.edu	37	8	144873996	144873997	+	Intron	DEL	CA	-	-	rs6982642		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144873996_144873997delCA	uc003yzp.1	-						SCRIB_uc003yzn.1_Intron|SCRIB_uc003yzo.1_Intron	NM_015356	NP_056171			scribble isoform b						activation of Rac GTPase activity|apoptosis involved in morphogenesis|cell migration|cell proliferation|cell-cell adhesion|establishment of apical/basal cell polarity|interspecies interaction between organisms|mammary gland duct morphogenesis|negative regulation of mitotic cell cycle|positive chemotaxis|positive regulation of apoptosis|positive regulation of receptor recycling|protein localization to adherens junction	cell-cell adherens junction|Scrib-APC-beta-catenin complex	protein binding			urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)|pancreas(1)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)															---	---	---	---
SCRIB	23513	broad.mit.edu	37	8	144873997	144873997	+	Intron	DEL	A	-	-	rs6982642		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144873997delA	uc003yzp.1	-						SCRIB_uc003yzn.1_Intron|SCRIB_uc003yzo.1_Intron	NM_015356	NP_056171			scribble isoform b						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	144940081	144940081	+	Intron	DEL	C	-	-	rs60421625		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144940081delC	uc003zaa.1	-							NM_031308	NP_112598			epiplakin 1							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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	145120889	145120889	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145120889delT								OPLAH (5305 upstream) : EXOSC4 (12633 downstream)																																			---	---	---	---
CYC1	1537	broad.mit.edu	37	8	145147008	145147009	+	5'Flank	DEL	TT	-	-	rs75977954		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145147008_145147009delTT	uc003zaz.3	+						CYC1_uc003zay.2_5'Flank	NM_001916	NP_001907			cytochrome c-1						respiratory electron transport chain|transport	cell junction|integral to membrane|mitochondrial inner membrane|respiratory chain	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme 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;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	145179526	145179529	+	IGR	DEL	AAAA	-	-	rs112316436		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145179526_145179529delAAAA								KIAA1875 (6308 upstream) : C8orf30A (13143 downstream)																																			---	---	---	---
HEATR7A	727957	broad.mit.edu	37	8	145218997	145219002	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145218997_145219002delTTTTTT	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																		---	---	---	---
HEATR7A	727957	broad.mit.edu	37	8	145230252	145230252	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145230252delC	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																		---	---	---	---
HEATR7A	727957	broad.mit.edu	37	8	145231116	145231116	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145231116delA	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																		---	---	---	---
HEATR7A	727957	broad.mit.edu	37	8	145256920	145256920	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145256920delC	uc003zbk.3	+						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																		---	---	---	---
HEATR7A	727957	broad.mit.edu	37	8	145273913	145273913	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145273913delT	uc003zbk.3	+						HEATR7A_uc011lla.1_Intron|HEATR7A_uc010mft.2_Intron	NM_032450	NP_115826			HEAT repeat containing 7A isoform 1								binding				0																		---	---	---	---
HSF1	3297	broad.mit.edu	37	8	145525850	145525850	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145525850delA	uc003zbt.3	+						HSF1_uc003zbu.3_Intron	NM_005526	NP_005517			heat shock transcription factor 1							cytoplasm	protein binding|sequence-specific DNA binding transcription factor 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;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	145565576	145565577	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145565576_145565577delAC								SCRT1 (5633 upstream) : C8ORFK29 (11310 downstream)																																			---	---	---	---
GPT	2875	broad.mit.edu	37	8	145730103	145730103	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145730103delC	uc011lli.1	+						GPT_uc011llj.1_Intron|GPT_uc003zdh.3_Intron	NM_005309	NP_005300			glutamic pyruvate transaminase						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)													---	---	---	---
MFSD3	113655	broad.mit.edu	37	8	145733043	145733043	+	5'Flank	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145733043delG	uc003zdi.1	+							NM_138431	NP_612440			major facilitator superfamily domain containing						transmembrane transport	integral to membrane				central_nervous_system(2)	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)															---	---	---	---
RECQL4	9401	broad.mit.edu	37	8	145738582	145738584	+	Intron	DEL	GGG	-	-	rs67678060		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145738582_145738584delGGG	uc003zdj.2	-							NM_004260	NP_004251			RecQ protein-like 4						DNA duplex unwinding|DNA recombination|DNA repair	cytoplasm|nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding			breast(2)|lung(1)|skin(1)	4	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)					N|F|S			osteosarcoma|skin basal and sqamous cell		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	RAPADILINO_syndrome|Rothmund-Thomson_syndrome|Baller-Gerold_syndrome				---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145813039	145813045	+	Intron	DEL	TTTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145813039_145813045delTTTTTTT	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	145893880	145893880	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145893880delT	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																		---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145898602	145898602	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145898602delA	uc011llk.1	-							NM_025251	NP_079527			KIAA1688 protein						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	145929299	145929299	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145929299delT								ARHGAP39 (18105 upstream) : ZNF251 (16996 downstream)																																			---	---	---	---
ZNF34	80778	broad.mit.edu	37	8	146009548	146009549	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146009548_146009549delAA	uc003zdy.3	-						ZNF34_uc003zdx.3_Intron	NM_030580	NP_085057			zinc finger protein 34						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.221)	OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;5.18e-38)|all cancers(56;4.41e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.0179)														---	---	---	---
RPL8	6132	broad.mit.edu	37	8	146019916	146019916	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146019916delA	uc003zeb.2	-						RPL8_uc003zdz.2_5'Flank|RPL8_uc003zea.2_5'Flank|RPL8_uc003zec.2_5'Flank|RPL8_uc010mgc.2_5'Flank|RPL8_uc011lll.1_5'Flank	NM_033301	NP_150644			ribosomal protein L8						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	rRNA binding|structural constituent of ribosome				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)	GBM - Glioblastoma multiforme(99;0.191)														---	---	---	---
COMMD5	28991	broad.mit.edu	37	8	146079716	146079716	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146079716delA	uc003zem.2	-						COMMD5_uc003zel.1_5'Flank|COMMD5_uc003zen.2_5'Flank|COMMD5_uc003zeo.3_5'Flank|COMMD5_uc010mgf.2_Intron	NM_001081004	NP_001074473			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)															---	---	---	---
COMMD5	28991	broad.mit.edu	37	8	146087776	146087776	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146087776delT	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)															---	---	---	---
DOCK8	81704	broad.mit.edu	37	9	332832	332832	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:332832delT	uc003zgf.2	+						DOCK8_uc011lls.1_Intron|DOCK8_uc010mgu.2_Intron|DOCK8_uc010mgv.2_Intron|DOCK8_uc003zgg.2_Intron|DOCK8_uc003zgh.2_Intron	NM_203447	NP_982272			dedicator of cytokinesis 8						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)														---	---	---	---
KANK1	23189	broad.mit.edu	37	9	501080	501080	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:501080delA	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)														---	---	---	---
KANK1	23189	broad.mit.edu	37	9	541632	541632	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:541632delA	uc003zgl.1	+						KANK1_uc003zgm.2_Intron|KANK1_uc003zgn.1_Intron	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)														---	---	---	---
KANK1	23189	broad.mit.edu	37	9	710630	710630	+	Intron	DEL	C	-	-	rs68161748		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:710630delC	uc003zgl.1	+						KANK1_uc003zgm.2_Intron|KANK1_uc003zgn.1_Intron|KANK1_uc003zgo.1_Intron|KANK1_uc003zgp.1_Intron|KANK1_uc003zgq.2_Intron|KANK1_uc003zgr.1_Intron|KANK1_uc003zgs.1_Intron	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)														---	---	---	---
DMRT1	1761	broad.mit.edu	37	9	902346	902346	+	Intron	DEL	C	-	-	rs2057430	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:902346delC	uc003zgv.2	+							NM_021951	NP_068770			doublesex and mab-3 related transcription factor						cell differentiation|male gonad development|sex determination	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(10;2.66e-10)|Lung NSC(10;2.82e-10)|Breast(48;0.232)		Lung(218;0.037)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	1537349	1537350	+	IGR	INS	-	T	T	rs141990570	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1537349_1537350insT								DMRT2 (479796 upstream) : SMARCA2 (477992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1577136	1577137	+	IGR	DEL	AC	-	-	rs73641756		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1577136_1577137delAC								DMRT2 (519583 upstream) : SMARCA2 (438205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1704923	1704924	+	IGR	INS	-	ATAC	ATAC	rs139217166	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1704923_1704924insATAC								DMRT2 (647370 upstream) : SMARCA2 (310418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1908669	1908670	+	IGR	DEL	AA	-	-	rs76409104		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1908669_1908670delAA								DMRT2 (851116 upstream) : SMARCA2 (106672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1915099	1915099	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1915099delA								DMRT2 (857546 upstream) : SMARCA2 (100243 downstream)																																			---	---	---	---
SMARCA2	6595	broad.mit.edu	37	9	2036177	2036178	+	Intron	INS	-	GT	GT	rs140964092	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2036177_2036178insGT	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	2086517	2086518	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2086517_2086518insG	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	2160212	2160214	+	Intron	DEL	TTT	-	-	rs147266408		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2160212_2160214delTTT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron|SMARCA2_uc011llw.1_Intron|SMARCA2_uc003zhf.2_Intron|SMARCA2_uc011llx.1_Intron|SMARCA2_uc003zhe.2_Intron|SMARCA2_uc003zhg.2_Intron|SMARCA2_uc010mhb.2_5'Flank	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	2161562	2161562	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2161562delT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron|SMARCA2_uc011llw.1_Intron|SMARCA2_uc003zhf.2_Intron|SMARCA2_uc011llx.1_Intron|SMARCA2_uc003zhe.2_Intron|SMARCA2_uc003zhg.2_Intron|SMARCA2_uc010mhb.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)														---	---	---	---
FLJ35024	401491	broad.mit.edu	37	9	2482942	2482942	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2482942delA	uc003zhh.1	-						FLJ35024_uc003zhi.2_Intron					Homo sapiens cDNA FLJ35024 fis, clone OCBBF2015233.												0																		---	---	---	---
VLDLR	7436	broad.mit.edu	37	9	2639688	2639688	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2639688delA	uc003zhk.1	+						VLDLR_uc003zhl.1_Intron|VLDLR_uc003zhm.1_Intron|VLDLR_uc003zhn.1_Intron	NM_003383	NP_003374			very low density lipoprotein receptor isoform a						cholesterol metabolic process|endocytosis|lipid transport|memory|very-low-density lipoprotein particle clearance	coated pit|integral to membrane|membrane fraction|plasma membrane|very-low-density lipoprotein particle	apolipoprotein binding|calcium ion binding|low-density lipoprotein receptor activity|very-low-density lipoprotein particle receptor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)														---	---	---	---
KCNV2	169522	broad.mit.edu	37	9	2719473	2719473	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2719473delT	uc003zho.1	+							NM_133497	NP_598004			potassium channel, subfamily V, member 2							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(50;0.0257)														---	---	---	---
KCNV2	169522	broad.mit.edu	37	9	2726490	2726490	+	Intron	DEL	A	-	-	rs111252100		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2726490delA	uc003zho.1	+							NM_133497	NP_598004			potassium channel, subfamily V, member 2							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(50;0.0257)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	2994832	2994832	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2994832delA								KIAA0020 (150702 upstream) : RFX3 (229817 downstream)																																			---	---	---	---
RFX3	5991	broad.mit.edu	37	9	3508956	3508957	+	Intron	INS	-	AC	AC	rs144609712	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3508956_3508957insAC	uc003zhr.2	-						RFX3_uc010mhd.2_Intron|RFX3_uc003zhs.1_Intron|RFX3_uc010mhe.1_Intron	NM_134428	NP_602304			regulatory factor X3 isoform b						cell maturation|ciliary cell motility|cilium assembly|cilium movement involved in determination of left/right asymmetry|endocrine pancreas development|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|regulation of insulin secretion	nuclear chromatin	protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	3532424	3532424	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3532424delT								RFX3 (6441 upstream) : GLIS3 (291704 downstream)																																			---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	3907620	3907625	+	Intron	DEL	ACACAG	-	-	rs71324274		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3907620_3907625delACACAG	uc003zhw.1	-						GLIS3_uc003zhx.1_Intron|GLIS3_uc010mhf.1_Intron|GLIS3_uc003zhv.1_Intron|GLIS3_uc003zhy.1_Intron|GLIS3_uc003zhz.1_Intron	NM_152629	NP_689842			GLIS family zinc finger 3 isoform b						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)														---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	3933182	3933183	+	Intron	DEL	TT	-	-	rs76720349		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3933182_3933183delTT	uc003zhw.1	-						GLIS3_uc003zhx.1_Intron|GLIS3_uc010mhf.1_Intron|GLIS3_uc003zhv.1_Intron|GLIS3_uc003zhy.1_Intron|GLIS3_uc003zhz.1_Intron	NM_152629	NP_689842			GLIS family zinc finger 3 isoform b						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)														---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	4235717	4235717	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4235717delA	uc003zhx.1	-						GLIS3_uc003zic.1_Intron|GLIS3_uc003zie.1_Intron|GLIS3_uc010mhh.1_Intron|GLIS3_uc003zid.1_Intron|GLIS3_uc010mhi.1_Intron|GLIS3_uc003zif.1_Intron|GLIS3_uc003zig.1_Intron|GLIS3_uc003zih.1_Intron	NM_001042413	NP_001035878			GLIS family zinc finger 3 isoform a						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	4462635	4462648	+	IGR	DEL	ACACGCACACACAC	-	-	rs56233060		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4462635_4462648delACACGCACACACAC								GLIS3 (162600 upstream) : SLC1A1 (27796 downstream)																																			---	---	---	---
C9orf68	55064	broad.mit.edu	37	9	4612012	4612012	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4612012delT	uc011llz.1	-						C9orf68_uc003zik.2_Intron|C9orf68_uc003zil.2_Intron|C9orf68_uc010mhj.2_Intron|C9orf68_uc011lly.1_Intron	NM_001039395	NP_001034484			hypothetical protein LOC55064												0		Breast(48;0.0456)		GBM - Glioblastoma multiforme(50;0.0222)														---	---	---	---
CDC37L1	55664	broad.mit.edu	37	9	4697084	4697084	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4697084delT	uc003zio.2	+							NM_017913	NP_060383			cell division cycle 37 homolog (S.							cytoplasm					0	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)														---	---	---	---
RCL1	10171	broad.mit.edu	37	9	4835376	4835377	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4835376_4835377delGT	uc003zis.2	+						RCL1_uc003zit.2_Intron|RCL1_uc010mhk.1_Intron	NM_005772	NP_005763			RNA terminal phosphate cyclase-like 1						ribosome biogenesis|RNA processing	nucleolus	RNA-3'-phosphate cyclase activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0206)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0244)														---	---	---	---
JAK2	3717	broad.mit.edu	37	9	5005578	5005579	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5005578_5005579insT	uc010mhm.2	+						JAK2_uc003ziw.2_Intron	NM_004972	NP_004963			Janus kinase 2						actin filament polymerization|activation of caspase activity by protein phosphorylation|activation of JAK2 kinase activity|blood coagulation|cellular component movement|erythrocyte differentiation|interferon-gamma-mediated signaling pathway|interleukin-12-mediated signaling pathway|JAK-STAT cascade involved in growth hormone signaling pathway|mammary gland epithelium development|mesoderm development|negative regulation of cell proliferation|negative regulation of DNA binding|positive regulation of apoptosis|positive regulation of cell-substrate adhesion|positive regulation of growth hormone receptor signaling pathway|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|protein autophosphorylation|regulation of inflammatory response|regulation of interferon-gamma-mediated signaling pathway|response to antibiotic|response to lipopolysaccharide|STAT protein import into nucleus|tumor necrosis factor-mediated signaling pathway|tyrosine phosphorylation of STAT protein	caveola|cytoskeleton|cytosol|endomembrane system|nucleus	ATP binding|growth hormone receptor binding|heme binding|histone binding|histone kinase activity (H3-Y41 specific)|interleukin-12 receptor binding|non-membrane spanning protein tyrosine kinase activity|protein kinase binding|SH2 domain binding		PCM1/JAK2(30)|PAX5/JAK2(18)|ETV6/JAK2(11)|BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)	haematopoietic_and_lymphoid_tissue(28629)|lung(5)|breast(5)|ovary(1)|liver(1)	28641	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)			1	T|Mis|O	ETV6|PCM1|BCR	ALL|AML|MPD| CML				Polycythemia_Vera_Familial				---	---	---	---
Unknown	0	broad.mit.edu	37	9	5312722	5312722	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5312722delA								RLN2 (8142 upstream) : RLN1 (22247 downstream)																																			---	---	---	---
CD274	29126	broad.mit.edu	37	9	5454414	5454415	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5454414_5454415delTT	uc003zje.2	+						C9orf46_uc003zjd.2_Intron|CD274_uc011lmb.1_Intron|CD274_uc010mhn.2_5'Flank|CD274_uc003zjf.2_5'Flank	NM_014143	NP_054862			CD274 molecule precursor						cell proliferation|cell surface receptor linked signaling pathway|immune response|T cell costimulation	endomembrane system|integral to membrane	receptor activity			lung(1)|central_nervous_system(1)	2	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)				T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
CD274	29126	broad.mit.edu	37	9	5464318	5464318	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5464318delT	uc003zje.2	+						C9orf46_uc003zjd.2_Intron|CD274_uc011lmb.1_Intron|CD274_uc010mhn.2_Intron|CD274_uc003zjf.2_Intron	NM_014143	NP_054862			CD274 molecule precursor						cell proliferation|cell surface receptor linked signaling pathway|immune response|T cell costimulation	endomembrane system|integral to membrane	receptor activity			lung(1)|central_nervous_system(1)	2	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)				T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
C9orf46	55848	broad.mit.edu	37	9	5479753	5479753	+	Intron	DEL	A	-	-	rs77594304		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5479753delA	uc003zjd.2	-							NM_018465	NP_060935			hypothetical protein LOC55848							integral to membrane				ovary(1)	1	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.00106)|Lung(218;0.125)														---	---	---	---
KIAA1432	57589	broad.mit.edu	37	9	5651358	5651358	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5651358delT	uc003zjh.2	+							NM_001135920	NP_001129392			connexin 43-interacting protein 150 isoform b							integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)														---	---	---	---
KIAA1432	57589	broad.mit.edu	37	9	5696258	5696259	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5696258_5696259delTT	uc003zji.2	+						KIAA1432_uc003zjh.2_Intron|KIAA1432_uc003zjl.3_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)														---	---	---	---
KIAA1432	57589	broad.mit.edu	37	9	5736814	5736814	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5736814delA	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)														---	---	---	---
KIAA1432	57589	broad.mit.edu	37	9	5750764	5750764	+	Intron	DEL	T	-	-	rs34121638		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5750764delT	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	5812235	5812235	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5812235delA	uc003zjm.1	-						ERMP1_uc011lme.1_Intron|ERMP1_uc010mhs.1_Intron	NM_024896	NP_079172			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	5873992	5873992	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5873992delA								ERMP1 (40911 upstream) : MLANA (16917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	6318340	6318340	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6318340delA								IL33 (60358 upstream) : TPD52L3 (10035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	6513703	6513706	+	IGR	DEL	TTTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6513703_6513706delTTTC								UHRF2 (6654 upstream) : GLDC (18760 downstream)																																			---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6603235	6603235	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6603235delA	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)													---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	6723631	6723633	+	Intron	DEL	AAA	-	-	rs4008336		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6723631_6723633delAAA	uc010mhu.2	+						KDM4C_uc003zkd.2_RNA|KDM4C_uc003zke.2_RNA	NM_001146696	NP_001140168			jumonji domain containing 2C isoform 4						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	6725323	6725324	+	Intron	INS	-	GTGT	GTGT	rs146693341	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6725323_6725324insGTGT	uc010mhu.2	+							NM_001146696	NP_001140168			jumonji domain containing 2C isoform 4						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	7001733	7001733	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7001733delT	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc011lmi.1_Intron|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	7128976	7128976	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7128976delT	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	7289351	7289352	+	IGR	DEL	AG	-	-	rs12238025		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7289351_7289352delAG								KDM4C (113704 upstream) : C9orf123 (507141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	7746780	7746780	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7746780delA								KDM4C (571133 upstream) : C9orf123 (49713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	8215975	8215975	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8215975delA								C9orf123 (416176 upstream) : PTPRD (98272 downstream)																																			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8428665	8428665	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8428665delA	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	8477810	8477811	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8477810_8477811delAA	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	8832104	8832105	+	Intron	INS	-	TG	TG	rs147517262	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8832104_8832105insTG	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	9203231	9203232	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9203231_9203232delAC	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	9264645	9264645	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9264645delA	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	9272640	9272640	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9272640delT	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	9528460	9528460	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9528460delA	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	9923097	9923097	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9923097delA	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	10090960	10090961	+	Intron	DEL	AT	-	-	rs142872656		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10090960_10090961delAT	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	10143823	10143823	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10143823delT	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	10199058	10199058	+	Intron	DEL	T	-	-	rs76628991		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10199058delT	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	10583343	10583343	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10583343delT	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	10653316	10653318	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10653316_10653318delAAA								PTPRD (40593 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	10762922	10762922	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10762922delT								PTPRD (150199 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11042738	11042738	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11042738delT								PTPRD (430015 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11124962	11124962	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11124962delT								PTPRD (512239 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11142597	11142597	+	IGR	DEL	T	-	-	rs79452819		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11142597delT								PTPRD (529874 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12136438	12136439	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12136438_12136439insT								None (None upstream) : TYRP1 (556947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12498734	12498734	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12498734delT								None (None upstream) : TYRP1 (194652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12606297	12606297	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12606297delT								None (None upstream) : TYRP1 (87089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12617879	12617879	+	IGR	DEL	A	-	-	rs149699081		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12617879delA								None (None upstream) : TYRP1 (75507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12899493	12899493	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12899493delT								C9orf150 (76435 upstream) : MPDZ (206216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	13388532	13388532	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13388532delA								MPDZ (108969 upstream) : NFIB (693316 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	13990195	13990196	+	IGR	INS	-	TGTG	TGTG	rs34387845		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13990195_13990196insTGTG								MPDZ (710632 upstream) : NFIB (91652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	14034215	14034217	+	IGR	DEL	AAA	-	-	rs138150746		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14034215_14034217delAAA								MPDZ (754652 upstream) : NFIB (47631 downstream)																																			---	---	---	---
NFIB	4781	broad.mit.edu	37	9	14245464	14245464	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14245464delA	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								---	---	---	---
NFIB	4781	broad.mit.edu	37	9	14307943	14307943	+	Intron	DEL	T	-	-	rs34670899		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14307943delT	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								---	---	---	---
ZDHHC21	340481	broad.mit.edu	37	9	14601397	14601399	+	Intron	DEL	TCA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14601397_14601399delTCA	uc003zlg.1	-											Homo sapiens HSPC097 mRNA, partial cds.						nitric oxide metabolic process|regulation of nitric-oxide synthase activity	Golgi membrane|integral to membrane	palmitoyltransferase activity|zinc ion binding				0				GBM - Glioblastoma multiforme(50;4.31e-06)														---	---	---	---
ZDHHC21	340481	broad.mit.edu	37	9	14638672	14638672	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14638672delA	uc003zli.2	-						ZDHHC21_uc003zlg.1_Intron	NM_178566	NP_848661			zinc finger, DHHC-type containing 21						nitric oxide metabolic process|regulation of nitric-oxide synthase activity	Golgi membrane|integral to membrane	palmitoyltransferase activity|zinc ion binding				0				GBM - Glioblastoma multiforme(50;4.31e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	14696690	14696690	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14696690delC								ZDHHC21 (3221 upstream) : CER1 (23044 downstream)																																			---	---	---	---
FREM1	158326	broad.mit.edu	37	9	14760855	14760855	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14760855delT	uc003zlm.2	-						FREM1_uc010mic.2_Intron|FREM1_uc003zlk.2_Intron|FREM1_uc003zll.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	15007924	15007924	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15007924delT	uc003zln.1	-						LOC389705_uc010mid.1_Intron					Homo sapiens cDNA FLJ46077 fis, clone TESTI2003768, weakly  similar to Chloride channel protein 3.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	15106353	15106353	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15106353delA	uc003zln.1	-											Homo sapiens cDNA FLJ46077 fis, clone TESTI2003768, weakly  similar to Chloride channel protein 3.																														---	---	---	---
TTC39B	158219	broad.mit.edu	37	9	15186697	15186697	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15186697delT	uc003zlr.1	-						TTC39B_uc003zlq.1_Intron|TTC39B_uc011lmp.1_Intron|TTC39B_uc010mie.1_Intron|TTC39B_uc011lmq.1_Intron|TTC39B_uc011lmr.1_Intron|TTC39B_uc010mif.1_3'UTR|TTC39B_uc003zlp.1_Intron	NM_152574	NP_689787			tetratricopeptide repeat domain 39B								binding			ovary(1)	1																		---	---	---	---
TTC39B	158219	broad.mit.edu	37	9	15189047	15189047	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15189047delA	uc003zlr.1	-						TTC39B_uc003zlq.1_Intron|TTC39B_uc011lmp.1_Intron|TTC39B_uc010mie.1_Intron|TTC39B_uc011lmq.1_Intron|TTC39B_uc011lmr.1_Intron|TTC39B_uc010mif.1_Intron|TTC39B_uc003zls.1_Intron|TTC39B_uc010mig.1_Intron|TTC39B_uc003zlp.1_5'Flank	NM_152574	NP_689787			tetratricopeptide repeat domain 39B								binding			ovary(1)	1																		---	---	---	---
PSIP1	11168	broad.mit.edu	37	9	15487004	15487005	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15487004_15487005delTT	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	15657002	15657002	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15657002delA	uc003zmd.2	+						C9orf93_uc010mih.1_Intron|C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron|C9orf93_uc003zmc.2_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15670261	15670261	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15670261delA	uc003zmd.2	+						C9orf93_uc010mih.1_Intron|C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15735433	15735433	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15735433delT	uc003zmd.2	+						C9orf93_uc010mih.1_Intron|C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15778788	15778788	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15778788delT	uc003zmd.2	+						C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron|C9orf93_uc003zmf.1_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15779366	15779367	+	Intron	INS	-	T	T	rs28576757		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15779366_15779367insT	uc003zmd.2	+						C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron|C9orf93_uc003zmf.1_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15880462	15880462	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15880462delT	uc003zmd.2	+						C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	16155548	16155548	+	IGR	DEL	T	-	-	rs112069431		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16155548delT								C9orf93 (183653 upstream) : BNC2 (253954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	16162003	16162004	+	IGR	INS	-	A	A	rs79124263	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16162003_16162004insA								C9orf93 (190108 upstream) : BNC2 (247498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	16377797	16377797	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16377797delA								C9orf93 (405902 upstream) : BNC2 (31705 downstream)																																			---	---	---	---
BNC2	54796	broad.mit.edu	37	9	16687204	16687204	+	Intron	DEL	T	-	-	rs150069561		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16687204delT	uc003zml.2	-						BNC2_uc011lmw.1_Intron|BNC2_uc003zmm.2_Intron|BNC2_uc003zmq.1_Intron|BNC2_uc003zmr.1_Intron|BNC2_uc003zmp.1_Intron|BNC2_uc010mij.1_Intron|BNC2_uc003zmu.1_Intron|BNC2_uc010mim.1_Intron|BNC2_uc010min.1_Intron|BNC2_uc003zmo.1_Intron|BNC2_uc003zms.1_Intron|BNC2_uc010mik.1_Intron|BNC2_uc010mil.1_Intron|BNC2_uc003zmt.1_Intron	NM_017637	NP_060107			basonuclin 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)														---	---	---	---
BNC2	54796	broad.mit.edu	37	9	16780569	16780570	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16780569_16780570delAA	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	16921743	16921744	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16921743_16921744insA								BNC2 (50957 upstream) : CNTLN (213294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	16944979	16944979	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16944979delA								BNC2 (74193 upstream) : CNTLN (190059 downstream)																																			---	---	---	---
CNTLN	54875	broad.mit.edu	37	9	17338168	17338168	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	18346318	18346319	+	IGR	INS	-	TC	TC	rs145512415	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18346318_18346319insTC								SH3GL2 (549198 upstream) : ADAMTSL1 (127785 downstream)																																			---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18609712	18609712	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18609712delC	uc003zne.3	+						ADAMTSL1_uc003znb.2_Intron|ADAMTSL1_uc003znc.3_Intron	NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18795080	18795080	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18795080delC	uc003zne.3	+							NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18818788	18818788	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18818788delA	uc003zne.3	+							NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18853917	18853918	+	Intron	INS	-	CA	CA	rs71333070		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18853917_18853918insCA	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)														---	---	---	---
DENND4C	55667	broad.mit.edu	37	9	19328010	19328010	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19328010delT	uc003znq.2	+						DENND4C_uc011lnc.1_Intron	NM_017925	NP_060395			DENN/MADD domain containing 4C							integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
SLC24A2	25769	broad.mit.edu	37	9	19555166	19555166	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19555166delA	uc003zoa.1	-						SLC24A2_uc003zob.1_Intron	NM_020344	NP_065077			solute carrier family 24						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)														---	---	---	---
SLC24A2	25769	broad.mit.edu	37	9	19608876	19608876	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19608876delG	uc003zoa.1	-						SLC24A2_uc003zob.1_Intron	NM_020344	NP_065077			solute carrier family 24						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	20064511	20064511	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20064511delA								SLC24A2 (275703 upstream) : MLLT3 (280457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	20189821	20189822	+	IGR	DEL	AA	-	-	rs150978811		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20189821_20189822delAA								SLC24A2 (401013 upstream) : MLLT3 (155146 downstream)																																			---	---	---	---
MLLT3	4300	broad.mit.edu	37	9	20418613	20418613	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20418613delT	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	20553439	20553439	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20553439delA	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								---	---	---	---
Unknown	0	broad.mit.edu	37	9	20642303	20642304	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20642303_20642304delGA								MLLT3 (19789 upstream) : KIAA1797 (16005 downstream)																																			---	---	---	---
PTPLAD2	401494	broad.mit.edu	37	9	21011382	21011382	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21011382delT	uc010miq.1	-						PTPLAD2_uc003zoj.1_Intron|PTPLAD2_uc010mir.1_Intron	NM_001010915	NP_001010915			protein tyrosine phosphatase-like A domain						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	lyase activity			skin(1)	1				Lung(24;6.02e-14)|LUSC - Lung squamous cell carcinoma(38;1.29e-10)														---	---	---	---
KLHL9	55958	broad.mit.edu	37	9	21330920	21330920	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21330920delA	uc003zow.2	-						KLHL9_uc003zox.2_Intron					Homo sapiens mRNA for KIAA1354 protein, partial cds.						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	21687786	21687787	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21687786_21687787delTT								LOC554202 (127954 upstream) : MTAP (114848 downstream)																																			---	---	---	---
MTAP	4507	broad.mit.edu	37	9	21916051	21916054	+	Intron	DEL	GAGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21916051_21916054delGAGG	uc003zpi.1	+							NM_002451	NP_002442			5'-methylthioadenosine phosphorylase						nucleoside metabolic process	cytoplasm	phosphorylase activity|S-methyl-5-thioadenosine phosphorylase activity			central_nervous_system(1)	1		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)	Adenine(DB00173)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	22121194	22121194	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22121194delA								CDKN2BAS (103 upstream) : DMRTA1 (325646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	22320715	22320716	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22320715_22320716insT								CDKN2BAS (199624 upstream) : DMRTA1 (126124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	22391675	22391675	+	IGR	DEL	A	-	-	rs80133826		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22391675delA								CDKN2BAS (270584 upstream) : DMRTA1 (55165 downstream)																																			---	---	---	---
DMRTA1	63951	broad.mit.edu	37	9	22451039	22451039	+	Intron	DEL	T	-	-	rs41270141	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									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	22576213	22576213	+	IGR	DEL	A	-	-	rs12380518		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22576213delA								DMRTA1 (123741 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	22992977	22992978	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22992977_22992978insA								DMRTA1 (540505 upstream) : ELAVL2 (697127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23431495	23431496	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23431495_23431496insA								DMRTA1 (979023 upstream) : ELAVL2 (258609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23442675	23442675	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23442675delA								DMRTA1 (990203 upstream) : ELAVL2 (247430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23551172	23551172	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23551172delT	uc003zpr.2	-											Homo sapiens mRNA; cDNA DKFZp781D1719 (from clone DKFZp781D1719).																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	23658657	23658657	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23658657delT	uc003zpr.2	-											Homo sapiens mRNA; cDNA DKFZp781D1719 (from clone DKFZp781D1719).																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	23968797	23968798	+	IGR	INS	-	TT	TT	rs139340664	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23968797_23968798insTT								ELAVL2 (142734 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23977538	23977538	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23977538delA								ELAVL2 (151475 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	24907621	24907622	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24907621_24907622delTG								None (None upstream) : TUSC1 (768772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25458580	25458581	+	IGR	INS	-	ACACAC	ACACAC	rs139675666	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25458580_25458581insACACAC								None (None upstream) : TUSC1 (217813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25625416	25625416	+	IGR	DEL	T	-	-	rs140918278		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25625416delT								None (None upstream) : TUSC1 (50978 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26258566	26258566	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26258566delT								TUSC1 (579710 upstream) : C9orf82 (582118 downstream)																																			---	---	---	---
PLAA	9373	broad.mit.edu	37	9	26915212	26915213	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26915212_26915213delAA	uc003zqd.2	-						PLAA_uc003zqe.2_Intron	NM_001031689	NP_001026859			phospholipase A2-activating protein						phospholipid metabolic process|signal transduction		phospholipase A2 activator activity				0		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)														---	---	---	---
IFT74	80173	broad.mit.edu	37	9	27036682	27036682	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27036682delA	uc010mja.2	+						IFT74_uc010mjb.2_Intron|IFT74_uc003zqf.3_3'UTR|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	27208346	27208346	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27208346delT	uc003zqi.3	+						TEK_uc011lno.1_Intron|TEK_uc011lnp.1_Intron|TEK_uc003zqj.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	27231318	27231318	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27231318delA								TEK (1147 upstream) : NCRNA00032 (14366 downstream)																																			---	---	---	---
MOBKL2B	79817	broad.mit.edu	37	9	27432259	27432259	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27432259delT	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	27441278	27441279	+	Intron	INS	-	A	A	rs141975347	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27441278_27441279insA	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	27444152	27444153	+	Intron	INS	-	GAAG	GAAG	rs146325733	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27444152_27444153insGAAG	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	27454966	27454967	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27454966_27454967insT	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	27457690	27457691	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27457690_27457691delTT	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	27502031	27502031	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27502031delT	uc003zqn.2	-							NM_024761	NP_079037			MOB1, Mps One Binder kinase activator-like 2B								metal ion binding|protein binding			ovary(1)|pleura(1)	2		all_neural(11;9.12e-11)		Lung(218;6.54e-05)|LUSC - Lung squamous cell carcinoma(38;0.000397)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	27541342	27541342	+	IGR	DEL	T	-	-	rs71856589		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27541342delT								MOBKL2B (11492 upstream) : C9orf72 (5202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	27579679	27579680	+	IGR	INS	-	T	T	rs140453473	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27579679_27579680insT								C9orf72 (5837 upstream) : LINGO2 (368848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	27656760	27656760	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27656760delA								C9orf72 (82918 upstream) : LINGO2 (291768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	27821182	27821182	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27821182delA								C9orf72 (247340 upstream) : LINGO2 (127346 downstream)																																			---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28171844	28171844	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28171844delA	uc003zqu.1	-						LINGO2_uc010mjf.1_Intron|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	28189647	28189648	+	Intron	INS	-	AGGA	AGGA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28189647_28189648insAGGA	uc003zqu.1	-						LINGO2_uc010mjf.1_Intron|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	28361650	28361650	+	Intron	DEL	A	-	-	rs113971802		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28361650delA	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	28659457	28659458	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28659457_28659458delTT	uc003zqv.1	-							NM_152570	NP_689783			leucine rich repeat and Ig domain containing 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)														---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28659849	28659849	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28659849delA	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	29211578	29211579	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29211578_29211579delTC								MIR873 (322625 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	29449341	29449341	+	IGR	DEL	T	-	-	rs72060282		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29449341delT								MIR873 (560388 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	29626510	29626511	+	IGR	INS	-	CT	CT	rs148591198	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29626510_29626511insCT								MIR873 (737557 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	29884220	29884220	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29884220delT								MIR873 (995267 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30013556	30013556	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30013556delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30288067	30288067	+	IGR	DEL	A	-	-	rs76968689		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30288067delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30419958	30419958	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30419958delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30439021	30439021	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30439021delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30682624	30682624	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30682624delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30774794	30774795	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30774794_30774795delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30882406	30882406	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30882406delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30917275	30917275	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30917275delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	31531185	31531185	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31531185delA								None (None upstream) : ACO1 (853416 downstream)																																			---	---	---	---
TOPORS	10210	broad.mit.edu	37	9	32541246	32541246	+	3'UTR	DEL	A	-	-	rs78113455		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32541246delA	uc003zrb.2	-	3					TOPORS_uc003zrc.2_3'UTR	NM_005802	NP_005793			topoisomerase I binding, arginine/serine-rich						DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)														---	---	---	---
TOPORS	10210	broad.mit.edu	37	9	32547036	32547037	+	Intron	INS	-	AAAC	AAAC	rs148602976	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32547036_32547037insAAAC	uc003zrb.2	-						TOPORS_uc003zrc.2_Intron	NM_005802	NP_005793			topoisomerase I binding, arginine/serine-rich						DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	32844888	32844888	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32844888delT								TMEM215 (55691 upstream) : APTX (127721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	32916768	32916768	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32916768delC								TMEM215 (127571 upstream) : APTX (55841 downstream)																																			---	---	---	---
APTX	54840	broad.mit.edu	37	9	33023220	33023222	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33023220_33023222delTTT	uc003zrz.2	-						DNAJA1_uc003zsd.1_5'Flank|DNAJA1_uc011lnt.1_5'Flank	NM_175071	NP_778241			aprataxin isoform d						cell death|double-strand break repair|regulation of protein stability|response to hydrogen peroxide|single strand break repair	chromatin|nucleolus|nucleoplasm	chromatin binding|damaged DNA binding|DNA 5'-adenosine monophosphate hydrolase activity|double-stranded DNA binding|double-stranded RNA binding|phosphoglycolate phosphatase activity|phosphoprotein binding|polynucleotide 3'-phosphatase activity|protein N-terminus binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)									Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
B4GALT1	2683	broad.mit.edu	37	9	33128095	33128096	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33128095_33128096delCT	uc003zsg.2	-							NM_001497	NP_001488			UDP-Gal:betaGlcNAc beta 1,4-						oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	basolateral plasma membrane|brush border membrane|desmosome|external side of plasma membrane|extracellular region|glycocalyx|Golgi cisterna membrane|Golgi trans cisterna|integral to membrane	alpha-tubulin binding|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|beta-tubulin binding|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity|protein binding|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
B4GALT1	2683	broad.mit.edu	37	9	33135908	33135909	+	Intron	DEL	TA	-	-	rs34931533		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33135908_33135909delTA	uc003zsg.2	-							NM_001497	NP_001488			UDP-Gal:betaGlcNAc beta 1,4-						oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	basolateral plasma membrane|brush border membrane|desmosome|external side of plasma membrane|extracellular region|glycocalyx|Golgi cisterna membrane|Golgi trans cisterna|integral to membrane	alpha-tubulin binding|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|beta-tubulin binding|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity|protein binding|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
SUGT1P1	441394	broad.mit.edu	37	9	33239442	33239442	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33239442delA	uc010mjq.1	-						SPINK4_uc003zsh.2_5'Flank	NR_003667				Homo sapiens suppressor of G2 allele of SKP1 pseudogene (S. cerevisiae) (SUGT1P), non-coding RNA.												0																		---	---	---	---
CHMP5	51510	broad.mit.edu	37	9	33270523	33270523	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33270523delT	uc003zsl.3	+						SUGT1P1_uc010mjq.1_Intron|CHMP5_uc003zsm.3_Intron|CHMP5_uc011lnv.1_Intron|CHMP5_uc003zsn.2_5'Flank	NM_016410	NP_057494			chromatin modifying protein 5						cellular membrane organization|protein transport	cytosol|endosome membrane	protein binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)															---	---	---	---
NFX1	4799	broad.mit.edu	37	9	33291901	33291901	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33291901delA	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	33323766	33323767	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33323766_33323767insA	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	33342124	33342125	+	Intron	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33342124_33342125insCA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	33606597	33606597	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33606597delA								SUGT1P1 (95550 upstream) : ANXA2P2 (17626 downstream)																																			---	---	---	---
PTENP1	11191	broad.mit.edu	37	9	33675365	33675365	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33675365delA	uc003zth.3	-	1						NR_023917				SubName: Full=Phosphatase and tensin homolog 2; Flags: Fragment;												0																		---	---	---	---
UBE2R2	54926	broad.mit.edu	37	9	33887000	33887000	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33887000delT	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)														---	---	---	---
UBE2R2	54926	broad.mit.edu	37	9	33906112	33906114	+	Intron	DEL	TGT	-	-	rs72326956		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33906112_33906114delTGT	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)														---	---	---	---
DNAI1	27019	broad.mit.edu	37	9	34483525	34483525	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34483525delT	uc003zum.2	+						DNAI1_uc011lom.1_Intron	NM_012144	NP_036276			dynein, axonemal, intermediate chain 1						cell projection organization	cilium axoneme|cytoplasm|dynein complex|microtubule	motor activity				0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)										Kartagener_syndrome				---	---	---	---
DNAI1	27019	broad.mit.edu	37	9	34489849	34489849	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34489849delA	uc003zum.2	+							NM_012144	NP_036276			dynein, axonemal, intermediate chain 1						cell projection organization	cilium axoneme|cytoplasm|dynein complex|microtubule	motor activity				0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)										Kartagener_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	9	34604440	34604440	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34604440delA								CNTFR (14718 upstream) : C9orf23 (6053 downstream)																																			---	---	---	---
SIGMAR1	10280	broad.mit.edu	37	9	34634867	34634868	+	3'UTR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34634867_34634868insC	uc003zvb.2	-	4					SIGMAR1_uc003zva.3_3'UTR|SIGMAR1_uc003zuz.2_3'UTR|SIGMAR1_uc003zvc.2_3'UTR|SIGMAR1_uc003zvd.2_RNA	NM_005866	NP_005857			sigma non-opioid intracellular receptor 1						ergosterol biosynthetic process|lipid transport	cell junction|endoplasmic reticulum membrane|growth cone|integral to plasma membrane|lipid particle|nuclear inner membrane|nuclear outer membrane	C-8 sterol isomerase activity|drug binding				0					Dextromethorphan(DB00514)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	34642711	34642712	+	IGR	INS	-	A	A	rs113085977		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34642711_34642712insA								SIGMAR1 (4943 upstream) : GALT (3923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	34678329	34678333	+	IGR	DEL	TTTTT	-	-	rs10538850		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34678329_34678333delTTTTT								CCL27 (15640 upstream) : CCL19 (11236 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	34866549	34866549	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34866549delA								C9orf144 (27966 upstream) : KIAA1045 (90972 downstream)																																			---	---	---	---
KIAA1045	23349	broad.mit.edu	37	9	34955412	34955413	+	5'Flank	INS	-	CG	CG	rs112275283		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34955412_34955413insCG	uc003zvq.2	+						KIAA1045_uc003zvr.2_5'Flank	NM_015297	NP_056112			hypothetical protein LOC23349								calcium ion binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00575)															---	---	---	---
KIAA1045	23349	broad.mit.edu	37	9	34979253	34979255	+	3'UTR	DEL	AGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34979253_34979255delAGA	uc003zvq.2	+	8					KIAA1045_uc003zvr.2_3'UTR	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	35136925	35136925	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35136925delT								KIAA1539 (21032 upstream) : UNC13B (25064 downstream)																																			---	---	---	---
ATP8B5P	158381	broad.mit.edu	37	9	35419683	35419683	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35419683delA	uc010mkn.1	+						ATP8B5P_uc010mko.2_Intron|ATP8B5P_uc010mkp.2_Intron|ATP8B5P_uc003zwu.2_Intron					Homo sapiens cDNA, FLJ17320.												0																		---	---	---	---
RUSC2	9853	broad.mit.edu	37	9	35539569	35539576	+	Intron	DEL	CATGCATG	-	-	rs113956351		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35539569_35539576delCATGCATG	uc003zww.2	+						RUSC2_uc010mkq.2_Intron|RUSC2_uc003zwx.3_Intron	NM_014806	NP_055621			RUN and SH3 domain containing 2							cytosol				ovary(1)	1			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
CD72	971	broad.mit.edu	37	9	35632180	35632181	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35632180_35632181delTT	uc010mkw.1	-											Homo sapiens mRNA for CD72 antigen variant protein.						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)															---	---	---	---
CA9	768	broad.mit.edu	37	9	35677613	35677613	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35677613delA	uc003zxo.3	+						C9orf100_uc003zxl.2_5'Flank|CA9_uc003zxp.3_Intron	NM_001216	NP_001207			carbonic anhydrase IX precursor						one-carbon metabolic process	integral to membrane|microvillus membrane|nucleolus	carbonate dehydratase activity|zinc ion binding			ovary(4)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
CA9	768	broad.mit.edu	37	9	35680370	35680370	+	Intron	DEL	T	-	-	rs113198393		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35680370delT	uc003zxo.3	+						CA9_uc003zxp.3_Intron	NM_001216	NP_001207			carbonic anhydrase IX precursor						one-carbon metabolic process	integral to membrane|microvillus membrane|nucleolus	carbonate dehydratase activity|zinc ion binding			ovary(4)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
GBA2	57704	broad.mit.edu	37	9	35741459	35741459	+	Intron	DEL	T	-	-	rs74748138		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35741459delT	uc003zxw.2	-						GBA2_uc003zxx.1_5'Flank|GBA2_uc011lpb.1_Intron|GBA2_uc011lpc.1_Intron|GBA2_uc011lpd.1_Intron|GBA2_uc003zxy.1_Intron	NM_020944	NP_065995			bile acid beta-glucosidase						bile acid metabolic process|glucosylceramide catabolic process|O-glycoside catabolic process	integral to membrane|microsome|plasma membrane|smooth endoplasmic reticulum	beta-glucosidase activity|glucosylceramidase activity			ovary(3)|skin(1)	4	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
OR2S2	56656	broad.mit.edu	37	9	35960805	35960806	+	5'Flank	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35960805_35960806delGT	uc011lpi.1	-							NM_019897	NP_063950			olfactory receptor, family 2, subfamily S,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	35980634	35980635	+	IGR	INS	-	G	G	rs148511329	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35980634_35980635insG								OR2S2 (22483 upstream) : RECK (56275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	36031401	36031402	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36031401_36031402insG								OR2S2 (73250 upstream) : RECK (5508 downstream)																																			---	---	---	---
RECK	8434	broad.mit.edu	37	9	36073211	36073220	+	Intron	DEL	ACACACAGAC	-	-	rs67440113		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36073211_36073220delACACACAGAC	uc003zyv.2	+						RECK_uc010mld.2_Intron|RECK_uc003zyu.3_Intron|RECK_uc003zyw.2_Intron|RECK_uc003zyx.2_Intron	NM_021111	NP_066934			RECK protein precursor							anchored to membrane|peripheral to membrane of membrane fraction|plasma membrane	metalloendopeptidase inhibitor activity|serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)	3			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
CLTA	1211	broad.mit.edu	37	9	36189844	36189844	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36189844delT	uc003zzc.2	+						CLTA_uc003zzd.2_5'Flank|CLTA_uc003zze.2_5'Flank|CLTA_uc011lpk.1_5'Flank|CLTA_uc003zzf.1_5'Flank	NM_007096	NP_009027			clathrin, light polypeptide A isoform b						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol	structural molecule activity			central_nervous_system(1)	1			STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
RNF38	152006	broad.mit.edu	37	9	36353341	36353342	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36353341_36353342delAA	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	36432140	36432140	+	IGR	DEL	T	-	-	rs72439934		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36432140delT								RNF38 (30945 upstream) : MELK (140765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	36533489	36533490	+	IGR	INS	-	G	G	rs150317535	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36533489_36533490insG								RNF38 (132294 upstream) : MELK (39415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	36824717	36824718	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36824717_36824718insT								MELK (147039 upstream) : PAX5 (13813 downstream)																																			---	---	---	---
PAX5	5079	broad.mit.edu	37	9	36963906	36963906	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36963906delA	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		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	37042487	37042487	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37042487delA								PAX5 (8011 upstream) : ZCCHC7 (77982 downstream)																																			---	---	---	---
ZCCHC7	84186	broad.mit.edu	37	9	37167257	37167259	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37167257_37167259delTTT	uc003zzq.2	+						ZCCHC7_uc011lqh.1_Intron|ZCCHC7_uc011lqi.1_Intron|ZCCHC7_uc010mlt.2_Intron|ZCCHC7_uc003zzs.1_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	37405001	37405002	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37405001_37405002insC								ZCCHC7 (46858 upstream) : GRHPR (17679 downstream)																																			---	---	---	---
POLR1E	64425	broad.mit.edu	37	9	37489233	37489233	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37489233delA	uc003zzz.1	+						POLR1E_uc011lqj.1_Intron|POLR1E_uc003zzy.1_Intron|POLR1E_uc011lqk.1_Intron	NM_022490	NP_071935			RNA polymerase I associated factor 53						rRNA transcription	cell junction|cytoplasm|nucleolus	DNA binding|DNA-directed RNA polymerase activity|protein binding				0				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)														---	---	---	---
FRMPD1	22844	broad.mit.edu	37	9	37669991	37669991	+	Intron	DEL	A	-	-	rs75935147		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37669991delA	uc004aag.1	+						FRMPD1_uc004aah.1_Intron	NM_014907	NP_055722			FERM and PDZ domain containing 1							cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	38120892	38120892	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38120892delA								SHB (51682 upstream) : ALDH1B1 (271810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	38477914	38477914	+	IGR	DEL	A	-	-	rs79212902		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38477914delA								IGFBPL1 (53470 upstream) : C9orf122 (143171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	39052219	39052219	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39052219delA								C9orf122 (428944 upstream) : CNTNAP3 (20547 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	39052537	39052537	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39052537delG								C9orf122 (429262 upstream) : CNTNAP3 (20229 downstream)																																			---	---	---	---
CNTNAP3	79937	broad.mit.edu	37	9	39121763	39121763	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39121763delA	uc004abi.2	-						CNTNAP3_uc004abj.2_Intron|CNTNAP3_uc011lqr.1_Intron|CNTNAP3_uc004abk.1_Intron|CNTNAP3_uc011lqs.1_Intron	NM_033655	NP_387504			cell recognition molecule CASPR3 precursor						cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	40053887	40053888	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40053887_40053888delAA								FAM74A1 (146647 upstream) : FAM75A3 (646403 downstream)																																			---	---	---	---
ZNF658	26149	broad.mit.edu	37	9	40762155	40762155	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40762155delT	uc010mmm.1	-							NM_033160	NP_149350			zinc finger protein 658						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)														---	---	---	---
ZNF658	26149	broad.mit.edu	37	9	40771888	40771888	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40771888delT	uc004abs.2	-	5					ZNF658_uc010mmm.1_Intron|ZNF658_uc010mmn.1_3'UTR	NM_033160	NP_149350			zinc finger protein 658						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)														---	---	---	---
AQP7P3	441432	broad.mit.edu	37	9	42870268	42870268	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:42870268delT	uc004acq.3	+							NR_026558				Homo sapiens aquaporin 7 pseudogene 1, mRNA (cDNA clone IMAGE:6191443).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	44126392	44126393	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44126392_44126393insA								FAM75A6 (495662 upstream) : FAM27C (863843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	45362789	45362791	+	IGR	DEL	TTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:45362789_45362791delTTC								FAM27C (371298 upstream) : FAM27A (364238 downstream)																																			---	---	---	---
KGFLP1	387628	broad.mit.edu	37	9	46719111	46719111	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:46719111delA	uc011lrd.1	+							NR_003674				Homo sapiens unknown protein mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	46799875	46799875	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:46799875delT	uc004ads.2	+											Homo sapiens cDNA FLJ44092 fis, clone TESTI4041985.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	65786775	65786775	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:65786775delA								FAM74A4 (292389 upstream) : LOC442421 (709695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66333354	66333354	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66333354delG								FAM74A4 (838968 upstream) : LOC442421 (163116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66333430	66333430	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66333430delA								FAM74A4 (839044 upstream) : LOC442421 (163040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66491787	66491788	+	IGR	INS	-	A	A	rs145157912	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66491787_66491788insA								FAM74A4 (997401 upstream) : LOC442421 (4682 downstream)																																			---	---	---	---
AQP7P1	375719	broad.mit.edu	37	9	67286211	67286211	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67286211delA	uc004aen.1	-						AQP7P1_uc004aeo.1_Intron|AQP7P1_uc004aep.1_Intron					Homo sapiens cDNA FLJ46364 fis, clone TESTI4051015.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	67890665	67890665	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67890665delA								FAM27B (96476 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	67899672	67899672	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67899672delT								FAM27B (105483 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	67909808	67909808	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67909808delA								FAM27B (115619 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68218431	68218431	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68218431delT								FAM27B (424242 upstream) : MIR1299 (783808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68411860	68411861	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	68989452	68989452	+	IGR	DEL	G	-	-	rs71498602		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68989452delG								None (None upstream) : MIR1299 (12787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69428145	69428145	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69428145delT	uc010mnx.1	+							NM_001098806	NP_001092276			coiled-coil domain containing 29																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	69814659	69814660	+	IGR	INS	-	T	T	rs147599302	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69814659_69814660insT								LOC100133920 (149710 upstream) : FOXD4L5 (361049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69828717	69828717	+	IGR	DEL	C	-	-	rs59138657		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69828717delC								LOC100133920 (163768 upstream) : FOXD4L5 (346992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	70163632	70163632	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70163632delA								LOC100133920 (498683 upstream) : FOXD4L5 (12077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	70619758	70619758	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70619758delA								CBWD3 (119695 upstream) : FOXD4L3 (298025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	70949829	70949830	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70949829_70949830insA								FOXD4L3 (29829 upstream) : LOC572558 (20281 downstream)																																			---	---	---	---
PGM5	5239	broad.mit.edu	37	9	71047530	71047530	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71047530delT	uc004agr.2	+							NM_021965	NP_068800			phosphoglucomutase 5						cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2																		---	---	---	---
PIP5K1B	8395	broad.mit.edu	37	9	71545516	71545516	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71545516delT	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	71836476	71836476	+	Intron	DEL	T	-	-	rs113816166		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71836476delT	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																		---	---	---	---
TJP2	9414	broad.mit.edu	37	9	71839701	71839701	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71839701delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	71874071	71874073	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71874071_71874073delAAA								TJP2 (3953 upstream) : FAM189A2 (65415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	71892582	71892582	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71892582delT								TJP2 (22464 upstream) : FAM189A2 (46906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	71925907	71925907	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71925907delT								TJP2 (55789 upstream) : FAM189A2 (13581 downstream)																																			---	---	---	---
APBA1	320	broad.mit.edu	37	9	72220185	72220185	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72220185delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	72294793	72294793	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72294793delT								APBA1 (7518 upstream) : PTAR1 (29646 downstream)																																			---	---	---	---
C9orf135	138255	broad.mit.edu	37	9	72479270	72479271	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72479270_72479271insT	uc004ahl.2	+						C9orf135_uc011lrw.1_Intron|C9orf135_uc010moq.2_Intron|C9orf135_uc011lrx.1_Intron|C9orf135_uc010mop.2_Intron	NM_001010940	NP_001010940			hypothetical protein LOC138255							integral to membrane				ovary(1)	1																		---	---	---	---
MAMDC2	256691	broad.mit.edu	37	9	72656174	72656175	+	5'Flank	DEL	AA	-	-	rs67591361		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72656174_72656175delAA	uc004ahm.2	+						MAMDC2_uc004ahn.2_5'Flank	NM_153267	NP_694999			MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
SMC5	23137	broad.mit.edu	37	9	72933006	72933006	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72933006delA	uc004ahr.2	+						uc004ahs.1_5'Flank	NM_015110	NP_055925			SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
SMC5	23137	broad.mit.edu	37	9	72958064	72958066	+	Intron	DEL	TTT	-	-	rs71681650		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72958064_72958066delTTT	uc004ahr.2	+							NM_015110	NP_055925			SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
KLF9	687	broad.mit.edu	37	9	73012390	73012391	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73012390_73012391delAA	uc004aht.2	-							NM_001206	NP_001197			Kruppel-like factor 9						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	73060396	73060397	+	IGR	INS	-	TTC	TTC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73060396_73060397insTTC								KLF9 (30823 upstream) : TRPM3 (89571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	73062894	73062895	+	IGR	DEL	AA	-	-	rs80166731		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73062894_73062895delAA								KLF9 (33321 upstream) : TRPM3 (87073 downstream)																																			---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73305286	73305286	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73305286delA	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_Intron	NM_001007471	NP_001007472			transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73366915	73366916	+	Intron	INS	-	GTGTGTATGT	GTGTGTATGT	rs76327451		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73366915_73366916insGTGTGTATGT	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_Intron	NM_001007471	NP_001007472			transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73516361	73516361	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73516361delT	uc004aid.2	-						TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron|TRPM3_uc004aii.2_Intron	NM_001007471	NP_001007472			transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73711210	73711210	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73711210delA	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	74415528	74415528	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74415528delA								TMEM2 (31728 upstream) : FAM108B1 (61842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	74650887	74650888	+	IGR	DEL	AA	-	-	rs35818031		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74650887_74650888delAA								C9orf85 (51497 upstream) : C9orf57 (15410 downstream)																																			---	---	---	---
GDA	9615	broad.mit.edu	37	9	74777458	74777460	+	Intron	DEL	GGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74777458_74777460delGGA	uc004aiq.2	+						GDA_uc011lse.1_Intron|GDA_uc011lsf.1_Intron|GDA_uc004air.2_Intron|GDA_uc010mow.1_Intron|GDA_uc004ais.2_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)														---	---	---	---
GDA	9615	broad.mit.edu	37	9	74788735	74788736	+	Intron	INS	-	GT	GT	rs142196983	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74788735_74788736insGT	uc004aiq.2	+						GDA_uc011lse.1_Intron|GDA_uc011lsf.1_Intron|GDA_uc004air.2_Intron|GDA_uc010mow.1_Intron|GDA_uc004ais.2_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)														---	---	---	---
TMC1	117531	broad.mit.edu	37	9	75186761	75186762	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75186761_75186762delTT	uc004aiz.1	+							NM_138691	NP_619636			transmembrane channel-like 1						sensory perception of sound	integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	75460926	75460927	+	IGR	INS	-	A	A	rs141008047	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75460926_75460927insA								TMC1 (9659 upstream) : ALDH1A1 (54661 downstream)																																			---	---	---	---
ALDH1A1	216	broad.mit.edu	37	9	75653953	75653953	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75653953delG	uc011lsh.1	-							NM_000689	NP_000680			aldehyde dehydrogenase 1A1						cellular aldehyde metabolic process|ethanol oxidation|xenobiotic metabolic process	cytosol	aldehyde dehydrogenase (NAD) activity|androgen binding|Ras GTPase activator activity|retinal dehydrogenase activity			ovary(3)|lung(1)	4					NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	75828320	75828321	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75828320_75828321delAG								ANXA1 (43013 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	75934314	75934315	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75934314_75934315delAA								ANXA1 (149007 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76108131	76108131	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76108131delT								ANXA1 (322824 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76197178	76197178	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76197178delT								ANXA1 (411871 upstream) : RORB (915074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76504173	76504173	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76504173delT								ANXA1 (718866 upstream) : RORB (608079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	77064454	77064454	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77064454delT								None (None upstream) : RORB (47798 downstream)																																			---	---	---	---
RORB	6096	broad.mit.edu	37	9	77169493	77169494	+	Intron	DEL	AA	-	-	rs112005785		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77169493_77169494delAA	uc004ajh.2	+							NM_006914	NP_008845			RAR-related orphan receptor B						eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	77313002	77313002	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77313002delT								RORB (10887 upstream) : TRPM6 (24409 downstream)																																			---	---	---	---
TRPM6	140803	broad.mit.edu	37	9	77420710	77420710	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77420710delA	uc004ajl.1	-						TRPM6_uc004ajk.1_Intron|TRPM6_uc010mpb.1_Intron|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron	NM_017662	NP_060132			transient receptor potential cation channel,						response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	77663039	77663039	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77663039delA								C9orf41 (19729 upstream) : C9orf95 (13079 downstream)																																			---	---	---	---
OSTF1	26578	broad.mit.edu	37	9	77715339	77715339	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77715339delT	uc004ajv.3	+						OSTF1_uc004ajw.3_Intron|OSTF1_uc004ajx.3_Intron	NM_012383	NP_036515			osteoclast stimulating factor 1						ossification|signal transduction	cytoplasm	identical protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	78019137	78019137	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78019137delT								OSTF1 (257024 upstream) : PCSK5 (486423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78080526	78080526	+	IGR	DEL	T	-	-	rs34720748		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78080526delT								OSTF1 (318413 upstream) : PCSK5 (425034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78176171	78176171	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78176171delT								OSTF1 (414058 upstream) : PCSK5 (329389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78962680	78962680	+	Intron	DEL	A	-	-	rs5898474		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78962680delA	uc004akc.1	+											Homo sapiens cDNA FLJ16215 fis, clone CTONG2025610, moderately similar to PC6B.																														---	---	---	---
GCNT1	2650	broad.mit.edu	37	9	79078802	79078802	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79078802delA	uc010mpf.2	+						GCNT1_uc010mpg.2_Intron|GCNT1_uc010mph.2_Intron|GCNT1_uc004akf.3_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	79137317	79137318	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79137317_79137318insT								GCNT1 (14987 upstream) : PRUNE2 (88975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	79150379	79150380	+	IGR	INS	-	CA	CA	rs34509730		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79150379_79150380insCA								GCNT1 (28049 upstream) : PRUNE2 (75913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	79161457	79161458	+	IGR	INS	-	T	T	rs143859783	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79161457_79161458insT								GCNT1 (39127 upstream) : PRUNE2 (64835 downstream)																																			---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79309097	79309097	+	Intron	DEL	T	-	-	rs112987798		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79309097delT	uc010mpk.2	-						PRUNE2_uc011lsk.1_5'Flank|PRUNE2_uc011lsl.1_5'Flank|PRUNE2_uc011lsm.1_5'Flank|PRUNE2_uc004akj.3_Intron|PRUNE2_uc010mpl.1_Intron	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	79390875	79390876	+	Intron	INS	-	A	A	rs150213381	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79390875_79390876insA	uc010mpk.2	-						PCA3_uc010mpm.1_Intron|PCA3_uc004akm.2_Intron|PCA3_uc010mpn.1_Intron	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	79400650	79400651	+	Intron	DEL	TG	-	-	rs67593286		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79400650_79400651delTG	uc010mpk.2	-						PCA3_uc010mpm.1_RNA|PCA3_uc004akm.2_RNA|PCA3_uc010mpn.1_RNA	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	79467723	79467738	+	Intron	DEL	TCTATCTATCTATCTA	-	-	rs112890852		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79467723_79467738delTCTATCTATCTATCTA	uc010mpk.2	-						PRUNE2_uc004akn.2_Intron	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	79525252	79525252	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79525252delA								PRUNE2 (4249 upstream) : FOXB2 (109319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	79534356	79534356	+	IGR	DEL	C	-	-	rs66879716		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79534356delC								PRUNE2 (13353 upstream) : FOXB2 (100215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	79620107	79620108	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79620107_79620108delAA								PRUNE2 (99104 upstream) : FOXB2 (14463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	79709320	79709320	+	IGR	DEL	A	-	-	rs10114058	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79709320delA								FOXB2 (73451 upstream) : VPS13A (83041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	79734305	79734305	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79734305delA								FOXB2 (98436 upstream) : VPS13A (58056 downstream)																																			---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79962780	79962780	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79962780delT	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron	NM_033305	NP_150648			vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
GNA14	9630	broad.mit.edu	37	9	80061554	80061554	+	Intron	DEL	G	-	-	rs7042331	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80061554delG	uc004aku.2	-							NM_004297	NP_004288			G alpha 14						activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	80278363	80278364	+	IGR	INS	-	A	A	rs71358616		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80278363_80278364insA								GNA14 (15131 upstream) : GNAQ (53275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	80295462	80295462	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80295462delA								GNA14 (32230 upstream) : GNAQ (36177 downstream)																																			---	---	---	---
GNAQ	2776	broad.mit.edu	37	9	80339111	80339111	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80339111delT	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	80342920	80342921	+	Intron	INS	-	T	T	rs149823277	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80342920_80342921insT	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	80358202	80358203	+	Intron	INS	-	A	A	rs141984612	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80358202_80358203insA	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	80437850	80437853	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80437850_80437853delTTTT	uc004akw.2	-						GNAQ_uc011lso.1_5'UTR	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	80444866	80444867	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80444866_80444867insT	uc004akw.2	-							NM_002072	NP_002063			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity			eye(136)|skin(44)|meninges(11)|ovary(1)|kidney(1)	193								Mis		uveal melanoma								---	---	---	---
Unknown	0	broad.mit.edu	37	9	80707043	80707043	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80707043delA								GNAQ (60851 upstream) : CEP78 (143948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	80731360	80731360	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80731360delA								GNAQ (85168 upstream) : CEP78 (119631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	80965198	80965198	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80965198delT								PSAT1 (20191 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	80993417	80993417	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80993417delA								PSAT1 (48410 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81168748	81168749	+	IGR	INS	-	AG	AG	rs147912226	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81168748_81168749insAG								PSAT1 (223741 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81548497	81548498	+	IGR	INS	-	GA	GA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81548497_81548498insGA								PSAT1 (603490 upstream) : TLE4 (638380 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81596762	81596764	+	IGR	DEL	TTT	-	-	rs111669500		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81596762_81596764delTTT								PSAT1 (651755 upstream) : TLE4 (590114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82928906	82928913	+	IGR	DEL	TCTGTCTG	-	-	rs78471095	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82928906_82928913delTCTGTCTG								TLE4 (587249 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83074851	83074851	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83074851delA								TLE4 (733194 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83076030	83076030	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83076030delT								TLE4 (734373 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83187024	83187024	+	IGR	DEL	A	-	-	rs79150585		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83187024delA								TLE4 (845367 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83411067	83411067	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83411067delA								None (None upstream) : TLE1 (787533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83540151	83540151	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83540151delA								None (None upstream) : TLE1 (658449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83693384	83693385	+	IGR	DEL	TT	-	-	rs2779622	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83693384_83693385delTT								None (None upstream) : TLE1 (505215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83766478	83766478	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83766478delA								None (None upstream) : TLE1 (432122 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83789594	83789594	+	IGR	DEL	A	-	-	rs147946047		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83789594delA								None (None upstream) : TLE1 (409006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83925570	83925570	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83925570delG								None (None upstream) : TLE1 (273030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84007085	84007092	+	IGR	DEL	CCCATGCA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84007085_84007092delCCCATGCA								None (None upstream) : TLE1 (191508 downstream)																																			---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84199018	84199018	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84199018delT	uc004aly.2	-	20					TLE1_uc004alz.2_3'UTR|TLE1_uc011lsr.1_3'UTR	NM_005077	NP_005068			transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84231237	84231238	+	Intron	DEL	AA	-	-	rs113282087	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84231237_84231238delAA	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_Intron|TLE1_uc011lss.1_Intron	NM_005077	NP_005068			transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84231498	84231499	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84231498_84231499insT	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_Intron|TLE1_uc011lss.1_Intron	NM_005077	NP_005068			transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84280436	84280436	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84280436delA	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_Intron|TLE1_uc011lss.1_Intron|TLE1_uc004amb.2_Intron	NM_005077	NP_005068			transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84296467	84296467	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84296467delA	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_Intron|TLE1_uc011lss.1_Intron|TLE1_uc004amb.2_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	84817515	84817515	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84817515delT								FLJ46321 (207345 upstream) : RASEF (779802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85014509	85014509	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85014509delA								FLJ46321 (404339 upstream) : RASEF (582808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85147831	85147831	+	IGR	DEL	A	-	-	rs79938685		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85147831delA								FLJ46321 (537661 upstream) : RASEF (449486 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85270386	85270387	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85270386_85270387delAC								FLJ46321 (660216 upstream) : RASEF (326930 downstream)																																			---	---	---	---
RASEF	158158	broad.mit.edu	37	9	85621424	85621424	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85621424delA	uc004amo.1	-							NM_152573	NP_689786			RAS and EF-hand domain containing						protein transport|small GTPase mediated signal transduction	perinuclear region of cytoplasm	calcium ion binding|GTP binding			upper_aerodigestive_tract(1)|lung(1)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	85779529	85779529	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85779529delA								RASEF (101486 upstream) : FRMD3 (78376 downstream)																																			---	---	---	---
FRMD3	257019	broad.mit.edu	37	9	85861558	85861559	+	Intron	DEL	TC	-	-	rs150401940	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85861558_85861559delTC	uc004amr.1	-						FRMD3_uc004amq.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	85943987	85943987	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85943987delA	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	85996970	85996970	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85996970delA	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	86075856	86075857	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86075856_86075857delAA	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																		---	---	---	---
UBQLN1	29979	broad.mit.edu	37	9	86277986	86277987	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86277986_86277987delAA	uc004amv.2	-						UBQLN1_uc004amw.2_Intron	NM_013438	NP_038466			ubiquilin 1 isoform 1						apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0																		---	---	---	---
UBQLN1	29979	broad.mit.edu	37	9	86297543	86297544	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86297543_86297544insA	uc004amv.2	-						UBQLN1_uc004amw.2_Intron	NM_013438	NP_038466			ubiquilin 1 isoform 1						apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0																		---	---	---	---
KIF27	55582	broad.mit.edu	37	9	86533239	86533240	+	Intron	DEL	GG	-	-	rs66698705		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86533239_86533240delGG	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																		---	---	---	---
HNRNPK	3190	broad.mit.edu	37	9	86584096	86584096	+	3'UTR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86584096delC	uc004ang.3	-	17					HNRNPK_uc011lsw.1_3'UTR|HNRNPK_uc004and.3_3'UTR|HNRNPK_uc004ank.3_3'UTR|HNRNPK_uc004anf.3_3'UTR|HNRNPK_uc004anh.3_3'UTR|HNRNPK_uc011lsx.1_3'UTR|HNRNPK_uc004ani.3_3'UTR|HNRNPK_uc004anj.3_3'UTR|HNRNPK_uc004ann.3_3'UTR|HNRNPK_uc004anl.3_3'UTR|HNRNPK_uc004anm.3_3'UTR	NM_031262	NP_112552			heterogeneous nuclear ribonucleoprotein K						interspecies interaction between organisms|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of receptor-mediated endocytosis|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of low-density lipoprotein particle clearance|signal transduction	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nuclear chromatin|nucleoplasm	protein binding|RNA binding|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|single-stranded DNA binding			skin(1)	1																		---	---	---	---
HNRNPK	3190	broad.mit.edu	37	9	86592043	86592044	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86592043_86592044insA	uc004ang.3	-						HNRNPK_uc011lsw.1_5'Flank|HNRNPK_uc004and.3_5'Flank|HNRNPK_uc004ank.3_Intron|HNRNPK_uc004anf.3_Intron|HNRNPK_uc004anh.3_Intron|HNRNPK_uc011lsx.1_Intron|HNRNPK_uc004ani.3_Intron|HNRNPK_uc004anj.3_Intron|HNRNPK_uc004ann.3_Intron|HNRNPK_uc004anl.3_Intron|HNRNPK_uc004anm.3_Intron	NM_031262	NP_112552			heterogeneous nuclear ribonucleoprotein K						interspecies interaction between organisms|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of receptor-mediated endocytosis|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of low-density lipoprotein particle clearance|signal transduction	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nuclear chromatin|nucleoplasm	protein binding|RNA binding|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|single-stranded DNA binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	86885921	86885922	+	IGR	DEL	CA	-	-	rs71807247		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86885921_86885922delCA								RMI1 (266939 upstream) : SLC28A3 (7170 downstream)																																			---	---	---	---
SLC28A3	64078	broad.mit.edu	37	9	86976664	86976664	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86976664delA	uc004anu.1	-							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	87143179	87143179	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87143179delT								SLC28A3 (159766 upstream) : NTRK2 (140287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87221108	87221109	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87221108_87221109delAA								SLC28A3 (237695 upstream) : NTRK2 (62357 downstream)																																			---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87591643	87591643	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87591643delA	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	87833943	87833943	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87833943delA								NTRK2 (195438 upstream) : AGTPBP1 (327512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87860667	87860670	+	IGR	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87860667_87860670delAAAA								NTRK2 (222162 upstream) : AGTPBP1 (300785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87979992	87979992	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87979992delT								NTRK2 (341487 upstream) : AGTPBP1 (181463 downstream)																																			---	---	---	---
AGTPBP1	23287	broad.mit.edu	37	9	88182507	88182507	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88182507delA	uc011ltd.1	-						AGTPBP1_uc004aod.3_Intron|AGTPBP1_uc011ltc.1_Intron|AGTPBP1_uc010mqc.2_Intron|AGTPBP1_uc011lte.1_Intron	NM_015239	NP_056054			ATP/GTP binding protein 1						C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7																		---	---	---	---
AGTPBP1	23287	broad.mit.edu	37	9	88306451	88306452	+	Intron	INS	-	GT	GT	rs147512485	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88306451_88306452insGT	uc011ltd.1	-						AGTPBP1_uc010mqc.2_Intron|AGTPBP1_uc011lte.1_Intron	NM_015239	NP_056054			ATP/GTP binding protein 1						C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	88368144	88368144	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88368144delA								AGTPBP1 (11200 upstream) : NAA35 (187913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	88469643	88469643	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88469643delA								AGTPBP1 (112699 upstream) : NAA35 (86414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89064276	89064276	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89064276delA								ZCCHC6 (94898 upstream) : GAS1 (495003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89274453	89274454	+	IGR	INS	-	TTC	TTC	rs147635049	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89274453_89274454insTTC								ZCCHC6 (305075 upstream) : GAS1 (284825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89569590	89569590	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89569590delA	uc004aoy.2	+											Homo sapiens, clone IMAGE:5309572, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	89601038	89601038	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89601038delT	uc004aoy.2	+											Homo sapiens, clone IMAGE:5309572, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	89717103	89717103	+	IGR	DEL	T	-	-	rs71507716		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89717103delT								LOC440173 (60062 upstream) : C9orf170 (46456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89855622	89855623	+	Intron	DEL	AA	-	-	rs72287915		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89855622_89855623delAA	uc004apb.1	-											Homo sapiens cDNA clone IMAGE:30346008.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	89936898	89936898	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89936898delT								C9orf170 (162257 upstream) : DAPK1 (175760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	90709108	90709108	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90709108delC								CDK20 (119441 upstream) : SPIN1 (293732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	90812182	90812183	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90812182_90812183insT								CDK20 (222515 upstream) : SPIN1 (190657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	90958034	90958034	+	IGR	DEL	A	-	-	rs35168291		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90958034delA								CDK20 (368367 upstream) : SPIN1 (44806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91367868	91367869	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91367868_91367869delAG								LOC286238 (100793 upstream) : C9orf47 (237909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91621971	91621971	+	RNA	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91621971delT	uc004aqf.1	-	1		c.3345delA								Homo sapiens cDNA FLJ45325 fis, clone BRHIP3006717.																														---	---	---	---
SHC3	53358	broad.mit.edu	37	9	91689767	91689768	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91689767_91689768delTT	uc004aqg.2	-							NM_016848	NP_058544			src homology 2 domain-containing transforming						central nervous system development|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	protein binding|signal transducer activity			lung(3)|skin(1)	4																		---	---	---	---
SHC3	53358	broad.mit.edu	37	9	91780175	91780176	+	Intron	INS	-	TG	TG	rs146748449	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91780175_91780176insTG	uc004aqg.2	-							NM_016848	NP_058544			src homology 2 domain-containing transforming						central nervous system development|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	protein binding|signal transducer activity			lung(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	91810400	91810400	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91810400delA								SHC3 (16718 upstream) : CKS2 (115713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91894261	91894261	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91894261delA								SHC3 (100579 upstream) : CKS2 (31852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91899063	91899064	+	IGR	INS	-	A	A	rs144387977	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91899063_91899064insA								SHC3 (105381 upstream) : CKS2 (27049 downstream)																																			---	---	---	---
SECISBP2	79048	broad.mit.edu	37	9	91934385	91934385	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91934385delA	uc004aqj.1	+						SECISBP2_uc010mqn.1_Intron|SECISBP2_uc004aqi.1_Intron|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	92113512	92113512	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92113512delT	uc004aqp.1	-							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	92150189	92150190	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92150189_92150190delTG								SEMA4D (37301 upstream) : GADD45G (69737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	92523697	92523697	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92523697delT								LOC100129066 (189023 upstream) : DIRAS2 (848417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	92759836	92759836	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92759836delA								LOC100129066 (425162 upstream) : DIRAS2 (612278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	92999256	92999256	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92999256delT								LOC100129066 (664582 upstream) : DIRAS2 (372858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	93150918	93150918	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93150918delA								LOC100129066 (816244 upstream) : DIRAS2 (221196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	93244485	93244486	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93244485_93244486delCA	uc004aqt.1	-											Homo sapiens cDNA FLJ46333 fis, clone TESTI4045701.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	93367173	93367174	+	IGR	INS	-	TT	TT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93367173_93367174insTT								None (None upstream) : DIRAS2 (4940 downstream)																																			---	---	---	---
SYK	6850	broad.mit.edu	37	9	93605039	93605046	+	Intron	DEL	GAGTGTGT	-	-	rs72442804		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93605039_93605046delGAGTGTGT	uc004aqz.2	+						SYK_uc004aqy.2_Intron|SYK_uc004ara.2_Intron|SYK_uc004arb.2_Intron|SYK_uc004arc.2_Intron|SYK_uc011ltr.1_5'Flank|SYK_uc011lts.1_5'Flank|SYK_uc011ltt.1_5'Flank	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	93846879	93846879	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93846879delA								SYK (186046 upstream) : AUH (129220 downstream)																																			---	---	---	---
AUH	549	broad.mit.edu	37	9	94028225	94028225	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94028225delT	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																		---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94635487	94635492	+	Intron	DEL	CTACCA	-	-	rs11278540		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94635487_94635492delCTACCA	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																		---	---	---	---
C9orf44	158314	broad.mit.edu	37	9	94904432	94904432	+	Intron	DEL	G	-	-	rs34310564		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94904432delG	uc004arp.1	+							NR_027341				Homo sapiens cDNA FLJ13600 fis, clone PLACE1009947.												0																		---	---	---	---
NOL8	55035	broad.mit.edu	37	9	95085870	95085870	+	Intron	DEL	A	-	-	rs75489638		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95085870delA	uc004arv.2	-						CENPP_uc004arz.2_5'Flank|CENPP_uc010mqx.2_5'Flank|NOL8_uc004arw.2_Intron|NOL8_uc011ltw.1_Intron|NOL8_uc004arx.2_Intron|CENPP_uc004ary.1_5'Flank	NM_017948	NP_060418			nucleolar protein 8						DNA replication|positive regulation of cell growth	nucleolus	nucleotide binding|protein binding|RNA binding			ovary(1)	1																		---	---	---	---
CENPP	401541	broad.mit.edu	37	9	95095094	95095094	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95095094delA	uc004arz.2	+						CENPP_uc010mqx.2_Intron|CENPP_uc004ary.1_Intron	NM_001012267	NP_001012267			centromere protein P						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2																		---	---	---	---
CENPP	401541	broad.mit.edu	37	9	95117548	95117549	+	Intron	INS	-	GG	GG	rs138076324	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95117548_95117549insGG	uc004arz.2	+						CENPP_uc010mqx.2_Intron|CENPP_uc004ary.1_Intron	NM_001012267	NP_001012267			centromere protein P						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2																		---	---	---	---
OMD	4958	broad.mit.edu	37	9	95179845	95179845	+	5'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95179845delT	uc004asd.3	-	2					CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron	NM_005014	NP_005005			osteomodulin precursor						cell adhesion	proteinaceous extracellular matrix				ovary(2)	2								T	USP6	aneurysmal bone cysts								---	---	---	---
ECM2	1842	broad.mit.edu	37	9	95279371	95279371	+	Intron	DEL	A	-	-	rs3841714		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95279371delA	uc004ash.2	-						CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ECM2_uc004asf.3_Intron|ECM2_uc011lty.1_Intron|ECM2_uc004asg.2_Intron|ECM2_uc004asi.2_3'UTR	NM_001393	NP_001384			extracellular matrix protein 2 precursor						cell-matrix adhesion		integrin binding			ovary(1)|skin(1)	2																		---	---	---	---
IPPK	64768	broad.mit.edu	37	9	95412308	95412309	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95412308_95412309delAA	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																		---	---	---	---
BICD2	23299	broad.mit.edu	37	9	95519989	95519989	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95519989delA	uc004aso.1	-						BICD2_uc004asp.1_Intron	NM_015250	NP_056065			bicaudal D homolog 2 isoform 2						microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule	cytoplasmic vesicle|cytoskeleton|Golgi apparatus|plasma membrane	Rab GTPase binding			skin(1)	1																		---	---	---	---
FGD3	89846	broad.mit.edu	37	9	95712701	95712702	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95712701_95712702delAA	uc004asw.2	+							NM_001083536	NP_001077005			FYVE, RhoGEF and PH domain containing 3						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	95781144	95781144	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95781144delT	uc004asw.2	+						FGD3_uc004asx.2_Intron|FGD3_uc004asz.2_Intron|FGD3_uc004ata.2_Intron|FGD3_uc011luc.1_Intron	NM_001083536	NP_001077005			FYVE, RhoGEF and PH domain containing 3						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																		---	---	---	---
C9orf89	84270	broad.mit.edu	37	9	95867474	95867479	+	Intron	DEL	GTGTGC	-	-	rs57409347	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95867474_95867479delGTGTGC	uc004atd.2	+						C9orf89_uc004ate.2_Intron|C9orf89_uc004atf.2_Intron	NM_032310	NP_115686			chromosome 9 open reading frame 89						negative regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|nucleus	CARD domain binding				0																		---	---	---	---
WNK2	65268	broad.mit.edu	37	9	96018922	96018923	+	Intron	INS	-	GT	GT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96018922_96018923insGT	uc004ati.1	+						WNK2_uc011lud.1_Intron|WNK2_uc004atj.2_Intron|WNK2_uc004atk.2_Intron|WNK2_uc010mrc.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																		---	---	---	---
FAM120A	23196	broad.mit.edu	37	9	96264848	96264849	+	Intron	DEL	AC	-	-	rs139110277		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96264848_96264849delAC	uc004atw.2	+						FAM120A_uc004atv.2_Intron|FAM120A_uc004atx.2_Intron|FAM120A_uc004aty.2_Intron	NM_014612	NP_055427			oxidative stress-associated Src activator							cytoplasm|plasma membrane	RNA binding				0																		---	---	---	---
PHF2	5253	broad.mit.edu	37	9	96345176	96345177	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96345176_96345177insT	uc004aub.2	+						PHF2_uc011lug.1_Intron	NM_005392	NP_005383			PHD finger protein 2						liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)														---	---	---	---
PHF2	5253	broad.mit.edu	37	9	96422612	96422612	+	Frame_Shift_Del	DEL	A	-	-	rs76832193		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96422612delA	uc004aub.2	+	12	1615	c.1468delA	c.(1468-1470)AAAfs	p.K490fs	PHF2_uc011lug.1_Frame_Shift_Del_p.K373fs|PHF2_uc004auc.2_5'Flank	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2	490	Pro-rich.|Lys-rich.				liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	96444747	96444747	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96444747delA								PHF2 (2880 upstream) : BARX1 (269164 downstream)																																	OREG0019324	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	96634048	96634053	+	IGR	DEL	ACACAC	-	-	rs150117345		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96634048_96634053delACACAC								PHF2 (192181 upstream) : BARX1 (79858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	96723227	96723227	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96723227delT								BARX1 (5619 upstream) : PTPDC1 (69849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	96750328	96750330	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96750328_96750330delAAA								BARX1 (32720 upstream) : PTPDC1 (42746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	96883552	96883552	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96883552delA								PTPDC1 (11416 upstream) : MIRLET7A1 (54687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	96900795	96900795	+	IGR	DEL	A	-	-	rs34156755		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96900795delA								PTPDC1 (28659 upstream) : MIRLET7A1 (37444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	97431511	97431511	+	IGR	DEL	A	-	-	rs35419759		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97431511delA								FBP1 (28980 upstream) : C9orf3 (57483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	97432476	97432476	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97432476delT								FBP1 (29945 upstream) : C9orf3 (56518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	97478775	97478775	+	IGR	DEL	A	-	-	rs80209381		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97478775delA								FBP1 (76244 upstream) : C9orf3 (10219 downstream)																																			---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97486739	97486739	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97486739delT	uc004auy.2	+						C9orf3_uc011lui.1_5'Flank|C9orf3_uc004aux.1_5'Flank	NM_032823	NP_116212			aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97609409	97609410	+	Intron	INS	-	ACAC	ACAC	rs150654352	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97609409_97609410insACAC	uc004ava.2	+						C9orf3_uc004aux.1_Intron|C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron	NM_032823	NP_116212			aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97635400	97635400	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97635400delA	uc004ava.2	+						C9orf3_uc004aux.1_Intron|C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron	NM_032823	NP_116212			aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97735221	97735221	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97735221delA	uc004ava.2	+						C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron|C9orf3_uc004avc.2_Intron	NM_032823	NP_116212			aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97746135	97746135	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97746135delC	uc004ava.2	+						C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron|C9orf3_uc004avc.2_Intron	NM_032823	NP_116212			aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97801686	97801686	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97801686delA	uc004ava.2	+						C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron|C9orf3_uc004avc.2_Intron|C9orf3_uc011luj.1_Intron|C9orf3_uc011luk.1_Intron|C9orf3_uc004avd.2_Intron	NM_032823	NP_116212			aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
FANCC	2176	broad.mit.edu	37	9	98021493	98021493	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98021493delA	uc004avh.2	-						FANCC_uc004avi.3_Intron|FANCC_uc010mrm.1_Intron|FANCC_uc011lul.1_Intron	NM_000136	NP_000127			Fanconi anemia, complementation group C						protein complex assembly	cytosol|nucleoplasm	protein binding			kidney(1)	1		Acute lymphoblastic leukemia(62;0.138)						D|Mis|N|F|S			AML|leukemia		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
Unknown	0	broad.mit.edu	37	9	98098700	98098700	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98098700delA								FANCC (18709 upstream) : PTCH1 (106566 downstream)																																			---	---	---	---
PTCH1	5727	broad.mit.edu	37	9	98270187	98270188	+	Intron	INS	-	ACAC	ACAC	rs139956254	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98270187_98270188insACAC	uc004avk.3	-						PTCH1_uc010mro.2_5'Flank|PTCH1_uc010mrp.2_5'Flank|PTCH1_uc010mrq.2_Intron|PTCH1_uc004avl.3_Intron|PTCH1_uc010mrr.2_Intron|PTCH1_uc004avm.3_Intron|PTCH1_uc010mrt.1_5'Flank|PTCH1_uc010mru.1_5'Flank|PTCH1_uc004avo.2_Intron|PTCH1_uc010mrv.1_Intron|PTCH1_uc010mrw.1_Intron	NM_000264	NP_000255			patched isoform L						embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity			skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1)	379		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)												Basal_Cell_Nevus_syndrome				---	---	---	---
C9orf130	100128782	broad.mit.edu	37	9	98574109	98574113	+	RNA	DEL	GGTGT	-	-	rs66798514		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98574109_98574113delGGTGT	uc004avp.3	-	3		c.2271_2275delACACC				NR_023390				Homo sapiens cDNA FLJ34818 fis, clone NT2NE2008077.												0																		---	---	---	---
C9orf102	375748	broad.mit.edu	37	9	98715123	98715124	+	Intron	DEL	AA	-	-	rs111777042		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98715123_98715124delAA	uc004avt.3	+						C9orf102_uc010mrx.1_Intron|C9orf102_uc011lum.1_Intron|C9orf102_uc010mry.1_Intron|C9orf102_uc010mrz.2_Intron|C9orf102_uc004avu.2_Intron	NM_001010895	NP_001010895			RAD26L hypothetical protein						DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding				0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	98894620	98894621	+	IGR	INS	-	TG	TG	rs140850322	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98894620_98894621insTG								NCRNA00092 (110583 upstream) : HSD17B3 (102968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98896641	98896641	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98896641delT								NCRNA00092 (112604 upstream) : HSD17B3 (100948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98922277	98922277	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98922277delG								NCRNA00092 (138240 upstream) : HSD17B3 (75312 downstream)																																			---	---	---	---
ZNF367	195828	broad.mit.edu	37	9	99164111	99164111	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99164111delA	uc004awf.2	-						ZNF367_uc004awg.2_Intron	NM_153695	NP_710162			zinc finger protein 367						regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0167)																---	---	---	---
HABP4	22927	broad.mit.edu	37	9	99209561	99209562	+	5'Flank	INS	-	ACACAA	ACACAA	rs72078524		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99209561_99209562insACACAA	uc010msg.2	+						HABP4_uc010msh.2_5'Flank	NM_014282	NP_055097			hyaluronan binding protein 4						platelet activation|platelet degranulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|extracellular region|nucleus	protein binding			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)																---	---	---	---
HABP4	22927	broad.mit.edu	37	9	99246224	99246224	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99246224delA	uc010msg.2	+						HABP4_uc010msh.2_Intron	NM_014282	NP_055097			hyaluronan binding protein 4						platelet activation|platelet degranulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|extracellular region|nucleus	protein binding			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	99423444	99423445	+	IGR	INS	-	T	T	rs112880252		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99423444_99423445insT								C9orf21 (5845 upstream) : LOC441455 (64658 downstream)																																			---	---	---	---
TMOD1	7111	broad.mit.edu	37	9	100356362	100356362	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100356362delA	uc004axk.1	+						TMOD1_uc004axl.1_Intron	NM_003275	NP_003266			tropomodulin 1						muscle filament sliding	cytosol	actin binding				0		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)														---	---	---	---
NCBP1	4686	broad.mit.edu	37	9	100420786	100420786	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100420786delT	uc004axq.2	+							NM_002486	NP_002477			nuclear cap binding protein subunit 1, 80kDa						gene silencing by RNA|histone mRNA metabolic process|mRNA 3'-end processing|mRNA capping|mRNA cleavage|mRNA export from nucleus|ncRNA metabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of mRNA 3'-end processing|positive regulation of viral transcription|regulation of translational initiation|spliceosomal snRNP assembly|termination of RNA polymerase II transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|mRNA cap binding complex|nucleoplasm|ribonucleoprotein complex	protein binding|RNA cap binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.158)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	100525873	100525874	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100525873_100525874insT								XPA (66182 upstream) : FOXE1 (89663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	100651145	100651145	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100651145delT								FOXE1 (32159 upstream) : C9orf156 (15627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	100653659	100653661	+	IGR	DEL	AGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100653659_100653661delAGG								FOXE1 (34673 upstream) : C9orf156 (13111 downstream)																																			---	---	---	---
ANP32B	10541	broad.mit.edu	37	9	100776138	100776138	+	Intron	DEL	A	-	-	rs77575974		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100776138delA	uc004aya.2	+							NM_006401	NP_006392			acidic (leucine-rich) nuclear phosphoprotein 32							cytoplasm|nucleus					0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
ANP32B	10541	broad.mit.edu	37	9	100777785	100777787	+	3'UTR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100777785_100777787delAAA	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	100784796	100784798	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100784796_100784798delTTT								ANP32B (6574 upstream) : NANS (23091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	100788640	100788642	+	IGR	DEL	TTT	-	-	rs56300336		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100788640_100788642delTTT								ANP32B (10418 upstream) : NANS (19247 downstream)																																			---	---	---	---
TRIM14	9830	broad.mit.edu	37	9	100876624	100876624	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100876624delT	uc004ayd.2	-						TRIM14_uc004ayf.1_Intron|TRIM14_uc004ayg.1_Intron|TRIM14_uc004ayh.1_Intron|TRIM14_uc004ayi.1_Intron|TRIM14_uc004ayj.1_Intron	NM_033220	NP_150089			tripartite motif protein TRIM14 isoform alpha							cytoplasm|intracellular	zinc ion binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101062312	101062312	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101062312delT	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101167402	101167402	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101167402delA	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101184899	101184899	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101184899delT	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101201382	101201382	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101201382delA	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101380023	101380023	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101380023delA	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	101564712	101564712	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101564712delT								ANKS6 (5918 upstream) : GALNT12 (5269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	101641434	101641434	+	IGR	DEL	T	-	-	rs77593605		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101641434delT								GALNT12 (29076 upstream) : COL15A1 (64704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	101649019	101649019	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101649019delA								GALNT12 (36661 upstream) : COL15A1 (57119 downstream)																																			---	---	---	---
COL15A1	1306	broad.mit.edu	37	9	101721880	101721881	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101721880_101721881delAA	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)																---	---	---	---
COL15A1	1306	broad.mit.edu	37	9	101776257	101776257	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101776257delT	uc004azb.1	+							NM_001855	NP_001846			alpha 1 type XV collagen precursor						angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	101860877	101860879	+	IGR	DEL	AAC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101860877_101860879delAAC								COL15A1 (27809 upstream) : TGFBR1 (6533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	102214959	102214960	+	IGR	DEL	TT	-	-	rs67190587		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102214959_102214960delTT								SEC61B (222059 upstream) : NR4A3 (369177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	102447831	102447832	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102447831_102447832insA	uc004bad.1	-											Homo sapiens cDNA FLJ32889 fis, clone TESTI2004560.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	102533501	102533501	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102533501delA	uc004bad.1	-											Homo sapiens cDNA FLJ32889 fis, clone TESTI2004560.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	102639772	102639772	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102639772delA								NR4A3 (10599 upstream) : STX17 (29143 downstream)																																			---	---	---	---
ERP44	23071	broad.mit.edu	37	9	102747989	102747990	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102747989_102747990insT	uc004bam.2	-						ERP44_uc010msy.2_Intron|ERP44_uc010msz.2_Intron	NM_015051	NP_055866			thioredoxin domain containing 4 (endoplasmic						cell redox homeostasis|glycoprotein metabolic process|protein folding|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|ER-Golgi intermediate compartment	protein binding|protein disulfide isomerase activity				0																		---	---	---	---
ERP44	23071	broad.mit.edu	37	9	102842922	102842922	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102842922delA	uc004bam.2	-						ERP44_uc010msy.2_Intron|ERP44_uc010msz.2_Intron	NM_015051	NP_055866			thioredoxin domain containing 4 (endoplasmic						cell redox homeostasis|glycoprotein metabolic process|protein folding|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|ER-Golgi intermediate compartment	protein binding|protein disulfide isomerase activity				0																		---	---	---	---
TEX10	54881	broad.mit.edu	37	9	103097490	103097490	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103097490delT	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)														---	---	---	---
MURC	347273	broad.mit.edu	37	9	103344616	103344617	+	Intron	INS	-	TT	TT	rs142050335	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103344616_103344617insTT	uc004bba.2	+							NM_001018116	NP_001018126			muscle-related coiled-coil protein						cell differentiation|muscle organ development|transcription, DNA-dependent					ovary(1)	1		Acute lymphoblastic leukemia(62;0.0461)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	103464575	103464576	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103464575_103464576delTT								MURC (114404 upstream) : LPPR1 (326455 downstream)																																			---	---	---	---
LPPR1	54886	broad.mit.edu	37	9	103808493	103808493	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103808493delT	uc004bbb.2	+						LPPR1_uc011lvi.1_Intron	NM_207299	NP_997182			plasticity related gene 3							integral to membrane	catalytic activity				0																		---	---	---	---
LPPR1	54886	broad.mit.edu	37	9	103813557	103813558	+	Intron	INS	-	CTA	CTA	rs28438480	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103813557_103813558insCTA	uc004bbb.2	+						LPPR1_uc011lvi.1_Intron	NM_207299	NP_997182			plasticity related gene 3							integral to membrane	catalytic activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	104805720	104805726	+	IGR	DEL	GTTTTTT	-	-	rs139239540	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104805720_104805726delGTTTTTT								GRIN3A (304858 upstream) : CYLC2 (951867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	104847732	104847733	+	IGR	INS	-	AG	AG	rs76844842	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104847732_104847733insAG								GRIN3A (346870 upstream) : CYLC2 (909860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	104896674	104896674	+	IGR	DEL	A	-	-	rs34402062		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104896674delA								GRIN3A (395812 upstream) : CYLC2 (860919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105427881	105427883	+	IGR	DEL	TTC	-	-	rs35875444		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105427881_105427883delTTC								GRIN3A (927019 upstream) : CYLC2 (329710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105920438	105920440	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105920438_105920440delTTT	uc004bbt.2	-											Homo sapiens cDNA clone IMAGE:5266449.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	105926116	105926116	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105926116delT	uc004bbt.2	-											Homo sapiens cDNA clone IMAGE:5266449.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	105955947	105955948	+	Intron	INS	-	T	T	rs72548360		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105955947_105955948insT	uc004bbt.2	-											Homo sapiens cDNA clone IMAGE:5266449.																														---	---	---	---
SMC2	10592	broad.mit.edu	37	9	106857181	106857190	+	Intron	DEL	TTGTGGAGAG	-	-	rs138893712		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106857181_106857190delTTGTGGAGAG	uc004bbv.2	+						SMC2_uc004bbu.1_Intron|SMC2_uc004bbw.2_Intron|SMC2_uc011lvl.1_Intron|SMC2_uc010mtg.1_Intron|SMC2_uc010mth.1_Intron|SMC2_uc004bbx.2_Intron	NM_001042551	NP_001036016			structural maintenance of chromosomes 2						cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9																		---	---	---	---
SMC2	10592	broad.mit.edu	37	9	106890446	106890446	+	Intron	DEL	T	-	-	rs77207733		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106890446delT	uc004bbv.2	+						SMC2_uc004bbw.2_Intron|SMC2_uc011lvl.1_Intron|SMC2_uc004bbx.2_Intron|SMC2_uc004bby.2_Intron	NM_001042551	NP_001036016			structural maintenance of chromosomes 2						cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	107167006	107167006	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107167006delT								SMC2 (263313 upstream) : OR13F1 (99538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107168606	107168606	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107168606delT								SMC2 (264913 upstream) : OR13F1 (97938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107182541	107182541	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107182541delT								SMC2 (278848 upstream) : OR13F1 (84003 downstream)																																			---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107615497	107615497	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107615497delT	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	107650339	107650340	+	Intron	INS	-	GT	GT	rs147762490	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107650339_107650340insGT	uc004bcl.2	-						ABCA1_uc004bcm.2_Intron	NM_005502	NP_005493			ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107680034	107680034	+	Intron	DEL	A	-	-	rs111680466		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107680034delA	uc004bcl.2	-						ABCA1_uc004bcm.2_Intron	NM_005502	NP_005493			ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	107773636	107773636	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107773636delT								ABCA1 (83200 upstream) : SLC44A1 (233293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107792508	107792508	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107792508delA								ABCA1 (102072 upstream) : SLC44A1 (214421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107869115	107869115	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107869115delT								ABCA1 (178679 upstream) : SLC44A1 (137814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107925700	107925700	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107925700delT								ABCA1 (235264 upstream) : SLC44A1 (81229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107975293	107975294	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107975293_107975294insA								ABCA1 (284857 upstream) : SLC44A1 (31635 downstream)																																			---	---	---	---
SLC44A1	23446	broad.mit.edu	37	9	108060393	108060393	+	Intron	DEL	A	-	-	rs113849669		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108060393delA	uc004bcn.2	+						SLC44A1_uc010mtk.1_Intron	NM_080546	NP_536856			CDW92 antigen							integral to membrane|mitochondrial outer membrane|plasma membrane	choline transmembrane transporter activity			breast(3)|ovary(1)	4					Choline(DB00122)													---	---	---	---
FSD1L	83856	broad.mit.edu	37	9	108227090	108227091	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108227090_108227091delAA	uc011lvv.1	+						FSD1L_uc011lvw.1_Intron|FSD1L_uc004bcq.2_Intron|FSD1L_uc004bcp.2_Intron	NM_001145313	NP_001138785			fibronectin type III and SPRY domain containing												0																		---	---	---	---
FSD1L	83856	broad.mit.edu	37	9	108228157	108228159	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108228157_108228159delTTT	uc011lvv.1	+						FSD1L_uc011lvw.1_Intron|FSD1L_uc004bcq.2_Intron|FSD1L_uc004bcp.2_Intron	NM_001145313	NP_001138785			fibronectin type III and SPRY domain containing												0																		---	---	---	---
FSD1L	83856	broad.mit.edu	37	9	108231720	108231720	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108231720delT	uc011lvv.1	+						FSD1L_uc011lvw.1_Intron|FSD1L_uc004bcq.2_Intron|FSD1L_uc004bcp.2_Intron	NM_001145313	NP_001138785			fibronectin type III and SPRY domain containing												0																		---	---	---	---
FKTN	2218	broad.mit.edu	37	9	108326333	108326333	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108326333delC	uc004bcr.2	+						FKTN_uc011lvx.1_Intron|FKTN_uc004bcs.2_Intron|FKTN_uc011lvy.1_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	108332976	108332976	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108332976delT	uc004bcr.2	+						FKTN_uc011lvx.1_Intron|FKTN_uc004bcs.2_Intron|FKTN_uc011lvy.1_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																		---	---	---	---
TMEM38B	55151	broad.mit.edu	37	9	108471136	108471136	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108471136delT	uc004bcu.1	+						TMEM38B_uc010mtn.1_Intron	NM_018112	NP_060582			transmembrane protein 38B							integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	108884703	108884706	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108884703_108884706delTTTT	uc004bcw.2	+											Homo sapiens, clone IMAGE:5538960, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109048501	109048501	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109048501delT	uc004bcw.2	+											Homo sapiens, clone IMAGE:5538960, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109140899	109140900	+	Intron	INS	-	A	A	rs35199494		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109140899_109140900insA	uc004bcw.2	+											Homo sapiens, clone IMAGE:5538960, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109184607	109184608	+	IGR	INS	-	A	A	rs138816683	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109184607_109184608insA								TMEM38B (647163 upstream) : ZNF462 (440770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	109333115	109333116	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109333115_109333116insA	uc004bcx.2	+											Homo sapiens, clone IMAGE:4246712, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109345163	109345164	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109345163_109345164insT	uc004bcx.2	+											Homo sapiens, clone IMAGE:4246712, mRNA.																														---	---	---	---
ZNF462	58499	broad.mit.edu	37	9	109660707	109660708	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109660707_109660708insG	uc004bcz.2	+							NM_021224	NP_067047			zinc finger protein 462						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	109892290	109892290	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109892290delA								ZNF462 (118501 upstream) : RAD23B (153254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	109958004	109958004	+	IGR	DEL	G	-	-	rs10978747		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109958004delG								ZNF462 (184215 upstream) : RAD23B (87540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110038345	110038346	+	IGR	DEL	TT	-	-	rs112060652	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110038345_110038346delTT								ZNF462 (264556 upstream) : RAD23B (7198 downstream)																																			---	---	---	---
RAD23B	5887	broad.mit.edu	37	9	110077785	110077786	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110077785_110077786insT	uc004bde.2	+						RAD23B_uc011lwa.1_Intron|RAD23B_uc011lwb.1_Intron	NM_002874	NP_002865			UV excision repair protein RAD23 homolog B						nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleoplasm|proteasome complex|XPC complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			ovary(1)	1													Direct_reversal_of_damage|NER					---	---	---	---
RAD23B	5887	broad.mit.edu	37	9	110081279	110081279	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110081279delT	uc004bde.2	+						RAD23B_uc011lwa.1_Intron|RAD23B_uc011lwb.1_Intron	NM_002874	NP_002865			UV excision repair protein RAD23 homolog B						nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleoplasm|proteasome complex|XPC complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			ovary(1)	1													Direct_reversal_of_damage|NER					---	---	---	---
Unknown	0	broad.mit.edu	37	9	110271839	110271840	+	IGR	DEL	GC	-	-	rs71732367		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110271839_110271840delGC								KLF4 (19792 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110308094	110308094	+	IGR	DEL	T	-	-	rs79002591		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110308094delT								KLF4 (56047 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110337002	110337003	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110337002_110337003delTT								KLF4 (84955 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110470955	110470956	+	IGR	INS	-	AAC	AAC	rs138040839	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110470955_110470956insAAC								KLF4 (218908 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110642170	110642170	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110642170delA								KLF4 (390123 upstream) : ACTL7B (974701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110775411	110775411	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110775411delA								KLF4 (523364 upstream) : ACTL7B (841460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110809054	110809055	+	IGR	INS	-	T	T	rs140513624	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110809054_110809055insT								KLF4 (557007 upstream) : ACTL7B (807816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110928445	110928445	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110928445delT								KLF4 (676398 upstream) : ACTL7B (688426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110960260	110960264	+	IGR	DEL	AAAAA	-	-	rs71897665		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110960260_110960264delAAAAA								KLF4 (708213 upstream) : ACTL7B (656607 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111031836	111031836	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111031836delA								KLF4 (779789 upstream) : ACTL7B (585035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111293835	111293835	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111293835delA								None (None upstream) : ACTL7B (323036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111469994	111469994	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111469994delG								None (None upstream) : ACTL7B (146877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111484689	111484690	+	IGR	INS	-	GA	GA	rs149291401	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111484689_111484690insGA								None (None upstream) : ACTL7B (132181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111572986	111572987	+	IGR	INS	-	A	A	rs143217811	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111572986_111572987insA								None (None upstream) : ACTL7B (43884 downstream)																																			---	---	---	---
IKBKAP	8518	broad.mit.edu	37	9	111661423	111661423	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111661423delA	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																		---	---	---	---
C9orf5	23731	broad.mit.edu	37	9	111812735	111812735	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111812735delA	uc004bdt.3	-						C9orf5_uc004bds.3_Intron|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401			hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)														---	---	---	---
C9orf5	23731	broad.mit.edu	37	9	111884172	111884172	+	5'Flank	DEL	T	-	-	rs111541495		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111884172delT	uc004bdt.3	-						C9orf5_uc004bdr.3_5'Flank	NM_032012	NP_114401			hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)														---	---	---	---
EPB41L4B	54566	broad.mit.edu	37	9	112035527	112035527	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112035527delT	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																		---	---	---	---
EPB41L4B	54566	broad.mit.edu	37	9	112065401	112065401	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112065401delA	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	112132391	112132391	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112132391delT								EPB41L4B (49370 upstream) : PTPN3 (5583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	112268761	112268764	+	IGR	DEL	TTCT	-	-	rs146228465	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112268761_112268764delTTCT								PTPN3 (8168 upstream) : PALM2 (134308 downstream)																																			---	---	---	---
PALM2	114299	broad.mit.edu	37	9	112480360	112480361	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112480360_112480361insT	uc004beg.2	+						PALM2_uc004bef.2_Intron	NM_001037293	NP_001032370			paralemmin 2 isoform b						regulation of cell shape	plasma membrane				ovary(2)	2																		---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112565379	112565380	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112565379_112565380insG	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	112626867	112626867	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112626867delG	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_5'Flank	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	112787067	112787068	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112787067_112787068delAA	uc004bei.2	+						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																		---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112878668	112878669	+	Intron	DEL	GC	-	-	rs497613		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112878668_112878669delGC	uc004bei.2	+						PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron|AKAP2_uc011lwi.1_Intron|AKAP2_uc004bem.2_Intron|PALM2-AKAP2_uc010mtw.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																		---	---	---	---
SVEP1	79987	broad.mit.edu	37	9	113274646	113274647	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113274646_113274647delTT	uc010mtz.2	-						SVEP1_uc010mua.1_Intron|SVEP1_uc004beu.2_Intron|SVEP1_uc004bev.2_3'UTR	NM_153366	NP_699197			polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7																		---	---	---	---
MUSK	4593	broad.mit.edu	37	9	113550983	113550984	+	Intron	INS	-	A	A	rs138576742	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113550983_113550984insA	uc004bey.2	+						MUSK_uc004bez.1_Intron	NM_005592	NP_005583			skeletal muscle receptor tyrosine kinase						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|ovary(2)|central_nervous_system(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	113903197	113903198	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113903197_113903198delAC								LPAR1 (101671 upstream) : OR2K2 (186566 downstream)																																			---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114135312	114135312	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114135312delA	uc004bfe.1	-							NM_001080398	NP_001073867			KIAA0368 protein												0																		---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114230857	114230858	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114230857_114230858insA	uc004bfe.1	-						KIAA0368_uc010muc.1_Intron	NM_001080398	NP_001073867			KIAA0368 protein												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	114370226	114370228	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114370226_114370228delTTT	uc004bfk.3	-											Homo sapiens chromosome 9 open reading frame 29, mRNA (cDNA clone MGC:39589 IMAGE:4838739), complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	114601047	114601049	+	IGR	DEL	TTT	-	-	rs35588187		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114601047_114601049delTTT								C9orf84 (43824 upstream) : UGCG (58157 downstream)																																			---	---	---	---
SUSD1	64420	broad.mit.edu	37	9	114905952	114905952	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114905952delA	uc004bfu.2	-						SUSD1_uc010mui.2_Intron|SUSD1_uc010muj.2_Intron	NM_022486	NP_071931			sushi domain containing 1 precursor							integral to membrane	calcium ion binding				0																		---	---	---	---
ROD1	9991	broad.mit.edu	37	9	114985973	114985975	+	3'UTR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114985973_114985975delAAA	uc004bfw.2	-	15					ROD1_uc004bfv.2_3'UTR|ROD1_uc004bfx.2_3'UTR|ROD1_uc011lwu.1_3'UTR|ROD1_uc004bfy.2_3'UTR|ROD1_uc004bfz.2_Intron	NM_005156	NP_005147			ROD1 regulator of differentiation 1 isoform 1						anatomical structure morphogenesis|mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1																		---	---	---	---
ROD1	9991	broad.mit.edu	37	9	115089492	115089493	+	Intron	DEL	AA	-	-	rs74373593		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115089492_115089493delAA	uc004bfw.2	-						ROD1_uc004bfv.2_Intron|ROD1_uc004bfx.2_Intron|ROD1_uc011lwu.1_Intron|ROD1_uc004bfy.2_Intron|ROD1_uc004bfz.2_Intron	NM_005156	NP_005147			ROD1 regulator of differentiation 1 isoform 1						anatomical structure morphogenesis|mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1																		---	---	---	---
ROD1	9991	broad.mit.edu	37	9	115094783	115094783	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115094783delA	uc004bfw.2	-						ROD1_uc004bfv.2_Intron|ROD1_uc004bfx.2_Intron|ROD1_uc011lwu.1_Intron|ROD1_uc004bfy.2_Intron|ROD1_uc004bfz.2_Intron	NM_005156	NP_005147			ROD1 regulator of differentiation 1 isoform 1						anatomical structure morphogenesis|mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1																		---	---	---	---
C9orf80	58493	broad.mit.edu	37	9	115468695	115468696	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115468695_115468696insT	uc004bgg.2	-						C9orf80_uc010muk.2_Intron	NM_021218	NP_067041			SOSSC protein						DNA repair|response to ionizing radiation	SOSS complex	protein binding				0																		---	---	---	---
SNX30	401548	broad.mit.edu	37	9	115550471	115550471	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115550471delT	uc004bgj.3	+							NM_001012994	NP_001013012			sorting nexin family member 30						cell communication|protein transport	cytoplasm	phosphatidylinositol binding				0																		---	---	---	---
SNX30	401548	broad.mit.edu	37	9	115572149	115572149	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
SNX30	401548	broad.mit.edu	37	9	115620036	115620039	+	Intron	DEL	GCAT	-	-	rs144243927		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115620036_115620039delGCAT	uc004bgj.3	+						SNX30_uc004bgi.3_Intron	NM_001012994	NP_001013012			sorting nexin family member 30						cell communication|protein transport	cytoplasm	phosphatidylinositol binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	115907172	115907173	+	IGR	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115907172_115907173insCA								C9orf109 (25048 upstream) : SLC31A2 (6065 downstream)																																			---	---	---	---
SLC31A2	1318	broad.mit.edu	37	9	115917977	115917977	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115917977delT	uc004bgq.2	+						SLC31A2_uc011lxb.1_Intron	NM_001860	NP_001851			solute carrier family 31 (copper transporters),							integral to plasma membrane	copper ion transmembrane transporter activity				0																		---	---	---	---
FKBP15	23307	broad.mit.edu	37	9	116030266	116030266	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116030266delA	uc010muu.1	-						CDC26_uc004bgw.2_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-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
ALAD	210	broad.mit.edu	37	9	116152317	116152318	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116152317_116152318insT	uc011lxf.1	-						ALAD_uc011lxe.1_Intron|ALAD_uc004bhl.3_Intron	NM_000031	NP_000022			delta-aminolevulinic acid dehydratase						heme biosynthetic process|protein homooligomerization	cytosol	identical protein binding|lead ion binding|porphobilinogen synthase activity|zinc ion binding				0					Aminolevulinic acid(DB00855)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	116169000	116169001	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116169000_116169001delAA								ALAD (5382 upstream) : POLE3 (517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	116196874	116196874	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116196874delT								C9orf43 (4997 upstream) : RGS3 (10137 downstream)																																			---	---	---	---
RGS3	5998	broad.mit.edu	37	9	116233856	116233856	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116233856delT	uc004bhq.2	+						RGS3_uc004bhr.2_Intron|RGS3_uc004bhs.2_Intron	NM_144488	NP_652759			regulator of G-protein signalling 3 isoform 6						inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	116426828	116426828	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116426828delA								RGS3 (66811 upstream) : ZNF618 (211734 downstream)																																			---	---	---	---
ZNF618	114991	broad.mit.edu	37	9	116666291	116666292	+	Intron	DEL	TT	-	-	rs80106051		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116666291_116666292delTT	uc004bid.2	+						ZNF618_uc004bib.1_Intron|ZNF618_uc004bic.2_Intron|ZNF618_uc011lxi.1_Intron|ZNF618_uc011lxj.1_Intron	NM_133374	NP_588615			zinc finger protein 618						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
COL27A1	85301	broad.mit.edu	37	9	117015575	117015576	+	Intron	INS	-	AAAG	AAAG	rs144800654	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117015575_117015576insAAAG	uc011lxl.1	+						COL27A1_uc004bii.2_Intron	NM_032888	NP_116277			collagen, type XXVII, alpha 1 precursor						cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	117321226	117321226	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117321226delT								DFNB31 (53496 upstream) : ATP6V1G1 (28768 downstream)																																			---	---	---	---
C9orf91	203197	broad.mit.edu	37	9	117401420	117401420	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117401420delT	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	117413556	117413556	+	IGR	DEL	T	-	-	rs74499238		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117413556delT								C9orf91 (4860 upstream) : TNFSF15 (138057 downstream)																																			---	---	---	---
TNC	3371	broad.mit.edu	37	9	117865709	117865709	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117865709delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	118167040	118167040	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118167040delA								DEC1 (2117 upstream) : C9orf27 (483506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	118639890	118639891	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118639890_118639891insT								DEC1 (474967 upstream) : C9orf27 (10655 downstream)																																			---	---	---	---
PAPPA	5069	broad.mit.edu	37	9	118946295	118946296	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118946295_118946296delAG	uc004bjn.2	+							NM_002581	NP_002572			pregnancy-associated plasma protein A						cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9																		---	---	---	---
PAPPA	5069	broad.mit.edu	37	9	119102989	119102989	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119102989delA	uc004bjn.2	+						PAPPA_uc011lxq.1_Intron	NM_002581	NP_002572			pregnancy-associated plasma protein A						cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	119179004	119179004	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119179004delA								PAPPA (14405 upstream) : ASTN2 (8503 downstream)																																			---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119194284	119194285	+	Intron	INS	-	A	A	rs146147807	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119194284_119194285insA	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|ASTN2_uc004bjo.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	119367321	119367322	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119367321_119367322delAG	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	119537865	119537868	+	Intron	DEL	AGGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119537865_119537868delAGGG	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	119596255	119596256	+	Intron	INS	-	AAA	AAA	rs142783305	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119596255_119596256insAAA	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	120148425	120148426	+	Intron	DEL	GA	-	-	rs113142800		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120148425_120148426delGA	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	120438777	120438777	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120438777delA								ASTN2 (261460 upstream) : TLR4 (27683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	120536281	120536281	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120536281delT								TLR4 (56517 upstream) : None (None downstream)																																			---	---	---	---
DBC1	1620	broad.mit.edu	37	9	121996138	121996138	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121996138delT	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	122786320	122786327	+	IGR	DEL	ACACACAC	-	-	rs66555312		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122786320_122786327delACACACAC								DBC1 (654581 upstream) : MIR147 (220930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122798503	122798503	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122798503delA								DBC1 (666764 upstream) : MIR147 (208754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122917311	122917330	+	IGR	DEL	AAGAAAGAAAGAAAGAAAGA	-	-	rs72437977		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122917311_122917330delAAGAAAGAAAGAAAGAAAGA								DBC1 (785572 upstream) : MIR147 (89927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	123359336	123359337	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123359336_123359337insT								CDK5RAP2 (16899 upstream) : MEGF9 (3754 downstream)																																			---	---	---	---
MEGF9	1955	broad.mit.edu	37	9	123421596	123421596	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123421596delT	uc004bkj.1	-						MEGF9_uc011lyb.1_Intron|MEGF9_uc004bkk.3_3'UTR	NM_001080497	NP_001073966			multiple EGF-like-domains 9							integral to membrane	calcium ion binding				0																		---	---	---	---
FBXW2	26190	broad.mit.edu	37	9	123538106	123538106	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123538106delT	uc004bkl.1	-						FBXW2_uc011lyc.1_Intron|FBXW2_uc004bkn.2_Intron|FBXW2_uc004bkm.1_Intron|FBXW2_uc010mvj.1_Intron	NM_012164	NP_036296			F-box and WD repeat domain containing 2						proteolysis		protein binding|ubiquitin-protein ligase activity			urinary_tract(1)|ovary(1)|pancreas(1)|skin(1)	4																		---	---	---	---
PSMD5	5711	broad.mit.edu	37	9	123582114	123582114	+	Intron	DEL	A	-	-	rs112375425		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123582114delA	uc004bko.2	-						PSMD5_uc011lye.1_Intron	NM_005047	NP_005038			proteasome 26S non-ATPase subunit 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|proteasome regulatory particle assembly|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	123700706	123700706	+	IGR	DEL	G	-	-	rs76817096	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123700706delG								TRAF1 (9227 upstream) : C5 (13910 downstream)																																			---	---	---	---
C5	727	broad.mit.edu	37	9	123751833	123751833	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123751833delT	uc004bkv.2	-							NM_001735	NP_001726			complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)													---	---	---	---
C5	727	broad.mit.edu	37	9	123795290	123795291	+	Intron	DEL	GG	-	-	rs111675093		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123795290_123795291delGG	uc004bkv.2	-						C5_uc010mvm.1_Intron|C5_uc010mvn.1_Intron	NM_001735	NP_001726			complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)													---	---	---	---
GSN	2934	broad.mit.edu	37	9	124074857	124074857	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124074857delA	uc004blf.1	+						GSN_uc004bld.1_Intron|GSN_uc010mvq.1_Intron|GSN_uc010mvr.1_Intron|GSN_uc010mvu.1_Intron|GSN_uc010mvt.1_Intron|GSN_uc010mvs.1_Intron|GSN_uc004ble.1_Intron|GSN_uc010mvv.1_Intron|GSN_uc011lyh.1_Intron|GSN_uc011lyi.1_Intron|GSN_uc011lyj.1_Intron|GSN_uc004blg.1_Intron	NM_000177	NP_000168			gelsolin isoform a precursor						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3																		---	---	---	---
GSN	2934	broad.mit.edu	37	9	124089775	124089775	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124089775delG	uc004blf.1	+						GSN_uc004bld.1_Intron|GSN_uc010mvq.1_Intron|GSN_uc010mvr.1_Intron|GSN_uc010mvu.1_Intron|GSN_uc010mvt.1_Intron|GSN_uc010mvs.1_Intron|GSN_uc004ble.1_Intron|GSN_uc010mvv.1_Intron|GSN_uc011lyh.1_Intron|GSN_uc011lyi.1_Intron|GSN_uc011lyj.1_Intron|GSN_uc004blg.1_Intron	NM_000177	NP_000168			gelsolin isoform a precursor						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3																		---	---	---	---
STOM	2040	broad.mit.edu	37	9	124127420	124127420	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124127420delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	124204990	124204991	+	IGR	INS	-	GTGT	GTGT	rs148747239	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124204990_124204991insGTGT								STOM (72445 upstream) : GGTA1 (2278 downstream)																																			---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124372336	124372337	+	Intron	DEL	TG	-	-	rs67948448		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124372336_124372337delTG	uc004bln.2	+							NM_032552	NP_115941			disabled homolog 2 interacting protein isoform						activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124452035	124452036	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124452035_124452036insC	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	124813028	124813028	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124813028delC	uc004blt.1	-						TTLL11_uc011lyl.1_Intron|TTLL11_uc004blr.2_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	124922805	124922805	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124922805delT	uc004blw.2	+						NDUFA8_uc004blv.2_5'Flank|MORN5_uc011lyn.1_Intron|MORN5_uc011lyo.1_Intron	NM_198469	NP_940871			MORN repeat containing 5												0																		---	---	---	---
MRRF	92399	broad.mit.edu	37	9	125048045	125048045	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125048045delT	uc004bmb.2	+						MRRF_uc004bmc.2_Intron|MRRF_uc011lyq.1_3'UTR|MRRF_uc010mvz.1_Intron|MRRF_uc010mwa.2_Intron|MRRF_uc011lyr.1_Intron|MRRF_uc004bmd.2_Intron|MRRF_uc004bme.2_Intron	NM_138777	NP_620132			mitochondrial ribosome recycling factor isoform						ribosome disassembly|translation	mitochondrion	sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	125111427	125111427	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125111427delT								MRRF (25687 upstream) : PTGS1 (21382 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	125216796	125216797	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125216796_125216797delAA								PTGS1 (58815 upstream) : OR1J2 (14043 downstream)																																	OREG0019465	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
OR1J2	26740	broad.mit.edu	37	9	125268087	125268087	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125268087delT	uc004bmj.1	+							NM_054107	NP_473448			olfactory receptor, family 1, subfamily J,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|pancreas(1)|breast(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	125345567	125345567	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125345567delA								OR1L8 (14811 upstream) : OR1Q1 (31450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	125534679	125534680	+	IGR	DEL	CA	-	-	rs113943492		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125534679_125534680delCA								OR1L6 (21619 upstream) : OR5C1 (16532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	125568901	125568902	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125568901_125568902delAA								OR1K1 (5550 upstream) : PDCL (11721 downstream)																																			---	---	---	---
PDCL	5082	broad.mit.edu	37	9	125583692	125583693	+	Intron	INS	-	AC	AC	rs148493349	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125583692_125583693insAC	uc004bmz.1	-						PDCL_uc004bna.2_Intron	NM_005388	NP_005379			phosducin-like						signal transduction|visual perception						0																		---	---	---	---
RC3H2	54542	broad.mit.edu	37	9	125613299	125613300	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125613299_125613300insT	uc010mwc.1	-						uc004bnb.1_5'Flank|RC3H2_uc004bnc.2_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																		---	---	---	---
ZBTB6	10773	broad.mit.edu	37	9	125675792	125675792	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125675792delT	uc004bnh.2	-							NM_006626	NP_006617			zinc finger and BTB domain containing 6						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
STRBP	55342	broad.mit.edu	37	9	126030153	126030153	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126030153delC	uc004bns.2	-						STRBP_uc004bnt.2_Intron|STRBP_uc004bnu.2_Intron|STRBP_uc004bnv.2_Intron	NM_018387	NP_060857			spermatid perinuclear RNA binding protein						multicellular organismal development	cytoplasm|nucleus	DNA binding			breast(1)|skin(1)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126180165	126180165	+	Intron	DEL	G	-	-	rs113918463		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126180165delG	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron|DENND1A_uc010mwh.1_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126212910	126212910	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126212910delT	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126308831	126308831	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126308831delA	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126515223	126515223	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126515223delT	uc004bnz.1	-						DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	126970031	126970033	+	IGR	DEL	TTT	-	-	rs72449391		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126970031_126970033delTTT								LHX2 (174589 upstream) : NEK6 (49853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	126979528	126979529	+	IGR	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126979528_126979529insCA								LHX2 (184086 upstream) : NEK6 (40357 downstream)																																			---	---	---	---
NR6A1	2649	broad.mit.edu	37	9	127303560	127303561	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127303560_127303561insA	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																		---	---	---	---
NR6A1	2649	broad.mit.edu	37	9	127334202	127334204	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127334202_127334204delAAA	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																		---	---	---	---
SCAI	286205	broad.mit.edu	37	9	127731224	127731227	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127731224_127731227delAAAA	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	127736560	127736560	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127736560delA	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	127765212	127765212	+	Intron	DEL	A	-	-	rs79884030		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127765212delA	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	127911822	127911822	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127911822delA	uc004bpg.3	-	7					PPP6C_uc010mwv.2_3'UTR|PPP6C_uc010mww.2_3'UTR|PPP6C_uc011lzr.1_3'UTR	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	128069548	128069551	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128069548_128069551delAAAA	uc010mwx.2	+						GAPVD1_uc004bpo.2_Intron|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	128179199	128179199	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128179199delT								GAPVD1 (51910 upstream) : MAPKAP1 (20475 downstream)																																			---	---	---	---
MAPKAP1	79109	broad.mit.edu	37	9	128306590	128306590	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128306590delT	uc004bpv.2	-						MAPKAP1_uc011lzt.1_Intron|MAPKAP1_uc010mwz.2_Intron|MAPKAP1_uc011lzu.1_Intron|MAPKAP1_uc011lzv.1_Intron|MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Intron|MAPKAP1_uc004bpz.2_Intron|MAPKAP1_uc010mxa.2_Intron|MAPKAP1_uc010mxb.1_Intron|MAPKAP1_uc004bqa.2_Intron	NM_001006617	NP_001006618			mitogen-activated protein kinase associated						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|response to stress|T cell costimulation	cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	Ras GTPase binding			ovary(2)|lung(2)	4																		---	---	---	---
MAPKAP1	79109	broad.mit.edu	37	9	128402392	128402392	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128402392delT	uc004bpv.2	-						MAPKAP1_uc011lzu.1_Intron|MAPKAP1_uc011lzv.1_Intron|MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Intron|MAPKAP1_uc004bpz.2_Intron|MAPKAP1_uc010mxa.2_Intron|MAPKAP1_uc010mxb.1_Intron|MAPKAP1_uc004bqa.2_Intron|MAPKAP1_uc010mxc.1_Intron	NM_001006617	NP_001006618			mitogen-activated protein kinase associated						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|response to stress|T cell costimulation	cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	Ras GTPase binding			ovary(2)|lung(2)	4																		---	---	---	---
FAM125B	89853	broad.mit.edu	37	9	129267933	129267934	+	3'UTR	INS	-	TG	TG	rs113188622		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129267933_129267934insTG	uc004bqh.1	+	10					FAM125B_uc011lzy.1_3'UTR|FAM125B_uc010mxd.2_3'UTR|FAM125B_uc010mxe.1_5'Flank	NM_033446	NP_258257			hypothetical protein LOC89853 isoform 1						protein transport	late endosome membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	129301027	129301027	+	IGR	DEL	C	-	-	rs7849116	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129301027delC								FAM125B (27328 upstream) : LMX1B (75721 downstream)																																			---	---	---	---
LMX1B	4010	broad.mit.edu	37	9	129391862	129391863	+	Intron	INS	-	TG	TG	rs141886141	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129391862_129391863insTG	uc004bqj.2	+						LMX1B_uc004bqi.2_Intron|LMX1B_uc011maa.1_Intron	NM_002316	NP_002307			LIM homeobox transcription factor 1, beta						dorsal/ventral pattern formation|in utero embryonic development	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														Nail-Patella_Syndrome				---	---	---	---
RALGPS1	9649	broad.mit.edu	37	9	129687837	129687838	+	Intron	DEL	AA	-	-	rs113554319		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129687837_129687838delAA	uc004bqo.1	+						RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.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																		---	---	---	---
RALGPS1	9649	broad.mit.edu	37	9	129714935	129714936	+	Intron	INS	-	GT	GT	rs58186926		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129714935_129714936insGT	uc004bqo.1	+						RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.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																		---	---	---	---
RALGPS1	9649	broad.mit.edu	37	9	129864808	129864808	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129864808delT	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																		---	---	---	---
GARNL3	84253	broad.mit.edu	37	9	130038660	130038660	+	Intron	DEL	T	-	-	rs34868250		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130038660delT	uc011mae.1	+						GARNL3_uc011mad.1_Intron	NM_032293	NP_115669			GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
STXBP1	6812	broad.mit.edu	37	9	130421912	130421912	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130421912delT	uc004brl.2	+						STXBP1_uc004brk.2_Intron	NM_001032221	NP_001027392			syntaxin binding protein 1 isoform b						axon target recognition|energy reserve metabolic process|glutamate secretion|negative regulation of synaptic transmission, GABAergic|neurotransmitter secretion|platelet aggregation|platelet degranulation|protein transport|regulation of insulin secretion|regulation of synaptic vesicle priming|synaptic vesicle maturation|vesicle docking involved in exocytosis	cytosol|mitochondrion|plasma membrane|platelet alpha granule|protein complex	identical protein binding|syntaxin-1 binding|syntaxin-2 binding			skin(1)	1																		---	---	---	---
STXBP1	6812	broad.mit.edu	37	9	130437469	130437470	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130437469_130437470insT	uc004brl.2	+						STXBP1_uc004brk.2_Intron	NM_001032221	NP_001027392			syntaxin binding protein 1 isoform b						axon target recognition|energy reserve metabolic process|glutamate secretion|negative regulation of synaptic transmission, GABAergic|neurotransmitter secretion|platelet aggregation|platelet degranulation|protein transport|regulation of insulin secretion|regulation of synaptic vesicle priming|synaptic vesicle maturation|vesicle docking involved in exocytosis	cytosol|mitochondrion|plasma membrane|platelet alpha granule|protein complex	identical protein binding|syntaxin-1 binding|syntaxin-2 binding			skin(1)	1																		---	---	---	---
FPGS	2356	broad.mit.edu	37	9	130574362	130574362	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130574362delA	uc004bsg.1	+						FPGS_uc004bsh.1_Intron|FPGS_uc011mal.1_Intron|FPGS_uc004bsi.1_Intron	NM_004957	NP_004948			folylpolyglutamate synthase isoform a precursor						folic acid metabolic process|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|one-carbon metabolic process	cytosol|mitochondrial matrix	ATP binding|tetrahydrofolylpolyglutamate synthase activity				0					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	130762913	130762913	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130762913delT								FAM102A (20418 upstream) : NAIF1 (60600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	130808739	130808739	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130808739delA								FAM102A (66244 upstream) : NAIF1 (14774 downstream)																																			---	---	---	---
SLC25A25	114789	broad.mit.edu	37	9	130838128	130838129	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130838128_130838129insA	uc004btb.2	+							NM_001006641	NP_001006642			solute carrier family 25, member 25 isoform b						transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding				0																		---	---	---	---
DNM1	1759	broad.mit.edu	37	9	131011936	131011936	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131011936delA	uc011mau.1	+						DNM1_uc011mat.1_Intron|DNM1_uc004bub.1_Intron|DNM1_uc004buc.1_Intron|DNM1_uc004bud.3_Intron	NM_004408	NP_004399			dynamin 1 isoform 1						receptor-mediated endocytosis	microtubule	GTP binding|GTPase activity			ovary(2)	2																		---	---	---	---
DNM1	1759	broad.mit.edu	37	9	131012114	131012114	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131012114delA	uc011mau.1	+						DNM1_uc011mat.1_Intron|DNM1_uc004bub.1_Intron|DNM1_uc004buc.1_Intron|DNM1_uc004bud.3_Intron	NM_004408	NP_004399			dynamin 1 isoform 1						receptor-mediated endocytosis	microtubule	GTP binding|GTPase activity			ovary(2)	2																		---	---	---	---
ODF2	4957	broad.mit.edu	37	9	131252567	131252567	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131252567delT	uc011mbd.1	+						ODF2_uc011maz.1_Intron|ODF2_uc011mbb.1_Intron|ODF2_uc011mbc.1_Intron|ODF2_uc004bva.2_Intron|ODF2_uc004bvb.2_Intron|ODF2_uc011mbe.1_Intron|ODF2_uc004bvc.2_Intron|ODF2_uc011mbf.1_Intron|ODF2_uc004bvd.3_Intron|ODF2_uc004bve.2_Intron	NM_002540	NP_002531			outer dense fiber of sperm tails 2 isoform 1						cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centriole|cilium|cytosol|microtubule|spindle pole	protein binding|structural molecule activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	131305980	131305980	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131305980delA								GLE1 (1401 upstream) : SPTAN1 (8886 downstream)																																			---	---	---	---
SPTAN1	6709	broad.mit.edu	37	9	131360554	131360556	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131360554_131360556delTTT	uc004bvl.3	+						SPTAN1_uc011mbg.1_Intron|SPTAN1_uc011mbh.1_Intron|SPTAN1_uc004bvm.3_Intron|SPTAN1_uc004bvn.3_Intron	NM_003127	NP_003118			spectrin, alpha, non-erythrocytic 1						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																		---	---	---	---
PKN3	29941	broad.mit.edu	37	9	131478876	131478880	+	Intron	DEL	CAAAA	-	-	rs10819432	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131478876_131478880delCAAAA	uc004bvw.2	+						PKN3_uc010myh.2_Intron|PKN3_uc011mbk.1_Intron	NM_013355	NP_037487			protein kinase PKNbeta						signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein binding|protein kinase C activity			stomach(2)|lung(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	131545104	131545104	+	IGR	DEL	T	-	-	rs4836626	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131545104delT								ZER1 (10906 upstream) : TBC1D13 (4406 downstream)																																			---	---	---	---
PHYHD1	254295	broad.mit.edu	37	9	131689650	131689650	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131689650delT	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)	---	---	---	---
PHYHD1	254295	broad.mit.edu	37	9	131692559	131692559	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131692559delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	132020415	132020415	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132020415delA								IER5L (79875 upstream) : C9orf106 (62880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132034828	132034828	+	IGR	DEL	C	-	-	rs34796865		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132034828delC								IER5L (94288 upstream) : C9orf106 (48467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132075640	132075640	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132075640delA								IER5L (135100 upstream) : C9orf106 (7655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132156475	132156476	+	IGR	INS	-	G	G	rs34978536		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132156475_132156476insG								C9orf106 (71593 upstream) : C9orf50 (218030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132203742	132203742	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132203742delT								C9orf106 (118860 upstream) : C9orf50 (170764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132328311	132328311	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132328311delT								C9orf106 (243429 upstream) : C9orf50 (46195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132338374	132338375	+	Intron	INS	-	CACA	CACA	rs148700093	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132338374_132338375insCACA	uc004bya.1	+											Homo sapiens cDNA clone IMAGE:4812570.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	132369756	132369757	+	IGR	INS	-	GTGT	GTGT	rs3054756		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132369756_132369757insGTGT								C9orf106 (284874 upstream) : C9orf50 (4749 downstream)																																			---	---	---	---
ASB6	140459	broad.mit.edu	37	9	132402445	132402445	+	Intron	DEL	A	-	-	rs34255049		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132402445delA	uc004byf.1	-						ASB6_uc004bye.1_Intron|ASB6_uc004byg.1_Intron|ASB6_uc011mbt.1_Intron|ASB6_uc010myx.1_Intron	NM_017873	NP_060343			ankyrin repeat and SOCS box-containing 6 isoform						intracellular signal transduction	cytoplasm					0		Ovarian(14;0.00556)																---	---	---	---
PTGES	9536	broad.mit.edu	37	9	132517154	132517155	+	5'Flank	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132517154_132517155delTT	uc004byi.2	-						PTGES_uc010myy.2_5'Flank|PTGES_uc004byj.2_5'Flank	NM_004878	NP_004869			prostaglandin E synthase						prostaglandin biosynthetic process|signal transduction	integral to membrane|membrane fraction	glutathione binding|prostaglandin-E synthase activity			skin(1)	1		Ovarian(14;0.00556)																---	---	---	---
USP20	10868	broad.mit.edu	37	9	132629876	132629876	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132629876delC	uc004bys.2	+						USP20_uc004byr.2_Intron|USP20_uc004byt.1_Intron	NM_001110303	NP_001103773			ubiquitin specific protease 20						endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|ubiquitin thiolesterase activity|zinc ion binding			lung(1)|breast(1)	2		Ovarian(14;0.00556)																---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132660778	132660778	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132660778delT	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc011mbu.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848			formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)				T	MLL	AML								---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132760794	132760795	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132760794_132760795delAA	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron	NM_015033	NP_055848			formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)				T	MLL	AML								---	---	---	---
NCS1	23413	broad.mit.edu	37	9	132992991	132992994	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132992991_132992994delAAAA	uc004bzi.2	+						NCS1_uc010myz.1_Intron	NM_014286	NP_055101			frequenin homolog isoform 1						negative regulation of calcium ion transport via voltage-gated calcium channel activity|regulation of neuron projection development	cell junction|Golgi cisterna membrane|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	133070899	133070899	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133070899delT								NCS1 (71316 upstream) : ASS1 (249195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	133226294	133226294	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133226294delA								NCS1 (226711 upstream) : ASS1 (93800 downstream)																																			---	---	---	---
EXOSC2	23404	broad.mit.edu	37	9	133579921	133579921	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133579921delA	uc004bzu.2	+	9					EXOSC2_uc011mbz.1_3'UTR|EXOSC2_uc011mca.1_RNA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	133852689	133852690	+	IGR	DEL	CA	-	-	rs34587625		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133852689_133852690delCA								FIBCD1 (38234 upstream) : LAMC3 (31814 downstream)																																			---	---	---	---
NUP214	8021	broad.mit.edu	37	9	134049820	134049822	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134049820_134049822delTTT	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								---	---	---	---
FAM78A	286336	broad.mit.edu	37	9	134144871	134144872	+	Intron	DEL	TT	-	-	rs111550579		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134144871_134144872delTT	uc004cak.2	-						FAM78A_uc004caj.2_Intron	NM_033387	NP_203745			hypothetical protein LOC286336											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	134597497	134597497	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134597497delA	uc004cbc.2	-						RAPGEF1_uc010mzn.2_Intron|RAPGEF1_uc004cbd.2_Intron	NM_005312	NP_005303			guanine nucleotide-releasing factor 2 isoform a						activation of MAPKK activity|nerve growth factor receptor signaling pathway|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome	guanyl-nucleotide exchange factor activity|SH3 domain binding			lung(3)|ovary(2)|breast(1)|skin(1)	7		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)														---	---	---	---
MED27	9442	broad.mit.edu	37	9	134953129	134953129	+	Intron	DEL	A	-	-	rs76460072		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134953129delA	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)														---	---	---	---
NTNG2	84628	broad.mit.edu	37	9	135108200	135108200	+	Intron	DEL	G	-	-	rs77960183		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135108200delG	uc004cbh.2	+							NM_032536	NP_115925			netrin G2 precursor						axonogenesis	anchored to plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)														---	---	---	---
C9orf171	389799	broad.mit.edu	37	9	135292506	135292506	+	Intron	DEL	T	-	-	rs71990783		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135292506delT	uc004cbn.2	+						C9orf171_uc004cbo.2_Intron	NM_207417	NP_997300			hypothetical protein LOC389799											ovary(4)|large_intestine(1)	5																		---	---	---	---
C9orf98	158067	broad.mit.edu	37	9	135690206	135690206	+	Intron	DEL	A	-	-	rs140406073		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135690206delA	uc004cbu.1	-						C9orf98_uc010mzx.1_Intron|C9orf98_uc004cbv.1_Intron	NM_152572	NP_689785			putative adenylate kinase-like protein C9orf98							cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;4.89e-06)|Epithelial(140;0.00016)														---	---	---	---
C9orf98	158067	broad.mit.edu	37	9	135695600	135695603	+	Intron	DEL	AAAA	-	-	rs66490117		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135695600_135695603delAAAA	uc004cbu.1	-						C9orf98_uc010mzx.1_Intron|C9orf98_uc004cbv.1_Intron	NM_152572	NP_689785			putative adenylate kinase-like protein C9orf98							cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;4.89e-06)|Epithelial(140;0.00016)														---	---	---	---
C9orf98	158067	broad.mit.edu	37	9	135713638	135713639	+	Intron	INS	-	A	A	rs147876772	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135713638_135713639insA	uc004cbu.1	-						C9orf98_uc010mzx.1_Intron|C9orf98_uc004cbv.1_Intron	NM_152572	NP_689785			putative adenylate kinase-like protein C9orf98							cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;4.89e-06)|Epithelial(140;0.00016)														---	---	---	---
TSC1	7248	broad.mit.edu	37	9	135790578	135790578	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135790578delA	uc004cca.2	-						TSC1_uc004ccb.3_Intron|TSC1_uc011mcq.1_Intron|TSC1_uc011mcr.1_Intron|TSC1_uc011mcs.1_Intron|TSC1_uc004ccc.1_Intron|TSC1_uc004ccd.2_Intron|TSC1_uc004cce.1_Intron	NM_000368	NP_000359			tuberous sclerosis 1 protein isoform 1						activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus	cell cortex|lamellipodium|membrane|TSC1-TSC2 complex	chaperone binding|protein N-terminus binding	p.?(1)		lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1)	14				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)				D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				---	---	---	---
RALGDS	5900	broad.mit.edu	37	9	136032047	136032047	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136032047delA	uc011mcw.1	-						GBGT1_uc004ccx.2_Intron|GBGT1_uc010nab.2_Intron|GBGT1_uc011mcx.1_Intron|GBGT1_uc004ccw.2_Intron|GBGT1_uc010nac.1_Intron|GBGT1_uc004ccy.1_Intron	NM_001042368	NP_001035827			ral guanine nucleotide dissociation stimulator						nerve growth factor receptor signaling pathway|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol	Ral guanyl-nucleotide exchange factor activity			large_intestine(1)|lung(1)|ovary(1)	3				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)				T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
Unknown	0	broad.mit.edu	37	9	136495224	136495224	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136495224delC								FAM163B (49879 upstream) : DBH (6261 downstream)																																			---	---	---	---
SARDH	1757	broad.mit.edu	37	9	136590812	136590813	+	Intron	INS	-	AAAC	AAAC	rs150689824	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136590812_136590813insAAAC	uc004cep.3	-						SARDH_uc004ceo.2_Intron|SARDH_uc011mdn.1_Intron|SARDH_uc011mdo.1_Intron	NM_001134707	NP_001128179			sarcosine dehydrogenase precursor						glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|sarcosine dehydrogenase activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)														---	---	---	---
SARDH	1757	broad.mit.edu	37	9	136601512	136601513	+	Intron	INS	-	T	T	rs141800614	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136601512_136601513insT	uc004cep.3	-						SARDH_uc004ceo.2_Intron|SARDH_uc011mdn.1_Intron|SARDH_uc011mdo.1_Intron	NM_001134707	NP_001128179			sarcosine dehydrogenase precursor						glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|sarcosine dehydrogenase activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)														---	---	---	---
VAV2	7410	broad.mit.edu	37	9	136694762	136694762	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136694762delT	uc004ces.2	-						VAV2_uc004cer.2_Intron	NM_001134398	NP_001127870			vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)														---	---	---	---
VAV2	7410	broad.mit.edu	37	9	136707081	136707082	+	Intron	INS	-	C	C	rs145290954	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136707081_136707082insC	uc004ces.2	-						VAV2_uc004cer.2_Intron	NM_001134398	NP_001127870			vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)														---	---	---	---
VAV2	7410	broad.mit.edu	37	9	136718743	136718743	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136718743delC	uc004ces.2	-						VAV2_uc004cer.2_Intron	NM_001134398	NP_001127870			vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	137376403	137376403	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137376403delA								RXRA (43972 upstream) : COL5A1 (157249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	137507402	137507405	+	IGR	DEL	ACAC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137507402_137507405delACAC								RXRA (174971 upstream) : COL5A1 (26247 downstream)																																			---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137567897	137567897	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137567897delT	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	137693635	137693637	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137693635_137693637delAAA	uc004cfe.2	+							NM_000093	NP_000084			alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	137920892	137920892	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137920892delA								FCN1 (111083 upstream) : OLFM1 (46197 downstream)																																			---	---	---	---
OLFM1	10439	broad.mit.edu	37	9	137983500	137983501	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137983500_137983501delCA	uc010nar.2	+						OLFM1_uc004cfl.3_Intron|OLFM1_uc004cfk.3_Intron|OLFM1_uc004cfm.3_Intron	NM_014279	NP_055094			olfactomedin related ER localized protein						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	138345438	138345438	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138345438delT								OLFM1 (332407 upstream) : KIAA0649 (26210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	138361604	138361606	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138361604_138361606delTTT	uc004cfp.3	-											Homo sapiens cDNA clone IMAGE:5295490.																														---	---	---	---
C9orf116	138162	broad.mit.edu	37	9	138389246	138389247	+	Intron	INS	-	T	T	rs139466485	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138389246_138389247insT	uc004cft.1	-						C9orf116_uc004cfs.1_Intron|C9orf116_uc004cfu.1_Intron	NM_001048265	NP_001041730			hypothetical protein LOC138162 isoform 1												0				OV - Ovarian serous cystadenocarcinoma(145;7.39e-08)|Epithelial(140;5.19e-07)|all cancers(34;1.04e-05)														---	---	---	---
SOHLH1	402381	broad.mit.edu	37	9	138588009	138588010	+	Intron	INS	-	C	C	rs138443831	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138588009_138588010insC	uc004cgl.2	-						SOHLH1_uc010nbe.2_Intron	NM_001012415	NP_001012415			spermatogenesis and oogenesis specific basic						cell differentiation|multicellular organismal development|oogenesis|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			breast(1)|central_nervous_system(1)	2		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)														---	---	---	---
KCNT1	57582	broad.mit.edu	37	9	138635671	138635671	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138635671delG	uc011mdq.1	+						KCNT1_uc011mdr.1_Intron|KCNT1_uc010nbf.2_Intron	NM_020822	NP_065873			potassium channel, subfamily T, member 1							membrane	binding|calcium-activated potassium channel activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)														---	---	---	---
NACC2	138151	broad.mit.edu	37	9	138972434	138972434	+	Intron	DEL	T	-	-	rs7044661	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138972434delT	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																		---	---	---	---
SNAPC4	6621	broad.mit.edu	37	9	139286008	139286015	+	Intron	DEL	GTCCTTAC	-	-	rs144719206		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139286008_139286015delGTCCTTAC	uc004chh.2	-							NM_003086	NP_003077			small nuclear RNA activating complex,						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	139339692	139339692	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139339692delA	uc004chx.2	-						SEC16A_uc004chp.2_Intron|SEC16A_uc004chq.2_Intron|SEC16A_uc011mea.1_Intron|SEC16A_uc004chr.2_Intron|SEC16A_uc004chs.2_Intron|SEC16A_uc004cht.2_Intron|SEC16A_uc004chu.2_Intron|SEC16A_uc004chv.3_Intron|SEC16A_uc004chw.2_Intron|SEC16A_uc010nbn.2_Intron	NM_014866	NP_055681			SEC16 homolog A						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane					0		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	139461466	139461467	+	IGR	INS	-	AAGGCGGACACGCGGGAAA	AAGGCGGACACGCGGGAAA	rs148354434	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139461466_139461467insAAGGCGGACACGCGGGAAA								NOTCH1 (21228 upstream) : EGFL7 (91841 downstream)																																			---	---	---	---
ENTPD2	954	broad.mit.edu	37	9	139946995	139946995	+	Intron	DEL	T	-	-	rs7024097	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139946995delT	uc004ckw.1	-						ENTPD2_uc004ckv.1_5'Flank|ENTPD2_uc004ckx.1_Intron	NM_203468	NP_982293			ectonucleoside triphosphate diphosphohydrolase 2							integral to membrane	ATP binding				0	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)														---	---	---	---
LOC100289341	100289341	broad.mit.edu	37	9	139979514	139979514	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139979514delT	uc004clb.3	-	1					MAN1B1_uc004clc.2_5'Flank|MAN1B1_uc011meo.1_5'Flank|MAN1B1_uc011mep.1_5'Flank|MAN1B1_uc004cld.2_5'Flank|MAN1B1_uc010ncc.2_5'Flank	NR_027447				SubName: Full=Putative uncharacterized protein; Flags: Fragment;												0																		---	---	---	---
MAN1B1	11253	broad.mit.edu	37	9	139989030	139989030	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139989030delA	uc004cld.2	+						MAN1B1_uc004clc.2_Intron|MAN1B1_uc011meo.1_Intron|MAN1B1_uc011mep.1_Intron|MAN1B1_uc010ncc.2_Intron	NM_016219	NP_057303			alpha 1,2-mannosidase						oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|endoplasmic reticulum quality control compartment|integral to membrane	alpha-mannosidase activity|calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(1)|central_nervous_system(1)	2	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)														---	---	---	---
COBRA1	25920	broad.mit.edu	37	9	140153484	140153484	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140153484delA	uc004cmm.3	+							NM_015456	NP_056271			cofactor of BRCA1						negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleoplasm	protein binding				0	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.137)	OV - Ovarian serous cystadenocarcinoma(145;9.42e-05)|Epithelial(140;0.000766)														---	---	---	---
EXD3	54932	broad.mit.edu	37	9	140221374	140221374	+	Intron	DEL	A	-	-	rs78800758		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140221374delA	uc004cmp.2	-						C9orf167_uc011mew.1_Intron|EXD3_uc010ncf.1_Intron	NM_017820	NP_060290			exonuclease 3'-5' domain containing 3						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0																		---	---	---	---
PNPLA7	375775	broad.mit.edu	37	9	140367902	140367902	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140367902delA	uc004cnf.2	-						C9orf167_uc011mew.1_Intron|PNPLA7_uc004cnd.1_Intron|PNPLA7_uc004cne.1_Intron|PNPLA7_uc011mfa.1_Intron|PNPLA7_uc010ncj.1_Intron	NM_152286	NP_689499			patatin-like phospholipase domain containing 7						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	140421744	140421745	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140421744_140421745insA	uc004cnf.2	-						PNPLA7_uc010ncj.1_Intron	NM_152286	NP_689499			patatin-like phospholipase domain containing 7						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	140553025	140553025	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140553025delT	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)														---	---	---	---
EHMT1	79813	broad.mit.edu	37	9	140649141	140649142	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140649141_140649142insT	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)														---	---	---	---
MIR602	693187	broad.mit.edu	37	9	140732961	140732961	+	RNA	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140732961delC	hsa-mir-602|MI0003615	+			c.91delC																				0																		---	---	---	---
CACNA1B	774	broad.mit.edu	37	9	140830235	140830235	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140830235delT	uc004cog.2	+							NM_000718	NP_000709			calcium channel, voltage-dependent, N type,						membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)													---	---	---	---
ZMYND11	10771	broad.mit.edu	37	10	188669	188670	+	Intron	DEL	TA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:188669_188670delTA	uc010pzt.1	+						ZMYND11_uc001ifk.2_Intron|ZMYND11_uc010pzu.1_Intron|ZMYND11_uc010pzv.1_Intron|ZMYND11_uc010pzw.1_Intron|ZMYND11_uc001ifm.2_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	749938	749938	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:749938delT								DIP2C (14330 upstream) : LARP4B (105546 downstream)																																			---	---	---	---
LARP4B	23185	broad.mit.edu	37	10	890939	890939	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:890939delT	uc001ifs.1	-	5	528	c.487delA	c.(487-489)ACAfs	p.T163fs		NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	163	HTH La-type RNA-binding.						nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1061538	1061570	+	Intron	DEL	CTGGGGTCCTGAGCGCTGAGCCTGGGAGTGGAC	-	-	rs71731536	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1061538_1061570delCTGGGGTCCTGAGCGCTGAGCCTGGGAGTGGAC	uc001ift.2	+						GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473			G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)														---	---	---	---
ADARB2	105	broad.mit.edu	37	10	1255478	1255495	+	Intron	DEL	CCCACACCCATGCCATCA	-	-	rs36221033		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1255478_1255495delCCCACACCCATGCCATCA	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	1588206	1588206	+	Intron	DEL	A	-	-	rs140592631		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1588206delA	uc009xhq.2	-						uc001ign.2_Intron	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	1652244	1652245	+	Intron	DEL	TT	-	-	rs111879447		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1652244_1652245delTT	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	2103592	2103593	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2103592_2103593delTG								ADARB2 (323874 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	5279052	5279052	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5279052delA								AKR1C4 (18142 upstream) : UCN3 (127924 downstream)																																			---	---	---	---
UCN3	114131	broad.mit.edu	37	10	5412923	5412924	+	Intron	INS	-	TA	TA	rs138555105	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5412923_5412924insTA	uc001ihx.1	+							NM_053049	NP_444277			urocortin 3 preproprotein							extracellular region	hormone activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	5618242	5618255	+	IGR	DEL	CTCTCTCTCTGTCT	-	-	rs72204145		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5618242_5618255delCTCTCTCTCTGTCT								CALML3 (50017 upstream) : ASB13 (62565 downstream)																																			---	---	---	---
C10orf18	54906	broad.mit.edu	37	10	5775462	5775462	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5775462delA	uc001iij.2	+						C10orf18_uc001iik.2_Intron	NM_017782	NP_060252			hypothetical protein LOC54906											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	5862951	5862951	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5862951delT								GDI2 (7439 upstream) : ANKRD16 (40740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	6320236	6320236	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6320236delT								PFKFB3 (42731 upstream) : PRKCQ (148869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	6706193	6706193	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6706193delT								PRKCQ (83955 upstream) : SFMBT2 (498056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	6735067	6735068	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6735067_6735068delGT								PRKCQ (112829 upstream) : SFMBT2 (469181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	7491619	7491619	+	IGR	DEL	C	-	-	rs2247230	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7491619delC								SFMBT2 (38169 upstream) : ITIH5 (110017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	7563495	7563498	+	IGR	DEL	CCTC	-	-	rs149663818	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7563495_7563498delCCTC								SFMBT2 (110045 upstream) : ITIH5 (38138 downstream)																																			---	---	---	---
ITIH2	3698	broad.mit.edu	37	10	7747059	7747060	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7747059_7747060insT	uc001ijs.2	+							NM_002216	NP_002207			inter-alpha globulin inhibitor H2 polypeptide						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
TAF3	83860	broad.mit.edu	37	10	7976915	7976915	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7976915delA	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	7994229	7994229	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7994229delA	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	8135111	8135111	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8135111delA								GATA3 (17949 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8265904	8265905	+	IGR	INS	-	CA	CA	rs150489892	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8265904_8265905insCA								GATA3 (148742 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8373992	8373995	+	IGR	DEL	ACAG	-	-	rs10536478		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8373992_8373995delACAG								GATA3 (256830 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8445161	8445161	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8445161delT								GATA3 (327999 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8586135	8586135	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8586135delT								GATA3 (468973 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8765017	8765017	+	IGR	DEL	T	-	-	rs113141388		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8765017delT								GATA3 (647855 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9200954	9200954	+	IGR	DEL	A	-	-	rs112998075		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9200954delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9968163	9968170	+	IGR	DEL	GAATGAAT	-	-	rs58593037		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9968163_9968170delGAATGAAT								None (None upstream) : SFTA1P (858232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10151399	10151400	+	IGR	DEL	CG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10151399_10151400delCG								None (None upstream) : SFTA1P (675002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10883510	10883510	+	IGR	DEL	T	-	-	rs79598260		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10883510delT								SFTA1P (46633 upstream) : LOC254312 (93394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10948681	10948684	+	IGR	DEL	TTTT	-	-	rs141649639		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10948681_10948684delTTTT								SFTA1P (111804 upstream) : LOC254312 (28220 downstream)																																			---	---	---	---
CELF2	10659	broad.mit.edu	37	10	11219385	11219385	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11219385delA	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|CELF2_uc010qbk.1_Intron|CELF2_uc010qbl.1_Intron|CELF2_uc010qbm.1_Intron|CELF2_uc001iko.3_Intron|CELF2_uc001ikp.3_Intron|CELF2_uc010qbn.1_Intron|CELF2_uc009xiw.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																		---	---	---	---
USP6NL	9712	broad.mit.edu	37	10	11552357	11552357	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11552357delT	uc001ikt.3	-						USP6NL_uc001iks.1_Intron	NM_014688	NP_055503			USP6 N-terminal like isoform 1							intracellular	Rab GTPase activator activity				0																		---	---	---	---
SEC61A2	55176	broad.mit.edu	37	10	12204197	12204197	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12204197delT	uc001ile.2	+						SEC61A2_uc010qbq.1_Intron|SEC61A2_uc001ilf.3_Intron|SEC61A2_uc001ilh.3_Intron|SEC61A2_uc001ilg.3_Intron	NM_018144	NP_060614			Sec61 alpha form 2 isoform a							endoplasmic reticulum membrane|integral to membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1		Renal(717;0.228)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	12368337	12368337	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12368337delT								CDC123 (75750 upstream) : CAMK1D (23246 downstream)																																			---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12406617	12406617	+	Intron	DEL	A	-	-	rs11299137		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12406617delA	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	12431193	12431194	+	Intron	INS	-	G	G	rs72511713	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12431193_12431194insG	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	12548521	12548522	+	Intron	INS	-	T	T	rs113048014		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12548521_12548522insT	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718			calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)														---	---	---	---
CCDC3	83643	broad.mit.edu	37	10	13018826	13018827	+	Intron	INS	-	AG	AG	rs146230192	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13018826_13018827insAG	uc001ilq.1	-						CCDC3_uc009xjb.1_Intron|CCDC3_uc001ilr.2_Intron|CCDC3_uc009xjc.1_Intron	NM_031455	NP_113643			coiled-coil domain containing 3 precursor							endoplasmic reticulum|extracellular region				ovary(1)	1		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	13348271	13348272	+	IGR	INS	-	AC	AC	rs148350622	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13348271_13348272insAC								PHYH (3859 upstream) : SEPHS1 (11811 downstream)																																			---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	14051312	14051312	+	Intron	DEL	T	-	-	rs112678116		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14051312delT	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imu.1_5'Flank	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	14415756	14415756	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14415756delT	uc001imv.2	-						FRMD4A_uc001imw.1_Intron					Homo sapiens mRNA for KIAA1294 protein, partial cds.							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3																		---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	14416888	14416897	+	Intron	DEL	GAAAGGGAAA	-	-	rs11277364	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14416888_14416897delGAAAGGGAAA	uc001imv.2	-						FRMD4A_uc001imw.1_Intron					Homo sapiens mRNA for KIAA1294 protein, partial cds.							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3																		---	---	---	---
FAM107B	83641	broad.mit.edu	37	10	14708572	14708572	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14708572delA	uc001ina.1	-						FAM107B_uc010qbu.1_Intron	NM_031453	NP_113641			hypothetical protein LOC83641											breast(4)	4																		---	---	---	---
ACBD7	414149	broad.mit.edu	37	10	15062370	15062370	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15062370delC	uc010qby.1	-											SubName: Full=cDNA FLJ52263, highly similar to Artemis protein (EC 3.1.-.-);								fatty-acyl-CoA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	15232723	15232724	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15232723_15232724insA								NMT2 (22028 upstream) : FAM171A1 (20923 downstream)																																			---	---	---	---
FAM171A1	221061	broad.mit.edu	37	10	15366736	15366736	+	Intron	DEL	A	-	-	rs77269403	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15366736delA	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	15762723	15762723	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15762723delT	uc001ioc.1	-						ITGA8_uc010qcb.1_5'Flank	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	15811888	15811888	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15811888delT								ITGA8 (50118 upstream) : FAM188A (8287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	16382086	16382088	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16382086_16382088delAAA								FAM188A (479567 upstream) : PTER (96879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	16451502	16451503	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16451502_16451503delCT								FAM188A (548983 upstream) : PTER (27464 downstream)																																			---	---	---	---
CUBN	8029	broad.mit.edu	37	10	17063118	17063118	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17063118delT	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)													---	---	---	---
VIM	7431	broad.mit.edu	37	10	17276623	17276623	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17276623delT	uc001iou.2	+						VIM_uc001iov.1_Intron|VIM_uc001iow.1_Intron|VIM_uc001iox.1_Intron|VIM_uc001ioy.1_Intron|VIM_uc001ioz.1_Intron|VIM_uc001ipb.1_Intron|VIM_uc009xjv.1_Intron|VIM_uc001ipc.1_Intron	NM_003380	NP_003371			vimentin						cellular component disassembly involved in apoptosis|cellular component movement|interspecies interaction between organisms|muscle filament sliding	cytosol|intermediate filament	protein C-terminus binding|structural constituent of cytoskeleton			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4																		---	---	---	---
VIM	7431	broad.mit.edu	37	10	17277960	17277960	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17277960delT	uc001iou.2	+						VIM_uc001iov.1_Intron|VIM_uc001iow.1_Intron|VIM_uc001iox.1_Intron|VIM_uc001ioy.1_Intron|VIM_uc001ioz.1_Intron|VIM_uc001ipb.1_Intron|VIM_uc009xjv.1_Intron|VIM_uc001ipc.1_Intron	NM_003380	NP_003371			vimentin						cellular component disassembly involved in apoptosis|cellular component movement|interspecies interaction between organisms|muscle filament sliding	cytosol|intermediate filament	protein C-terminus binding|structural constituent of cytoskeleton			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4																		---	---	---	---
ST8SIA6	338596	broad.mit.edu	37	10	17389504	17389504	+	Intron	DEL	A	-	-	rs77953361		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17389504delA	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron	NM_001004470	NP_001004470			ST8 alpha-N-acetyl-neuraminide						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	17664776	17664777	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17664776_17664777insA								PTPLA (5403 upstream) : STAM (21347 downstream)																																			---	---	---	---
CACNB2	783	broad.mit.edu	37	10	18672644	18672645	+	Intron	INS	-	T	T	rs145504929	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18672644_18672645insT	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)													---	---	---	---
ARL5B	221079	broad.mit.edu	37	10	18964316	18964316	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18964316delT	uc001iqd.1	+	6					uc001iqe.2_5'Flank	NM_178815	NP_848930			ADP-ribosylation factor-like 8						small GTPase mediated signal transduction	intracellular	GTP binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	19055275	19055275	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19055275delT								ARL5B (88335 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19412234	19412235	+	IGR	INS	-	TGTG	TGTG	rs145077546	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19412234_19412235insTGTG								ARL5B (445294 upstream) : PLXDC2 (693137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19922179	19922180	+	Intron	INS	-	AG	AG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19922179_19922180insAG	uc010qcr.1	+											Homo sapiens cDNA FLJ60310 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	20048889	20048889	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20048889delA								None (None upstream) : PLXDC2 (56483 downstream)																																			---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20455664	20455664	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20455664delT	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																		---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21093139	21093139	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21093139delA	uc001iqi.2	-						NEBL_uc001iqj.2_Intron|NEBL_uc001iqk.2_Intron	NM_006393	NP_006384			nebulette sarcomeric isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21124623	21124623	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21124623delA	uc001iqi.2	-						NEBL_uc001iqj.2_Intron|NEBL_uc001iqk.2_Intron|NEBL_uc001iql.1_Intron	NM_006393	NP_006384			nebulette sarcomeric isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21148586	21148586	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21148586delA	uc001iqi.2	-						NEBL_uc001iqj.2_Intron|NEBL_uc001iqk.2_Intron	NM_006393	NP_006384			nebulette sarcomeric isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	21568982	21568982	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21568982delA								NEBL (105866 upstream) : C10orf114 (214440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21571446	21571446	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21571446delA								NEBL (108330 upstream) : C10orf114 (211976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21638232	21638235	+	IGR	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21638232_21638235delAAAA								NEBL (175116 upstream) : C10orf114 (145187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21755472	21755472	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21755472delA								NEBL (292356 upstream) : C10orf114 (27950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21796951	21796951	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21796951delT								C10orf114 (10738 upstream) : C10orf140 (5460 downstream)																																			---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21877756	21877758	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21877756_21877758delTTT	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	21878832	21878837	+	Intron	DEL	CCCTTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21878832_21878837delCCCTTC	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								---	---	---	---
DNAJC1	64215	broad.mit.edu	37	10	22196240	22196241	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22196240_22196241delTT	uc001irc.2	-						DNAJC1_uc001ird.2_Intron	NM_022365	NP_071760			DnaJ (Hsp40) homolog, subfamily C, member 1						negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding			lung(1)	1		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)																---	---	---	---
DNAJC1	64215	broad.mit.edu	37	10	22217054	22217054	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22217054delG	uc001irc.2	-						DNAJC1_uc001ird.2_Intron	NM_022365	NP_071760			DnaJ (Hsp40) homolog, subfamily C, member 1						negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding			lung(1)	1		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)																---	---	---	---
DNAJC1	64215	broad.mit.edu	37	10	22247361	22247363	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22247361_22247363delTTT	uc001irc.2	-						DNAJC1_uc001ird.2_Intron	NM_022365	NP_071760			DnaJ (Hsp40) homolog, subfamily C, member 1						negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding			lung(1)	1		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	22421635	22421635	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22421635delT								DNAJC1 (128985 upstream) : COMMD3 (183664 downstream)																																			---	---	---	---
BMI1	648	broad.mit.edu	37	10	22607161	22607161	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22607161delT	uc001irh.2	+						COMMD3_uc001ire.2_Intron|COMMD3_uc001irf.2_Intron|COMMD3_uc001irg.2_Intron|BMI1_uc009xkg.2_Intron	NM_005180	NP_005171			BMI1 polycomb ring finger oncogene						hemopoiesis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fibroblast proliferation|positive regulation of ubiquitin-protein ligase activity|segment specification|transcription, DNA-dependent	cytoplasm|nucleolus|PcG protein complex|ubiquitin ligase complex	RING-like zinc finger domain binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	23057368	23057369	+	IGR	INS	-	TG	TG	rs138841064	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23057368_23057369insTG								PIP4K2A (53865 upstream) : ARMC3 (159585 downstream)																																			---	---	---	---
PTF1A	256297	broad.mit.edu	37	10	23479492	23479497	+	5'Flank	DEL	ACACAC	-	-	rs72173932		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23479492_23479497delACACAC	uc001irp.2	+							NM_178161	NP_835455			pancreas specific transcription factor, 1a						endocrine pancreas development|exocrine pancreas development|regulation of transcription, DNA-dependent|tissue development|transcription, DNA-dependent	cytoplasm|transcription factor complex				pancreas(1)|skin(1)	2																		---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24783886	24783886	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24783886delC	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																		---	---	---	---
ARHGAP21	57584	broad.mit.edu	37	10	24967036	24967036	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24967036delA	uc001isb.2	-						ARHGAP21_uc009xkl.1_Intron|ARHGAP21_uc001isc.1_Intron|ARHGAP21_uc001isd.1_Intron	NM_020824	NP_065875			Rho GTPase activating protein 21						signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	25060107	25060107	+	IGR	DEL	T	-	-	rs139278764		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25060107delT								ARHGAP21 (47510 upstream) : PRTFDC1 (77447 downstream)																																			---	---	---	---
PRTFDC1	56952	broad.mit.edu	37	10	25184183	25184184	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25184183_25184184delTT	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																		---	---	---	---
ENKUR	219670	broad.mit.edu	37	10	25348757	25348757	+	Intron	DEL	A	-	-	rs112899740		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25348757delA	uc001ish.1	-							NM_145010	NP_659447			enkurin							cilium|flagellum	calmodulin binding|SH3 domain binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	26187530	26187531	+	IGR	INS	-	T	T	rs144893223	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26187530_26187531insT								GPR158 (296375 upstream) : MYO3A (35471 downstream)																																			---	---	---	---
MYO3A	53904	broad.mit.edu	37	10	26324870	26324871	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26324870_26324871delTT	uc001isn.2	+						MYO3A_uc009xko.1_Intron|MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129			myosin IIIA						protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18																		---	---	---	---
MYO3A	53904	broad.mit.edu	37	10	26462760	26462760	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26462760delA	uc001isn.2	+	30	3927	c.3567delA	c.(3565-3567)CCAfs	p.P1189fs	MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1189					protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18																		---	---	---	---
APBB1IP	54518	broad.mit.edu	37	10	26724526	26724527	+	5'Flank	INS	-	TTGT	TTGT	rs146354052	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26724526_26724527insTTGT	uc001iss.2	+						APBB1IP_uc001isr.2_5'Flank|APBB1IP_uc009xks.1_5'Flank	NM_019043	NP_061916			amyloid beta (A4) precursor protein-binding,						blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7																		---	---	---	---
APBB1IP	54518	broad.mit.edu	37	10	26828337	26828337	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26828337delA	uc001iss.2	+						APBB1IP_uc009xks.1_Intron	NM_019043	NP_061916			amyloid beta (A4) precursor protein-binding,						blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7																		---	---	---	---
ABI1	10006	broad.mit.edu	37	10	27054256	27054256	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27054256delA	uc001isx.2	-						ABI1_uc001ite.2_Intron|ABI1_uc010qdh.1_Intron|ABI1_uc010qdi.1_Intron|ABI1_uc001isy.2_Intron|ABI1_uc001ita.2_Intron|ABI1_uc001isz.2_Intron|ABI1_uc001itb.2_Intron|ABI1_uc001itc.2_Intron|ABI1_uc010qdj.1_Intron|ABI1_uc001itd.2_Intron|ABI1_uc010qdk.1_Intron|ABI1_uc010qdg.1_Intron	NM_005470	NP_005461			abl-interactor 1 isoform a						actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome	cytoskeletal protein binding			central_nervous_system(1)	1																		---	---	---	---
ANKRD26	22852	broad.mit.edu	37	10	27295869	27295869	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27295869delT	uc001ith.2	-	33	5145	c.4973delA	c.(4972-4974)AATfs	p.N1658fs	ANKRD26_uc001itg.2_Frame_Shift_Del_p.N1345fs|ANKRD26_uc009xku.1_Frame_Shift_Del_p.N1659fs	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1658	Potential.					centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4																		---	---	---	---
ANKRD26	22852	broad.mit.edu	37	10	27356350	27356351	+	Intron	INS	-	T	T	rs111776754		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27356350_27356351insT	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	27408201	27408201	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27408201delA	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																		---	---	---	---
YME1L1	10730	broad.mit.edu	37	10	27409239	27409239	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
YME1L1	10730	broad.mit.edu	37	10	27431280	27431280	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27431280delT	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																		---	---	---	---
MASTL	84930	broad.mit.edu	37	10	27459254	27459254	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27459254delA	uc001itm.2	+	8	2005	c.1366delA	c.(1366-1368)AAAfs	p.K456fs	MASTL_uc001itl.2_Frame_Shift_Del_p.K456fs|MASTL_uc009xkw.1_Frame_Shift_Del_p.K456fs|MASTL_uc009xkx.1_RNA	NM_032844	NP_116233	Q96GX5	GWL_HUMAN	microtubule associated serine/threonine	456	Protein kinase.				cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus	centrosome|cleavage furrow|nucleus	ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	27684426	27684427	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27684426_27684427insG								LOC387646 (143191 upstream) : PTCHD3 (2690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	27786739	27786739	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27786739delA								PTCHD3 (83442 upstream) : RAB18 (6510 downstream)																																			---	---	---	---
MPP7	143098	broad.mit.edu	37	10	28488809	28488810	+	Intron	DEL	AC	-	-	rs150903701		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28488809_28488810delAC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	28639266	28639266	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28639266delA								MPP7 (47271 upstream) : WAC (182161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	28739804	28739805	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28739804_28739805insA								MPP7 (147809 upstream) : WAC (81622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	28775314	28775315	+	IGR	INS	-	TTTG	TTTG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28775314_28775315insTTTG								MPP7 (183319 upstream) : WAC (46112 downstream)																																			---	---	---	---
WAC	51322	broad.mit.edu	37	10	28824817	28824817	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28824817delT	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	28906457	28906458	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28906457_28906458insT	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																		---	---	---	---
WAC	51322	broad.mit.edu	37	10	28908453	28908453	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28908453delT	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	29029168	29029171	+	IGR	DEL	CTCT	-	-	rs56300405		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29029168_29029171delCTCT								BAMBI (57300 upstream) : LYZL1 (548819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29285564	29285568	+	IGR	DEL	TTTTT	-	-	rs72107648		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29285564_29285568delTTTTT								BAMBI (313696 upstream) : LYZL1 (292422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29452466	29452467	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29452466_29452467insA								BAMBI (480598 upstream) : LYZL1 (125523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29648443	29648444	+	IGR	DEL	TT	-	-	rs79409211		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29648443_29648444delTT								LYZL1 (48286 upstream) : LOC387647 (50039 downstream)																																			---	---	---	---
SVIL	6840	broad.mit.edu	37	10	29969848	29969848	+	Intron	DEL	A	-	-	rs66861329		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29969848delA	uc001iuu.1	-						SVIL_uc009xld.1_Intron	NM_003174	NP_003165			supervillin isoform 1						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)																---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30362576	30362577	+	Intron	INS	-	TCCT	TCCT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30362576_30362577insTCCT	uc001iuz.2	-											RecName: Full=Uncharacterized protein KIAA1462;											ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	30436061	30436061	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30436061delT								KIAA1462 (31641 upstream) : MTPAP (162670 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	31057040	31057040	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31057040delT								LYZL2 (138393 upstream) : ZNF438 (76527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	31364693	31364693	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31364693delT								ZNF438 (43827 upstream) : LOC220930 (240765 downstream)																																			---	---	---	---
ZEB1	6935	broad.mit.edu	37	10	31691040	31691042	+	Intron	DEL	TGT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31691040_31691042delTGT	uc001ivs.3	+						ZEB1_uc001ivr.3_Intron|ZEB1_uc010qee.1_Intron|ZEB1_uc010qef.1_Intron|ZEB1_uc009xlh.1_Intron|ZEB1_uc009xli.1_Intron|ZEB1_uc009xlj.1_Intron|ZEB1_uc010qeg.1_Intron|ZEB1_uc009xlk.1_Intron|ZEB1_uc001ivt.3_Intron|ZEB1_uc001ivu.3_Intron|ZEB1_uc001ivv.3_Intron|ZEB1_uc010qeh.1_Intron|ZEB1_uc009xll.2_Intron|ZEB1_uc009xlm.1_Intron|ZEB1_uc009xln.1_Intron|ZEB1_uc009xlo.1_Intron|ZEB1_uc009xlp.2_Intron	NM_030751	NP_110378			zinc finger E-box binding homeobox 1 isoform b						cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)																---	---	---	---
ARHGAP12	94134	broad.mit.edu	37	10	32208720	32208720	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32208720delA	uc001ivz.1	-						ARHGAP12_uc009xls.2_Intron|ARHGAP12_uc001iwb.1_Intron|ARHGAP12_uc001iwc.1_Intron|ARHGAP12_uc009xlq.1_Intron|ARHGAP12_uc001iwd.1_Intron|ARHGAP12_uc009xlr.1_Intron	NM_018287	NP_060757			Rho GTPase activating protein 12						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		Prostate(175;0.0199)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	32512782	32512782	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32512782delA								KIF5B (167411 upstream) : EPC1 (45077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	32530001	32530001	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32530001delT								KIF5B (184630 upstream) : EPC1 (27858 downstream)																																			---	---	---	---
C10orf68	79741	broad.mit.edu	37	10	33063218	33063219	+	Intron	DEL	CT	-	-	rs78436044	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33063218_33063219delCT	uc001iwn.3	+						C10orf68_uc001iwl.1_Intron|C10orf68_uc001iwm.1_Intron|C10orf68_uc010qei.1_Intron|C10orf68_uc001iwo.3_Intron	NM_024688	NP_078964			chromosome 10 open reading frame 68											skin(2)|ovary(1)	3																		---	---	---	---
ITGB1	3688	broad.mit.edu	37	10	33243141	33243141	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33243141delA	uc001iws.3	-						ITGB1_uc001iwt.3_Intron	NM_133376	NP_596867			integrin beta 1 isoform 1A precursor						axon guidance|blood coagulation|cell-cell adhesion mediated by integrin|cell-matrix adhesion|cellular defense response|homophilic cell adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|leukocyte migration|positive regulation of apoptosis|regulation of immune response	cell surface|cleavage furrow|focal adhesion|melanosome|neuromuscular junction|ruffle|sarcolemma	identical protein binding|protein heterodimerization activity|receptor activity			upper_aerodigestive_tract(1)|ovary(1)	2		Ovarian(717;1.34e-05)|Breast(68;0.0634)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	33266863	33266864	+	IGR	DEL	AA	-	-	rs74233157		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33266863_33266864delAA								ITGB1 (19570 upstream) : NRP1 (199556 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	33413489	33413489	+	IGR	DEL	T	-	-	rs112720840		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33413489delT								ITGB1 (166196 upstream) : NRP1 (52931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34050497	34050497	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34050497delG	uc001ixd.2	-											Homo sapiens cDNA clone IMAGE:4822215.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	34153682	34153682	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34153682delA								NRP1 (529676 upstream) : PARD3 (246416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34220055	34220056	+	IGR	INS	-	TTCCTTCCTTCC	TTCCTTCCTTCC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34220055_34220056insTTCCTTCCTTCC								NRP1 (596049 upstream) : PARD3 (180042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	35254139	35254140	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35254139_35254140delTT								PARD3 (150216 upstream) : CUL2 (44668 downstream)																																			---	---	---	---
CUL2	8453	broad.mit.edu	37	10	35320659	35320659	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35320659delT	uc001ixv.2	-						CUL2_uc009xma.2_Intron|CUL2_uc010qer.1_Intron|CUL2_uc001ixw.2_Intron|CUL2_uc010qes.1_Intron	NM_003591	NP_003582			cullin 2						cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	35412415	35412415	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35412415delA								CUL2 (32869 upstream) : CREM (3386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	35528224	35528224	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35528224delA								CREM (26339 upstream) : CCNY (7729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	35904916	35904916	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35904916delA								GJD4 (7053 upstream) : FZD8 (22261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	35956143	35956145	+	IGR	DEL	CAC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35956143_35956145delCAC								FZD8 (25781 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36399430	36399431	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36399430_36399431delGT								FZD8 (469068 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	37028321	37028321	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37028321delT								None (None upstream) : ANKRD30A (386464 downstream)																																			---	---	---	---
ANKRD30A	91074	broad.mit.edu	37	10	37482610	37482610	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37482610delT	uc001iza.1	+							NM_052997	NP_443723			ankyrin repeat domain 30A							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	38008096	38008096	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38008096delG								ANKRD30A (486601 upstream) : ZNF248 (82351 downstream)																																			---	---	---	---
ZNF248	57209	broad.mit.edu	37	10	38101247	38101247	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38101247delA	uc009xmc.2	-						ZNF248_uc001izb.2_Intron					SubName: Full=ZNF248 protein; SubName: Full=Zinc finger protein 248; SubName: Full=Zinc finger protein 248, isoform CRA_b;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	38916316	38916316	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38916316delA								LOC399744 (175236 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42631641	42631642	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42631641_42631642insT								None (None upstream) : LOC441666 (195673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42651830	42651835	+	IGR	DEL	ATGTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42651830_42651835delATGTTT								None (None upstream) : LOC441666 (175480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42695566	42695566	+	IGR	DEL	A	-	-	rs72785934	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42695566delA								None (None upstream) : LOC441666 (131749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	43356160	43356162	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43356160_43356162delAAA								BMS1 (25777 upstream) : RET (216355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	43545516	43545516	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43545516delA								BMS1 (215133 upstream) : RET (27001 downstream)																																			---	---	---	---
ZNF487	642819	broad.mit.edu	37	10	43976781	43976782	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43976781_43976782delAA	uc010qfb.1	+							NR_026693				SubName: Full=cDNA FLJ52643, weakly similar to Zinc finger protein 11B;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	43997971	43997971	+	IGR	DEL	A	-	-	rs7901252	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43997971delA								ZNF487 (19964 upstream) : ZNF239 (53824 downstream)																																			---	---	---	---
ZNF239	8187	broad.mit.edu	37	10	44054490	44054490	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44054490delA	uc001jaw.3	-						ZNF239_uc001jax.3_Intron|ZNF239_uc009xmj.2_Intron|ZNF239_uc009xmk.2_Intron	NM_005674	NP_005665			zinc finger protein 239						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|RNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	44137205	44137206	+	Intron	INS	-	G	G	rs150894567	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44137205_44137206insG	uc001jba.2	+											Homo sapiens chromosome 10 open reading frame 44, mRNA (cDNA clone IMAGE:4837462).																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	44812052	44812053	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44812052_44812053insC								HNRNPA3P1 (526187 upstream) : CXCL12 (53554 downstream)																																			---	---	---	---
CXCL12	6387	broad.mit.edu	37	10	44871967	44871967	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44871967delA	uc001jbf.2	-						CXCL12_uc001jbh.2_Intron	NM_000609	NP_000600			chemokine (C-X-C motif) ligand 12 (stromal						blood circulation|cell adhesion|cellular calcium ion homeostasis|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|negative regulation of leukocyte apoptosis|positive regulation of monocyte chemotaxis|regulation of actin polymerization or depolymerization|response to virus	extracellular space	chemokine activity|growth factor activity|signal transducer activity				0					Dexamethasone(DB01234)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	44973824	44973824	+	IGR	DEL	C	-	-	rs11284193		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44973824delC								CXCL12 (93282 upstream) : TMEM72 (432940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45061170	45061170	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45061170delA								CXCL12 (180628 upstream) : TMEM72 (345594 downstream)																																			---	---	---	---
MARCH8	220972	broad.mit.edu	37	10	45987746	45987746	+	Intron	DEL	T	-	-	rs74663458		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45987746delT	uc001jci.1	-						MARCH8_uc001jch.2_Intron|MARCH8_uc001jcj.1_Intron|MARCH8_uc001jck.1_Intron	NM_001002266	NP_001002266			cellular modulator of immune recognition isoform							cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
MARCH8	220972	broad.mit.edu	37	10	46074186	46074187	+	Intron	INS	-	A	A	rs148680468	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46074186_46074187insA	uc001jcj.1	-						MARCH8_uc001jck.1_Intron	NM_001002265	NP_001002265			cellular modulator of immune recognition isoform							cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
FAM21C	253725	broad.mit.edu	37	10	46233217	46233223	+	Intron	DEL	TTTTTTT	-	-	rs74128816		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46233217_46233223delTTTTTTT	uc001jcu.2	+						FAM21C_uc001jcs.1_Intron|FAM21C_uc001jct.2_Intron|FAM21C_uc010qfi.1_Intron	NM_015262	NP_056077			hypothetical protein LOC253725											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	46986921	46986921	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46986921delT								SYT15 (16320 upstream) : GPRIN2 (6625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	47010149	47010149	+	IGR	DEL	T	-	-	rs67707077		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47010149delT								GPRIN2 (4506 upstream) : ANXA8 (1604 downstream)																																			---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47028001	47028002	+	Intron	INS	-	CT	CT	rs149264405		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47028001_47028002insCT	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-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
MAPK8	5599	broad.mit.edu	37	10	49612720	49612720	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49612720delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	49876974	49876977	+	IGR	DEL	TATC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49876974_49876977delTATC								ARHGAP22 (12664 upstream) : WDFY4 (15944 downstream)																																			---	---	---	---
WDFY4	57705	broad.mit.edu	37	10	49943301	49943301	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49943301delA	uc001jha.3	+						WDFY4_uc001jgy.2_Intron	NM_020945	NP_065996			WDFY family member 4							integral to membrane	binding				0																		---	---	---	---
WDFY4	57705	broad.mit.edu	37	10	50111154	50111154	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50111154delA	uc001jha.3	+							NM_020945	NP_065996			WDFY family member 4							integral to membrane	binding				0																		---	---	---	---
C10orf72	196740	broad.mit.edu	37	10	50305496	50305496	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50305496delA	uc001jhf.2	-							NM_001031746	NP_001026916			hypothetical protein LOC196740 isoform 1							integral to membrane|plasma membrane					0																		---	---	---	---
C10orf72	196740	broad.mit.edu	37	10	50310018	50310019	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50310018_50310019delGT	uc001jhf.2	-							NM_001031746	NP_001026916			hypothetical protein LOC196740 isoform 1							integral to membrane|plasma membrane					0																		---	---	---	---
C10orf72	196740	broad.mit.edu	37	10	50311966	50311966	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50311966delG	uc001jhf.2	-						C10orf72_uc001jhh.2_Intron	NM_001031746	NP_001026916			hypothetical protein LOC196740 isoform 1							integral to membrane|plasma membrane					0																		---	---	---	---
C10orf71	118461	broad.mit.edu	37	10	50506391	50506391	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50506391delA	uc010qgp.1	+							NM_199459	NP_955629			hypothetical protein LOC118461 isoform 2												0																		---	---	---	---
ERCC6	2074	broad.mit.edu	37	10	50680934	50680934	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50680934delA	uc001jhs.3	-						ERCC6_uc009xod.2_Intron|ERCC6_uc010qgr.1_Intron|ERCC6_uc001jhr.3_Intron	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	50774905	50774906	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50774905_50774906insA								PGBD3 (27321 upstream) : CHAT (42235 downstream)																																			---	---	---	---
PARG	8505	broad.mit.edu	37	10	51581255	51581255	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51581255delT	uc001jih.2	-						uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|NCOA4_uc009xon.2_Intron|NCOA4_uc010qhd.1_Intron|NCOA4_uc001jis.3_Intron|NCOA4_uc010qhe.1_Intron|NCOA4_uc010qhf.1_Intron|NCOA4_uc001jit.2_Intron|NCOA4_uc009xoo.2_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	52486675	52486675	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52486675delC								SGMS1 (101752 upstream) : ASAH2B (13021 downstream)																																			---	---	---	---
A1CF	29974	broad.mit.edu	37	10	52566433	52566433	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52566433delT	uc001jjj.2	-	13					A1CF_uc010qhn.1_3'UTR|A1CF_uc001jji.2_3'UTR|A1CF_uc001jjh.2_3'UTR|A1CF_uc010qho.1_3'UTR|A1CF_uc009xov.2_3'UTR	NM_138932	NP_620310			apobec-1 complementation factor isoform 2						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																		---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53109684	53109684	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53109684delA	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_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	53195936	53195938	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53195936_53195938delTTT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_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	53396926	53396926	+	Intron	DEL	A	-	-	rs7071294	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53396926delA	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	54241264	54241264	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54241264delC								DKK1 (163848 upstream) : MBL2 (283877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	54930366	54930367	+	IGR	INS	-	AT	AT	rs140779279	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54930366_54930367insAT								MBL2 (398906 upstream) : PCDH15 (632168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	55254018	55254018	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55254018delT								MBL2 (722558 upstream) : PCDH15 (308517 downstream)																																			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55684269	55684269	+	Intron	DEL	C	-	-	rs34087235		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55684269delC	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	56098469	56098469	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56098469delT	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|PCDH15_uc001jjw.2_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	56361409	56361409	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56361409delA	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|PCDH15_uc001jjw.2_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	56401343	56401344	+	Intron	DEL	CA	-	-	rs71872318		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56401343_56401344delCA	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|PCDH15_uc001jjw.2_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)			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58206748	58206748	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58206748delT								ZWINT (85714 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58604940	58604941	+	IGR	INS	-	AC	AC	rs138040204	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58604940_58604941insAC								ZWINT (483906 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59359608	59359608	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59359608delT								None (None upstream) : IPMK (596010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59811902	59811902	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59811902delA								None (None upstream) : IPMK (143716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59827178	59827179	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59827178_59827179delTT								None (None upstream) : IPMK (128439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59922547	59922547	+	IGR	DEL	A	-	-	rs66475944		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59922547delA								None (None upstream) : IPMK (33071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	60700458	60700459	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60700458_60700459insA								BICC1 (111613 upstream) : PHYHIPL (235889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	61295966	61295966	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61295966delT								FAM13C (173305 upstream) : SLC16A9 (114556 downstream)																																			---	---	---	---
SLC16A9	220963	broad.mit.edu	37	10	61466388	61466389	+	Intron	INS	-	ACAC	ACAC	rs147040148	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61466388_61466389insACAC	uc010qig.1	-							NM_194298	NP_919274			solute carrier family 16 (monocarboxylic acid						urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3																		---	---	---	---
CCDC6	8030	broad.mit.edu	37	10	61593992	61593993	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61593992_61593993delAA	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)														---	---	---	---
TMEM26	219623	broad.mit.edu	37	10	63196058	63196058	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63196058delA	uc001jlo.2	-						TMEM26_uc010qij.1_Intron|TMEM26_uc001jlq.2_Intron	NM_178505	NP_848600			transmembrane protein 26							integral to membrane					0	Prostate(12;0.0112)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	63409864	63409864	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63409864delT								TMEM26 (196656 upstream) : C10orf107 (12855 downstream)																																			---	---	---	---
ARID5B	84159	broad.mit.edu	37	10	63712603	63712604	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63712603_63712604delGT	uc001jlt.1	+						ARID5B_uc010qil.1_Intron	NM_032199	NP_115575			AT rich interactive domain 5B (MRF1-like)						liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)																	---	---	---	---
RTKN2	219790	broad.mit.edu	37	10	64022583	64022583	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																	---	---	---	---
RTKN2	219790	broad.mit.edu	37	10	64024862	64024862	+	Intron	DEL	A	-	-	rs11357728		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64024862delA	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)																	---	---	---	---
EGR2	1959	broad.mit.edu	37	10	64575974	64575974	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64575974delT	uc010qim.1	-						EGR2_uc010qin.1_5'UTR|EGR2_uc001jmi.2_5'UTR|EGR2_uc010qio.1_Intron|EGR2_uc009xph.2_Intron	NM_001136177	NP_001129649			early growth response 2 protein isoform a						fat cell differentiation|protein export from nucleus|transcription from RNA polymerase II promoter	cytoplasm|nucleus	chromatin binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|ubiquitin protein ligase binding|zinc ion binding			ovary(2)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	64615057	64615057	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64615057delA								EGR2 (36130 upstream) : NRBF2 (277950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	64923515	64923515	+	IGR	DEL	T	-	-	rs78959322		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64923515delT								NRBF2 (8730 upstream) : JMJD1C (3475 downstream)																																			---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	65089300	65089301	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65089300_65089301delAA	uc001jmn.2	-						JMJD1C_uc009xpi.2_Intron	NM_032776	NP_116165			jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	65623034	65623035	+	IGR	INS	-	AC	AC	rs137943268	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65623034_65623035insAC								REEP3 (241063 upstream) : ANXA2P3 (962250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66103632	66103633	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66103632_66103633insG								REEP3 (721661 upstream) : ANXA2P3 (481652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66139970	66139971	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66139970_66139971insC								REEP3 (757999 upstream) : ANXA2P3 (445314 downstream)																																			---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68411217	68411218	+	Intron	INS	-	C	C	rs143646292	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68411217_68411218insC	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	68896318	68896319	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68896318_68896319delGA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	69634691	69634691	+	IGR	DEL	A	-	-	rs34328489		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69634691delA								DNAJC12 (36754 upstream) : SIRT1 (9736 downstream)																																			---	---	---	---
SIRT1	23411	broad.mit.edu	37	10	69676036	69676036	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69676036delT	uc001jnd.2	+	9	1983	c.1930delT	c.(1930-1932)TTTfs	p.F644fs	SIRT1_uc010qis.1_Frame_Shift_Del_p.F349fs|SIRT1_uc009xpp.2_Frame_Shift_Del_p.F452fs|SIRT1_uc001jne.2_Frame_Shift_Del_p.F341fs	NM_012238	NP_036370	Q96EB6	SIRT1_HUMAN	sirtuin 1 isoform a	644					apoptosis|cell aging|cellular response to hydrogen peroxide|cellular response to starvation|chromatin silencing at rDNA|DNA repair|DNA replication|establishment of chromatin silencing|histone H3 deacetylation|interspecies interaction between organisms|maintenance of chromatin silencing|muscle organ development|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of fat cell differentiation|negative regulation of helicase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine acetylation|peptidyl-lysine deacetylation|positive regulation of anti-apoptosis|positive regulation of chromatin silencing|positive regulation of DNA repair|regulation of apoptosis|regulation of cell proliferation|regulation of endodeoxyribonuclease activity|regulation of protein import into nucleus, translocation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|rRNA processing|transcription, DNA-dependent|triglyceride mobilization|white fat cell differentiation	chromatin silencing complex|cytoplasm|nuclear euchromatin|nuclear heterochromatin|nuclear inner membrane|nucleolus|PML body|rDNA heterochromatin	bHLH transcription factor binding|histone binding|HLH domain binding|identical protein binding|mitogen-activated protein kinase binding|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|p53 binding|protein C-terminus binding|transcription corepressor activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	69855709	69855709	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69855709delA								HERC4 (20606 upstream) : MYPN (10167 downstream)																																			---	---	---	---
MYPN	84665	broad.mit.edu	37	10	69881820	69881822	+	In_Frame_Del	DEL	TCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69881820_69881822delTCT	uc001jnm.3	+	3	810_812	c.625_627delTCT	c.(625-627)TCTdel	p.S210del	MYPN_uc001jnl.1_In_Frame_Del_p.S210del|MYPN_uc001jnn.3_Intron|MYPN_uc001jno.3_In_Frame_Del_p.S210del|MYPN_uc001jnp.1_In_Frame_Del_p.S210del|MYPN_uc009xps.2_In_Frame_Del_p.S210del|MYPN_uc009xpt.2_In_Frame_Del_p.S210del|MYPN_uc010qit.1_5'UTR|MYPN_uc010qiu.1_RNA	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin	210	Interaction with CARP.					nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70304123	70304124	+	IGR	DEL	TT	-	-	rs71716010		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70304123_70304124delTT								SLC25A16 (16539 upstream) : TET1 (15993 downstream)																																			---	---	---	---
TET1	80312	broad.mit.edu	37	10	70360728	70360728	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70360728delT	uc001jok.3	+							NM_030625	NP_085128			CXXC finger 6						DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9																		---	---	---	---
TET1	80312	broad.mit.edu	37	10	70392079	70392079	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70392079delA	uc001jok.3	+							NM_030625	NP_085128			CXXC finger 6						DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9																		---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70491620	70491620	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70491620delT	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																		---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70530835	70530836	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70530835_70530836delAA	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	70649625	70649625	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70649625delT	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																		---	---	---	---
DDX21	9188	broad.mit.edu	37	10	70727306	70727306	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70727306delA	uc001jov.1	+						DDX21_uc001jow.1_Intron	NM_004728	NP_004719			DEAD (Asp-Glu-Ala-Asp) box polypeptide 21							nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)	3																		---	---	---	---
KIAA1279	26128	broad.mit.edu	37	10	70775281	70775281	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70775281delT	uc001joy.2	+							NM_015634	NP_056449			KIF1 binding protein						cell differentiation|mitochondrial transport|nervous system development	mitochondrion	kinesin binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70796185	70796186	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70796185_70796186delAA								KIAA1279 (19451 upstream) : SRGN (51642 downstream)																																			---	---	---	---
VPS26A	9559	broad.mit.edu	37	10	70925703	70925703	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70925703delA	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	71107959	71107959	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71107959delA	uc001jpl.3	+						HK1_uc001jpg.3_Intron|HK1_uc001jph.3_Intron|HK1_uc001jpi.3_Intron|HK1_uc001jpj.3_Intron|HK1_uc001jpk.3_Intron|HK1_uc009xqd.2_Intron	NM_000188	NP_000179			hexokinase 1 isoform HKI						glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	71197806	71197806	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71197806delA								TACR2 (21132 upstream) : TSPAN15 (13420 downstream)																																			---	---	---	---
AIFM2	84883	broad.mit.edu	37	10	71863594	71863594	+	Intron	DEL	A	-	-	rs79992463	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71863594delA	uc010qjg.1	-						H2AFY2_uc001jqm.2_Intron|H2AFY2_uc001jqn.2_Intron	NM_032797	NP_116186			apoptosis-inducing factor (AIF)-like						apoptotic mitochondrial changes|chromosome condensation|induction of apoptosis	cytosol|integral to membrane|mitochondrial outer membrane	DNA binding|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding			central_nervous_system(1)	1																		---	---	---	---
AIFM2	84883	broad.mit.edu	37	10	71895209	71895209	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71895209delT	uc001jqp.1	-							NM_032797	NP_116186			apoptosis-inducing factor (AIF)-like						apoptotic mitochondrial changes|chromosome condensation|induction of apoptosis	cytosol|integral to membrane|mitochondrial outer membrane	DNA binding|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding			central_nervous_system(1)	1																		---	---	---	---
LRRC20	55222	broad.mit.edu	37	10	72062069	72062069	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72062069delA	uc001jqx.1	-						LRRC20_uc001jqy.1_Intron|LRRC20_uc001jqz.1_Intron	NM_207119	NP_997002			leucine rich repeat containing 20 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	72797294	72797295	+	IGR	INS	-	TA	TA	rs10629687		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72797294_72797295insTA								PCBD1 (148753 upstream) : UNC5B (175003 downstream)																																			---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73518803	73518804	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73518803_73518804insT	uc001jrx.3	+						C10orf54_uc001jsd.2_Intron|C10orf54_uc001jse.2_Intron|C10orf54_uc009xqm.2_Intron	NM_022124	NP_071407			cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
CHST3	9469	broad.mit.edu	37	10	73745423	73745423	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73745423delT	uc001jsn.2	+							NM_004273	NP_004264			chondroitin 6-sulfotransferase 3						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 6-sulfotransferase activity				0																		---	---	---	---
SPOCK2	9806	broad.mit.edu	37	10	73827960	73827961	+	Frame_Shift_Ins	INS	-	GGGG	GGGG	rs150310833	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73827960_73827961insGGGG	uc001jso.1	-	6	1018_1019	c.573_574insCCCC	c.(571-576)ACCGCCfs	p.T191fs	SPOCK2_uc001jsp.2_Frame_Shift_Ins_p.T191fs	NM_014767	NP_055582	Q92563	TICN2_HUMAN	sparc/osteonectin, cwcv and kazal-like domains	191_192					extracellular matrix organization|regulation of cell differentiation|signal transduction|synapse assembly	proteinaceous extracellular matrix	calcium ion binding				0																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73963045	73963046	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73963045_73963046delAA	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	74471467	74471468	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74471467_74471468delTT	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-4292-01	TCGA-BR-4292-01									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	74801600	74801600	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74801600delT	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)													---	---	---	---
ECD	11319	broad.mit.edu	37	10	74899608	74899615	+	Intron	DEL	TTTTTTTT	-	-	rs56403902	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74899608_74899615delTTTTTTTT	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)																	---	---	---	---
KIAA0913	23053	broad.mit.edu	37	10	75560546	75560546	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75560546delC	uc009xrl.2	+						KIAA0913_uc001jve.2_Intron|KIAA0913_uc001jvf.2_Intron|KIAA0913_uc001jvh.2_Intron|KIAA0913_uc001jvi.2_Intron|KIAA0913_uc010qkr.1_Intron|KIAA0913_uc001jvj.2_Intron|KIAA0913_uc009xrn.1_3'UTR	NM_015037	NP_055852			hypothetical protein LOC23053								zinc ion binding			breast(1)	1	Prostate(51;0.0112)																	---	---	---	---
VCL	7414	broad.mit.edu	37	10	75798660	75798660	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75798660delT	uc001jwd.2	+						VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Intron|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706			vinculin isoform meta-VCL						adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)																	---	---	---	---
VCL	7414	broad.mit.edu	37	10	75822827	75822827	+	Intron	DEL	A	-	-	rs137961314	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75822827delA	uc001jwd.2	+						VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Intron|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706			vinculin isoform meta-VCL						adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)																	---	---	---	---
AP3M1	26985	broad.mit.edu	37	10	75893990	75893990	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75893990delA	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)																	---	---	---	---
ADK	132	broad.mit.edu	37	10	76026334	76026334	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76026334delA	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	76288058	76288058	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76288058delA	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76649799	76649801	+	Intron	DEL	TTT	-	-	rs36105581		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76649799_76649801delTTT	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								---	---	---	---
Unknown	0	broad.mit.edu	37	10	77112771	77112772	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77112771_77112772insG	uc001jxd.1	+											Homo sapiens cDNA FLJ13383 fis, clone PLACE1001024.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	77312416	77312416	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77312416delT								MIR606 (105 upstream) : C10orf11 (230103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	77386485	77386485	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77386485delA								MIR606 (74174 upstream) : C10orf11 (156034 downstream)																																			---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	77884042	77884042	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77884042delA	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	77991110	77991110	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77991110delG	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	78356063	78356064	+	IGR	INS	-	A	A	rs151112388	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78356063_78356064insA								C10orf11 (38939 upstream) : KCNMA1 (273295 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	78566454	78566455	+	IGR	DEL	GC	-	-	rs147704296		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78566454_78566455delGC								C10orf11 (249330 upstream) : KCNMA1 (62904 downstream)																																			---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	79104344	79104344	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79104344delT	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
DLG5	9231	broad.mit.edu	37	10	79603069	79603069	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79603069delA	uc001jzk.2	-						DLG5_uc001jzj.2_Intron|DLG5_uc009xru.1_Intron|DLG5_uc001jzl.3_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)															---	---	---	---
DLG5	9231	broad.mit.edu	37	10	79646143	79646143	+	Intron	DEL	T	-	-	rs67258322		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79646143delT	uc001jzk.2	-						DLG5_uc009xru.1_Intron	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	79900520	79900520	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79900520delT								RPS24 (83950 upstream) : LOC283050 (802564 downstream)																																			---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	80874254	80874263	+	Intron	DEL	GTGTGTGTGC	-	-	rs72328497		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80874254_80874263delGTGTGTGTGC	uc001kaf.2	+							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)															---	---	---	---
MBL1P	8512	broad.mit.edu	37	10	81680656	81680656	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81680656delA	uc001kbf.2	+						MBL1P_uc001kbg.1_RNA					Homo sapiens mannose-binding protein-A pseudogene (MBL1P1) mRNA sequence.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	81885733	81885733	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81885733delA								C10orf57 (33427 upstream) : PLAC9 (6525 downstream)																																			---	---	---	---
ANXA11	311	broad.mit.edu	37	10	81916277	81916277	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81916277delT	uc001kbq.1	-						ANXA11_uc010qlx.1_Intron|ANXA11_uc001kbr.1_Intron|ANXA11_uc001kbs.1_Intron|ANXA11_uc001kbt.1_Intron|ANXA11_uc010qly.1_Intron|ANXA11_uc009xsq.1_Intron|ANXA11_uc001kbu.1_Intron	NM_145869	NP_665876			annexin A11						cell cycle|cytokinesis, completion of separation|phagocytosis|response to calcium ion	azurophil granule|melanosome|midbody|nuclear envelope|nucleoplasm|phagocytic vesicle|specific granule|spindle	calcium-dependent phospholipid binding|calcium-dependent protein binding|S100 alpha binding			ovary(1)	1	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	82095804	82095804	+	IGR	DEL	A	-	-	rs72815321	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82095804delA								MAT1A (46370 upstream) : DYDC1 (60 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82199571	82199572	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82199571_82199572delAC								C10orf58 (2702 upstream) : TSPAN14 (14466 downstream)																																			---	---	---	---
NRG3	10718	broad.mit.edu	37	10	84339347	84339348	+	Intron	INS	-	GT	GT	rs148283237	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84339347_84339348insGT	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	84518932	84518933	+	Intron	INS	-	TC	TC	rs147330192	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84518932_84518933insTC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	85669722	85669723	+	IGR	DEL	AA	-	-	rs35867689		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85669722_85669723delAA								NRG3 (922787 upstream) : GHITM (229462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85751275	85751277	+	IGR	DEL	AAA	-	-	rs78678541		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85751275_85751277delAAA								None (None upstream) : GHITM (147908 downstream)																																			---	---	---	---
FAM190B	54462	broad.mit.edu	37	10	86111000	86111000	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86111000delT	uc001kdh.1	+						FAM190B_uc001kdg.1_Intron|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	86931761	86931761	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86931761delA								FAM190B (653485 upstream) : GRID1 (427551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	87302843	87302844	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87302843_87302844delAA								None (None upstream) : GRID1 (56468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	88350328	88350328	+	IGR	DEL	A	-	-	rs80006353		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88350328delA								WAPAL (68787 upstream) : OPN4 (63986 downstream)																																			---	---	---	---
BMPR1A	657	broad.mit.edu	37	10	88666169	88666169	+	Intron	DEL	T	-	-	rs112473102		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88666169delT	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	88695240	88695240	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88695240delT								BMPR1A (10296 upstream) : MMRN2 (60 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	89508464	89508465	+	IGR	DEL	TT	-	-	rs12782128	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89508464_89508465delTT								PAPSS2 (1004 upstream) : ATAD1 (4410 downstream)																																			---	---	---	---
ATAD1	84896	broad.mit.edu	37	10	89514658	89514658	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89514658delA	uc001key.1	-						ATAD1_uc010qmr.1_Intron|ATAD1_uc009xth.1_Intron|ATAD1_uc001kez.1_Intron	NM_032810	NP_116199			ATPase family, AAA domain containing 1							peroxisome	ATP binding|nucleoside-triphosphatase activity			large_intestine(1)|ovary(1)	2		all_cancers(4;6.78e-12)|Prostate(4;3.56e-12)|all_epithelial(4;5.58e-09)|Melanoma(5;0.0273)|Breast(4;0.0424)|all_hematologic(4;0.0846)|Colorectal(252;0.207)|Glioma(4;0.217)|all_neural(4;0.224)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00131)|GBM - Glioblastoma multiforme(1;1.1e-32)|Lung(2;1.4e-05)|LUSC - Lung squamous cell carcinoma(2;2.69e-05)|Colorectal(12;7.09e-05)|COAD - Colon adenocarcinoma(12;0.000261)|STAD - Stomach adenocarcinoma(243;0.235)														---	---	---	---
RNLS	55328	broad.mit.edu	37	10	89929954	89929954	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89929954delA	uc010qms.1	-											SubName: Full=cDNA FLJ55083, highly similar to Renalase (EC 1.4.-.-);							extracellular region	oxidoreductase activity			ovary(1)	1																		---	---	---	---
RNLS	55328	broad.mit.edu	37	10	90034668	90034668	+	3'UTR	DEL	A	-	-	rs113106989		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90034668delA	uc001kfd.2	-	7					RNLS_uc010qms.1_Intron	NM_018363	NP_060833			renalase isoform 2							extracellular region	oxidoreductase activity			ovary(1)	1																		---	---	---	---
RNLS	55328	broad.mit.edu	37	10	90045392	90045392	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90045392delA	uc001kfe.2	-						RNLS_uc010qms.1_Intron|RNLS_uc001kfd.2_Intron|RNLS_uc009xtj.2_Intron	NM_001031709	NP_001026879			renalase isoform 1							extracellular region	oxidoreductase activity			ovary(1)	1																		---	---	---	---
SLC16A12	387700	broad.mit.edu	37	10	91213726	91213727	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91213726_91213727delTC	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	91467265	91467265	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91467265delT	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron	NM_016195	NP_057279			M-phase phosphoprotein 1						cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
KIF20B	9585	broad.mit.edu	37	10	91483767	91483767	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91483767delA	uc001kgs.1	+	14	1841	c.1769delA	c.(1768-1770)GAAfs	p.E590fs	KIF20B_uc001kgr.1_Frame_Shift_Del_p.E590fs|KIF20B_uc001kgt.1_5'UTR	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1	590	Potential.				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																		---	---	---	---
KIF20B	9585	broad.mit.edu	37	10	91483917	91483917	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	92291157	92291158	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92291157_92291158delAA								KIF20B (756457 upstream) : HTR7 (209420 downstream)																																			---	---	---	---
HTR7	3363	broad.mit.edu	37	10	92546123	92546123	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92546123delT	uc001kha.2	-						HTR7_uc001kgz.2_Intron|HTR7_uc001khb.2_Intron	NM_019859	NP_062873			5-hydroxytryptamine receptor 7 isoform d						blood circulation|circadian rhythm	integral to plasma membrane	protein binding|serotonin receptor activity			ovary(1)	1					Eletriptan(DB00216)|Methysergide(DB00247)|Ziprasidone(DB00246)													---	---	---	---
HTR7	3363	broad.mit.edu	37	10	92580891	92580892	+	Intron	INS	-	CACA	CACA	rs11186322		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92580891_92580892insCACA	uc001kha.2	-						HTR7_uc001kgz.2_Intron|HTR7_uc001khb.2_Intron	NM_019859	NP_062873			5-hydroxytryptamine receptor 7 isoform d						blood circulation|circadian rhythm	integral to plasma membrane	protein binding|serotonin receptor activity			ovary(1)	1					Eletriptan(DB00216)|Methysergide(DB00247)|Ziprasidone(DB00246)													---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93695681	93695681	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93695681delT	uc001khr.2	+						BTAF1_uc009xua.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)																---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93741816	93741816	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93748896	93748896	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93748896delT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	94124068	94124068	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94124068delA								MARCH5 (10347 upstream) : IDE (89532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	94338643	94338643	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94338643delT								IDE (4791 upstream) : KIF11 (14182 downstream)																																			---	---	---	---
EXOC6	54536	broad.mit.edu	37	10	94738165	94738166	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94738165_94738166insA	uc001kig.2	+						EXOC6_uc010qnr.1_Intron|EXOC6_uc001kie.2_Intron|EXOC6_uc009xub.2_Intron|EXOC6_uc009xuc.2_Intron|EXOC6_uc001kih.2_Intron|EXOC6_uc001kii.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)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	94969262	94969263	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94969262_94969263insA								CYP26A1 (131621 upstream) : MYOF (96924 downstream)																																			---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95173585	95173585	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95173585delA	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	95244278	95244279	+	5'Flank	INS	-	AAC	AAC	rs145567840	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95244278_95244279insAAC	uc001kin.2	-						MYOF_uc001kio.2_5'Flank|MYOF_uc001kip.3_5'Flank|MYOF_uc009xuf.2_5'Flank	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																		---	---	---	---
LGI1	9211	broad.mit.edu	37	10	95523037	95523038	+	Intron	DEL	AC	-	-	rs144378530	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95523037_95523038delAC	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	95792060	95792061	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95792060_95792061insA	uc001kjk.2	+						PLCE1_uc010qnx.1_Intron	NM_016341	NP_057425			phospholipase C, epsilon 1 isoform 1						activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)																---	---	---	---
PLCE1	51196	broad.mit.edu	37	10	95904072	95904073	+	Intron	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95904072_95904073insTG	uc001kjk.2	+						PLCE1_uc010qnx.1_Intron|PLCE1_uc001kjm.2_Intron	NM_016341	NP_057425			phospholipase C, epsilon 1 isoform 1						activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)																---	---	---	---
NOC3L	64318	broad.mit.edu	37	10	96094287	96094287	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																---	---	---	---
HELLS	3070	broad.mit.edu	37	10	96322552	96322552	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96322552delA	uc001kjt.2	+						HELLS_uc001kjs.2_Intron|HELLS_uc009xul.2_Intron|HELLS_uc009xum.2_Intron|HELLS_uc009xun.2_Intron|HELLS_uc009xuo.2_Intron|HELLS_uc001kju.2_Intron|HELLS_uc009xup.2_Intron|HELLS_uc009xuq.2_Intron|HELLS_uc009xur.2_Intron	NM_018063	NP_060533			helicase, lymphoid-specific						cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	97664557	97664558	+	Intron	DEL	AA	-	-	rs77444468		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97664557_97664558delAA	uc001klg.1	-											Homo sapiens cDNA FLJ34077 fis, clone FCBBF3003481, weakly similar to ZINC FINGER PROTEIN 195.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	97939598	97939599	+	IGR	INS	-	CTT	CTT	rs139762736	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97939598_97939599insCTT								ZNF518A (16088 upstream) : BLNK (11864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	98510007	98510008	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98510007_98510008delAA								PIK3AP1 (29728 upstream) : MIR607 (78418 downstream)																																			---	---	---	---
SLIT1	6585	broad.mit.edu	37	10	98780878	98780879	+	Intron	INS	-	CCTTGTTC	CCTTGTTC	rs140758802	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98780878_98780879insCCTTGTTC	uc001kmw.2	-							NM_003061	NP_003052			slit homolog 1 precursor						axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)														---	---	---	---
ARHGAP19	84986	broad.mit.edu	37	10	98992904	98992904	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98992904delA	uc001knb.2	-						ARHGAP19_uc001kmy.2_Intron|ARHGAP19_uc001kna.2_Intron|ARHGAP19_uc009xvi.2_Intron|ARHGAP19_uc009xvj.2_Intron|ARHGAP19_uc009xvk.2_Intron	NM_032900	NP_116289			Rho GTPase activating protein 19						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	GTPase activator activity				0		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)														---	---	---	---
PI4K2A	55361	broad.mit.edu	37	10	99353633	99353633	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99353633delT	uc010qoy.1	+						DHDPSL_uc001knx.2_Intron|DHDPSL_uc001kny.2_Intron|DHDPSL_uc001knz.2_Intron	NM_018425	NP_060895			phosphatidylinositol 4-kinase type 2 alpha						phosphatidylinositol biosynthetic process	cytoplasm|integral to plasma membrane|membrane raft	1-phosphatidylinositol 4-kinase activity|ATP binding|magnesium ion binding			lung(1)|skin(1)	2		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)														---	---	---	---
PI4K2A	55361	broad.mit.edu	37	10	99379120	99379120	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99379120delA	uc010qoy.1	+						MORN4_uc001kob.3_Intron|MORN4_uc001koc.3_Intron|MORN4_uc001kod.3_Intron|MORN4_uc001koe.2_Intron|uc001kof.1_Intron	NM_018425	NP_060895			phosphatidylinositol 4-kinase type 2 alpha						phosphatidylinositol biosynthetic process	cytoplasm|integral to plasma membrane|membrane raft	1-phosphatidylinositol 4-kinase activity|ATP binding|magnesium ion binding			lung(1)|skin(1)	2		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)														---	---	---	---
HPSE2	60495	broad.mit.edu	37	10	100226368	100226370	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100226368_100226370delAAA	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	100240401	100240401	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100240401delA	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	100787434	100787436	+	Intron	DEL	ACC	-	-	rs143852520		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100787434_100787436delACC	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	100893925	100893926	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100893925_100893926insA	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	100954284	100954284	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100954284delA	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)														---	---	---	---
SLC25A28	81894	broad.mit.edu	37	10	101412193	101412193	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101412193delT	uc001kpy.2	-											RecName: Full=Mitoferrin-2; AltName: Full=Mitochondrial iron transporter 2; AltName: Full=Solute carrier family 25 member 28; AltName: Full=Mitochondrial RNA-splicing protein 3/4 homolog;          Short=hMRS3/4;          Short=MRS3/4;						ion transport|iron ion homeostasis	integral to membrane|mitochondrial inner membrane					0		Colorectal(252;0.234)		Epithelial(162;2.57e-10)|all cancers(201;2.01e-08)														---	---	---	---
ABCC2	1244	broad.mit.edu	37	10	101579171	101579172	+	Intron	DEL	TG	-	-	rs5787360		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101579171_101579172delTG	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	103015325	103015325	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103015325delT	uc001ksy.1	-											Homo sapiens cDNA FLJ34886 fis, clone NT2NE2016766, weakly similar to Mus musculus nuclear localization signal binding protein (spot-1) mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	103061102	103061102	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103061102delT								LBX1 (72385 upstream) : BTRC (52723 downstream)																																			---	---	---	---
BTRC	8945	broad.mit.edu	37	10	103138019	103138019	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103138019delT	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)														---	---	---	---
FBXW4	6468	broad.mit.edu	37	10	103378650	103378650	+	Intron	DEL	A	-	-	rs75454639		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103378650delA	uc001kto.2	-							NM_022039	NP_071322			F-box and WD repeat domain containing 4						ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	ubiquitin ligase complex				skin(1)	1		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)														---	---	---	---
FBXW4	6468	broad.mit.edu	37	10	103379416	103379417	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103379416_103379417delAA	uc001kto.2	-							NM_022039	NP_071322			F-box and WD repeat domain containing 4						ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	ubiquitin ligase complex				skin(1)	1		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	103501060	103501065	+	IGR	DEL	AAAAAA	-	-	rs112507967		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103501060_103501065delAAAAAA								FBXW4 (46317 upstream) : FGF8 (28822 downstream)																																			---	---	---	---
C10orf76	79591	broad.mit.edu	37	10	103735185	103735185	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103735185delA	uc009xwy.1	-						C10orf76_uc009xwx.1_Intron	NM_024541	NP_078817			hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)														---	---	---	---
C10orf76	79591	broad.mit.edu	37	10	103735617	103735617	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103735617delA	uc009xwy.1	-						C10orf76_uc009xwx.1_Intron	NM_024541	NP_078817			hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)														---	---	---	---
C10orf76	79591	broad.mit.edu	37	10	103766491	103766491	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103766491delT	uc009xwy.1	-							NM_024541	NP_078817			hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)														---	---	---	---
LDB1	8861	broad.mit.edu	37	10	103871226	103871226	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103871226delG	uc009xwz.2	-	2	436	c.93delC	c.(91-93)CCCfs	p.P31fs	LDB1_uc001kuk.3_5'UTR|LDB1_uc001kul.3_5'UTR	NM_001113407	NP_001106878	Q86U70	LDB1_HUMAN	LIM domain binding 1 isoform 1	31					histone H3-K4 acetylation|negative regulation of erythrocyte differentiation|negative regulation of transcription, DNA-dependent|positive regulation of hemoglobin biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription elongation, DNA-dependent|transcription, DNA-dependent|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	nuclear chromatin|protein complex	LIM domain binding|protein homodimerization activity|transcription corepressor activity			large_intestine(1)	1		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	103977006	103977007	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103977006_103977007insA								NOLC1 (53379 upstream) : ELOVL3 (9136 downstream)																																			---	---	---	---
CUEDC2	79004	broad.mit.edu	37	10	104194954	104194954	+	5'Flank	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104194954delG	uc001kvn.2	-						MIR146B_hsa-mir-146b|MI0003129_5'Flank	NM_024040	NP_076945			CUE domain containing 2							cytoplasm|nucleus	protein binding				0		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
SUFU	51684	broad.mit.edu	37	10	104374315	104374316	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104374315_104374316delAA	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				---	---	---	---
CYP17A1	1586	broad.mit.edu	37	10	104590294	104590294	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104590294delA	uc001kwg.2	-	8					C10orf26_uc009xxg.1_Intron	NM_000102	NP_000093			cytochrome P450, family 17						androgen biosynthetic process|glucocorticoid biosynthetic process|sex differentiation|xenobiotic metabolic process	endoplasmic reticulum membrane	electron carrier activity|heme binding|oxygen binding|steroid 17-alpha-monooxygenase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	NADH(DB00157)|Progesterone(DB00396)													---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104746377	104746377	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104746377delA	uc001kwm.2	+						CNNM2_uc001kwn.2_Intron	NM_017649	NP_060119			cyclin M2 isoform 1						ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104812049	104812049	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104812049delA	uc001kwm.2	+						CNNM2_uc001kwn.2_Intron	NM_017649	NP_060119			cyclin M2 isoform 1						ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
NT5C2	22978	broad.mit.edu	37	10	104954779	104954779	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104954779delA	uc001kwo.2	-						NT5C2_uc001kwq.2_5'Flank|NT5C2_uc001kwp.2_5'Flank	NM_012229	NP_036361			5'-nucleotidase, cytosolic II						purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding				0		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	104988857	104988862	+	Intron	DEL	ACACAC	-	-	rs35353410		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104988857_104988862delACACAC	uc001kwr.2	-											Homo sapiens, clone IMAGE:5199023, mRNA.																														---	---	---	---
CALHM2	51063	broad.mit.edu	37	10	105208932	105208933	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105208932_105208933delAA	uc001kwz.2	-						CALHM2_uc001kxa.2_Intron|CALHM2_uc001kxc.2_Intron|CALHM2_uc001kxb.2_Intron|CALHM2_uc001kxd.1_3'UTR	NM_015916	NP_057000			calcium homeostasis modulator 2							integral to membrane				skin(1)	1																		---	---	---	---
SH3PXD2A	9644	broad.mit.edu	37	10	105356401	105356402	+	3'UTR	INS	-	AG	AG	rs67331275		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105356401_105356402insAG	uc001kxj.1	-	14					SH3PXD2A_uc010qqr.1_Intron|SH3PXD2A_uc010qqs.1_3'UTR|SH3PXD2A_uc010qqt.1_3'UTR|SH3PXD2A_uc009xxn.1_3'UTR|SH3PXD2A_uc010qqu.1_3'UTR	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)														---	---	---	---
SH3PXD2A	9644	broad.mit.edu	37	10	105391712	105391712	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105391712delA	uc001kxj.1	-						SH3PXD2A_uc010qqr.1_Intron|SH3PXD2A_uc010qqs.1_Intron|SH3PXD2A_uc010qqt.1_Intron|SH3PXD2A_uc009xxn.1_Intron|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)														---	---	---	---
SH3PXD2A	9644	broad.mit.edu	37	10	105452684	105452684	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105452684delC	uc001kxj.1	-						SH3PXD2A_uc010qqr.1_Intron|SH3PXD2A_uc010qqt.1_Intron|SH3PXD2A_uc009xxn.1_Intron|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)														---	---	---	---
C10orf79	80217	broad.mit.edu	37	10	105904407	105904407	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105904407delA	uc001kxw.2	-						C10orf79_uc009xxq.2_Intron	NM_025145	NP_079421			hypothetical protein LOC80217												0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	106309737	106309737	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106309737delT								CCDC147 (94898 upstream) : SORCS3 (91122 downstream)																																			---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106543489	106543490	+	Intron	INS	-	AG	AG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106543489_106543490insAG	uc001kyi.1	+							NM_014978	NP_055793			VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	107064896	107064896	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107064896delT								SORCS3 (39903 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107273966	107273967	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107273966_107273967delCA								SORCS3 (248973 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107361855	107361857	+	IGR	DEL	AAA	-	-	rs78773551		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107361855_107361857delAAA								SORCS3 (336862 upstream) : SORCS1 (971565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107757618	107757619	+	IGR	DEL	TG	-	-	rs61875571		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107757618_107757619delTG								SORCS3 (732625 upstream) : SORCS1 (575803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107821747	107821747	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107821747delA								SORCS3 (796754 upstream) : SORCS1 (511675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107882895	107882896	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107882895_107882896insT								SORCS3 (857902 upstream) : SORCS1 (450526 downstream)																																			---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108359125	108359126	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108359125_108359126insA	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	108708719	108708720	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108708719_108708720insA	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	108756794	108756794	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108756794delT	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	108904682	108904683	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108904682_108904683insA	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	109107528	109107528	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109107528delT								SORCS1 (183236 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	109353802	109353803	+	IGR	INS	-	AGAG	AGAG	rs147307394	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109353802_109353803insAGAG								SORCS1 (429510 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110516629	110516629	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110516629delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110760480	110760480	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110760480delT								None (None upstream) : XPNPEP1 (864044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110788481	110788481	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110788481delA								None (None upstream) : XPNPEP1 (836043 downstream)																																			---	---	---	---
XPNPEP1	7511	broad.mit.edu	37	10	111630199	111630199	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111630199delA	uc001kyp.1	-						XPNPEP1_uc009xxt.1_Intron|XPNPEP1_uc001kyq.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)														---	---	---	---
XPNPEP1	7511	broad.mit.edu	37	10	111651337	111651338	+	Intron	DEL	TT	-	-	rs112429910		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111651337_111651338delTT	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)														---	---	---	---
ADD3	120	broad.mit.edu	37	10	111799098	111799098	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111799098delA	uc001kyt.3	+						ADD3_uc001kys.3_Intron|ADD3_uc001kyu.2_Intron|ADD3_uc001kyv.2_Intron|ADD3_uc001kyw.2_Intron	NM_016824	NP_058432			adducin 3 (gamma) isoform a							cytoskeleton	actin binding|calmodulin binding|metal ion binding|structural constituent of cytoskeleton			ovary(2)|skin(2)|large_intestine(1)	5		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)														---	---	---	---
SMNDC1	10285	broad.mit.edu	37	10	112058387	112058387	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112058387delT	uc001kzc.3	-						SMNDC1_uc001kzb.2_Intron	NM_005871	NP_005862			survival motor neuron domain containing 1						apoptosis|induction of apoptosis|mRNA processing|RNA splicing, via transesterification reactions	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding|RNA binding			skin(1)	1		Breast(234;0.174)		Epithelial(162;6.86e-05)|all cancers(201;0.00149)|BRCA - Breast invasive adenocarcinoma(275;0.119)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	112076415	112076415	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112076415delC								SMNDC1 (11708 upstream) : DUSP5 (181210 downstream)																																			---	---	---	---
SMC3	9126	broad.mit.edu	37	10	112341962	112341962	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112341962delA	uc001kze.2	+							NM_005445	NP_005436			structural maintenance of chromosomes 3						cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	112802768	112802768	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112802768delT								SHOC2 (29344 upstream) : ADRA2A (34022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113096585	113096586	+	IGR	DEL	TT	-	-	rs33971261		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113096585_113096586delTT								ADRA2A (255925 upstream) : GPAM (813036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113567463	113567463	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113567463delA								ADRA2A (726803 upstream) : GPAM (342159 downstream)																																			---	---	---	---
VTI1A	143187	broad.mit.edu	37	10	114256330	114256330	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114256330delA	uc001kzy.2	+						VTI1A_uc001kzz.2_Intron	NM_145206	NP_660207			SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)														---	---	---	---
VTI1A	143187	broad.mit.edu	37	10	114297977	114297977	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114297977delT	uc001kzy.2	+						VTI1A_uc001kzz.2_Intron	NM_145206	NP_660207			SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)														---	---	---	---
VTI1A	143187	broad.mit.edu	37	10	114514068	114514069	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114514068_114514069insC	uc001kzz.2	+							NM_145206	NP_660207			SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114782581	114782582	+	Intron	INS	-	CT	CT	rs146676076	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114782581_114782582insCT	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)														---	---	---	---
DCLRE1A	9937	broad.mit.edu	37	10	115603845	115603845	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115603845delA	uc001law.2	-							NM_014881	NP_055696			DNA cross-link repair 1A						cell division|mitosis	nucleus	hydrolase activity			skin(2)	2				Epithelial(162;0.0157)|all cancers(201;0.0171)									Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
Unknown	0	broad.mit.edu	37	10	115708771	115708772	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115708771_115708772delAA								NHLRC2 (40319 upstream) : ADRB1 (95034 downstream)																																			---	---	---	---
ABLIM1	3983	broad.mit.edu	37	10	116302348	116302349	+	Intron	INS	-	GAAGGAGGAA	GAAGGAGGAA	rs145911227	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116302348_116302349insGAAGGAGGAA	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	116317597	116317598	+	Intron	DEL	AA	-	-	rs72063407		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116317597_116317598delAA	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)														---	---	---	---
FAM160B1	57700	broad.mit.edu	37	10	116608351	116608351	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116608351delT	uc001lcb.2	+						FAM160B1_uc001lcc.2_Intron	NM_020940	NP_065991			hypothetical protein LOC57700 isoform a											lung(1)	1																		---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117080978	117080978	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117080978delG	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	117128227	117128227	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117128227delT	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	117822065	117822065	+	3'UTR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117822065delC	uc001lcj.2	-	11					GFRA1_uc001lci.2_3'UTR|GFRA1_uc009xyr.2_3'UTR	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	118271736	118271737	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118271736_118271737delAA								PNLIPRP3 (34270 upstream) : PNLIP (33691 downstream)																																			---	---	---	---
VAX1	11023	broad.mit.edu	37	10	118897640	118897641	+	5'UTR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118897640_118897641insA	uc009xyx.2	-	1					VAX1_uc001ldb.1_5'UTR	NM_001112704	NP_001106175			ventral anterior homeobox 1 isoform a							nucleus	sequence-specific DNA binding			ovary(2)	2				all cancers(201;0.0108)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	118926060	118926060	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118926060delC								VAX1 (28248 upstream) : KCNK18 (30940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119179386	119179386	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119179386delA								PDZD8 (44449 upstream) : EMX2OS (64419 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119679489	119679489	+	IGR	DEL	T	-	-	rs76096448		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119679489delT								EMX2 (370433 upstream) : RAB11FIP2 (84940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119682115	119682116	+	IGR	INS	-	A	A	rs144793141	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119682115_119682116insA								EMX2 (373059 upstream) : RAB11FIP2 (82313 downstream)																																			---	---	---	---
CASC2	255082	broad.mit.edu	37	10	119887544	119887545	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119887544_119887545delCA	uc001ldm.3	+						CASC2_uc009xzc.2_Intron	NR_026939				Homo sapiens mRNA for IGM1 protein.												0																		---	---	---	---
CASC2	255082	broad.mit.edu	37	10	119921891	119921891	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119921891delT	uc001ldm.3	+						CASC2_uc009xzc.2_Intron	NR_026939				Homo sapiens mRNA for IGM1 protein.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	120058829	120058829	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120058829delT								CASC2 (89170 upstream) : C10orf84 (9743 downstream)																																			---	---	---	---
C10orf46	143384	broad.mit.edu	37	10	120467214	120467216	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120467214_120467216delAAA	uc001lds.1	-						C10orf46_uc010qst.1_Intron	NM_153810	NP_722517			chromosome 10 open reading frame 46						ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding				0		Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0131)														---	---	---	---
C10orf46	143384	broad.mit.edu	37	10	120515803	120515804	+	5'Flank	DEL	AA	-	-	rs77182521		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120515803_120515804delAA	uc001lds.1	-						C10orf46_uc010qst.1_5'Flank	NM_153810	NP_722517			chromosome 10 open reading frame 46						ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding				0		Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0131)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	120533533	120533535	+	IGR	DEL	TTT	-	-	rs79798702		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120533533_120533535delTTT								C10orf46 (18775 upstream) : NANOS1 (255693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	120773259	120773259	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120773259delA								C10orf46 (258501 upstream) : NANOS1 (15969 downstream)																																			---	---	---	---
EIF3A	8661	broad.mit.edu	37	10	120795796	120795797	+	Intron	DEL	AA	-	-	rs75955170		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120795796_120795797delAA	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)														---	---	---	---
FAM45A	404636	broad.mit.edu	37	10	120879760	120879760	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120879760delA	uc001ldw.2	+						FAM45A_uc010qsv.1_Intron|FAM45A_uc010qsw.1_Intron|FAM45A_uc010qsx.1_Intron|FAM45A_uc010qsy.1_Intron|FAM45A_uc010qsz.1_Intron	NM_207009	NP_996892			hypothetical protein LOC404636											ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)														---	---	---	---
FAM45A	404636	broad.mit.edu	37	10	120889526	120889526	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120889526delT	uc001ldw.2	+						FAM45A_uc010qsv.1_Intron|FAM45A_uc010qsw.1_Intron|FAM45A_uc010qsx.1_Intron|FAM45A_uc010qsy.1_Intron|FAM45A_uc010qsz.1_Intron	NM_207009	NP_996892			hypothetical protein LOC404636											ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)														---	---	---	---
PRDX3	10935	broad.mit.edu	37	10	120936633	120936634	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120936633_120936634insC	uc001lec.2	-	2	111_112	c.68_69insG	c.(67-69)GGCfs	p.G23fs		NM_006793	NP_006784	P30048	PRDX3_HUMAN	peroxiredoxin 3 isoform a precursor	23					cell redox homeostasis|hydrogen peroxide catabolic process|mitochondrion organization|myeloid cell differentiation|negative regulation of kinase activity|positive regulation of cell proliferation|positive regulation of NF-kappaB transcription factor activity|regulation of mitochondrial membrane potential|response to lipopolysaccharide	early endosome|mitochondrion	alkyl hydroperoxide reductase activity|caspase inhibitor activity|peroxidase activity|peroxiredoxin activity|protein C-terminus binding|protein kinase binding				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0245)														---	---	---	---
GRK5	2869	broad.mit.edu	37	10	121095955	121095955	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121095955delT	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)														---	---	---	---
INPP5F	22876	broad.mit.edu	37	10	121583273	121583273	+	Intron	DEL	T	-	-	rs80313489		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121583273delT	uc001leo.2	+						INPP5F_uc001lep.2_Intron	NM_014937	NP_055752			inositol polyphosphate-5-phosphatase F								phosphoric ester hydrolase activity			ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)														---	---	---	---
C10orf119	79892	broad.mit.edu	37	10	121609304	121609304	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121609304delT	uc001ler.2	-						C10orf119_uc001leq.1_Intron|C10orf119_uc001les.1_Intron|C10orf119_uc001let.1_Intron	NM_024834	NP_079110			chromosome 10 open reading frame 119						cell division|DNA-dependent DNA replication|mitosis|S phase of mitotic cell cycle|sister chromatid cohesion	nucleus	chromatin binding				0		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.0044)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	122094794	122094794	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122094794delA								SEC23IP (393549 upstream) : PPAPDC1A (121672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	122669856	122669857	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122669856_122669857delAG								WDR11 (821 upstream) : FGFR2 (567988 downstream)																																			---	---	---	---
FGFR2	2263	broad.mit.edu	37	10	123263119	123263119	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123263119delT	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_uc001lfg.3_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	123343545	123343546	+	Intron	INS	-	CAT	CAT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123343545_123343546insCAT	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				---	---	---	---
Unknown	0	broad.mit.edu	37	10	123435538	123435539	+	IGR	INS	-	CA	CA	rs147076704	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123435538_123435539insCA								FGFR2 (77566 upstream) : ATE1 (67087 downstream)																																			---	---	---	---
ATE1	11101	broad.mit.edu	37	10	123676354	123676356	+	Intron	DEL	AAA	-	-	rs113526423		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123676354_123676356delAAA	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)																---	---	---	---
BTBD16	118663	broad.mit.edu	37	10	124058504	124058504	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124058504delT	uc001lgc.1	+						BTBD16_uc001lgd.1_Intron	NM_144587	NP_653188			BTB (POZ) domain containing 16											skin(1)	1		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)														OREG0020592	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ACADSB	36	broad.mit.edu	37	10	124795611	124795611	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124795611delT	uc001lhb.2	+						ACADSB_uc010qub.1_Intron	NM_001609	NP_001600			acyl-Coenzyme A dehydrogenase, short/branched						branched chain family amino acid catabolic process|fatty acid metabolic process	mitochondrial matrix	flavin adenine dinucleotide binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.0811)|COAD - Colon adenocarcinoma(40;0.0835)	L-Isoleucine(DB00167)													---	---	---	---
HMX3	340784	broad.mit.edu	37	10	124895995	124895996	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124895995_124895996insC	uc010quc.1	+							NM_001105574	NP_001099044			H6 family homeobox 3						cell differentiation	nucleus	sequence-specific DNA binding transcription factor activity				0		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.122)|COAD - Colon adenocarcinoma(40;0.141)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	125208714	125208715	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125208714_125208715insA	uc001lhg.1	+											full-length cDNA clone CS0DD008YJ14 of Neuroblastoma Cot 50-normalized of Homo sapiens (human).																														---	---	---	---
CHST15	51363	broad.mit.edu	37	10	125840856	125840873	+	Intron	DEL	GCATGCACACACATGCAC	-	-	rs72197768		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125840856_125840873delGCATGCACACACATGCAC	uc001lhm.2	-						CHST15_uc001lhn.2_Intron|CHST15_uc010que.1_Intron|CHST15_uc001lho.2_Intron	NM_015892	NP_056976			B cell RAG associated protein						hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	126006397	126006398	+	IGR	DEL	AC	-	-	rs71988357		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126006397_126006398delAC								CHST15 (153191 upstream) : OAT (79474 downstream)																																			---	---	---	---
OAT	4942	broad.mit.edu	37	10	126100914	126100915	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126100914_126100915insA	uc001lhp.2	-						OAT_uc001lhq.2_Intron|OAT_uc001lhr.2_Intron	NM_000274	NP_000265			ornithine aminotransferase precursor						cellular amino acid biosynthetic process|visual perception	mitochondrial matrix	ornithine-oxo-acid transaminase activity|protein binding|pyridoxal phosphate binding				0		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	126142567	126142568	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126142567_126142568delTT								NKX1-2 (4017 upstream) : LHPP (7844 downstream)																																			---	---	---	---
LHPP	64077	broad.mit.edu	37	10	126190941	126190941	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126190941delT	uc001lhs.1	+						LHPP_uc001lht.1_Intron|LHPP_uc009yai.1_Intron	NM_022126	NP_071409			phospholysine phosphohistidine inorganic						protein dephosphorylation	cytosol|nucleus	inorganic diphosphatase activity|magnesium ion binding|phosphohistidine phosphatase activity|protein homodimerization activity				0		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	126561719	126561720	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126561719_126561720insT								FAM175B (36481 upstream) : ZRANB1 (67252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	126859586	126859586	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126859586delA								CTBP2 (9962 upstream) : LOC100169752 (403354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	126979745	126979745	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126979745delA								CTBP2 (130121 upstream) : LOC100169752 (283195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	127103574	127103574	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127103574delT								CTBP2 (253950 upstream) : LOC100169752 (159366 downstream)																																			---	---	---	---
FANK1	92565	broad.mit.edu	37	10	127606656	127606656	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127606656delA	uc001ljh.3	+						FANK1_uc010quk.1_Intron|FANK1_uc009yan.2_Intron	NM_145235	NP_660278			fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	128577216	128577216	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128577216delA								C10orf90 (218137 upstream) : DOCK1 (16807 downstream)																																			---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128821807	128821810	+	Intron	DEL	TTTT	-	-	rs72037531		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128821807_128821810delTTTT	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	129010925	129010925	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129010925delT	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	129060294	129060295	+	Intron	DEL	AT	-	-	rs35452674		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129060294_129060295delAT	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	129112437	129112437	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129112437delT	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)														---	---	---	---
PTPRE	5791	broad.mit.edu	37	10	129859191	129859191	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129859191delT	uc001lkb.2	+						PTPRE_uc009yat.2_Intron|PTPRE_uc010qup.1_Intron|PTPRE_uc009yau.2_Intron|PTPRE_uc001lkd.2_Intron|PTPRE_uc010quq.1_Intron	NM_006504	NP_006495			protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway|protein phosphorylation	cytoplasm|integral to membrane|intermediate filament cytoskeleton|nucleus|plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(1)	1		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	130195907	130195907	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130195907delC								MKI67 (271439 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130236811	130236812	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130236811_130236812delGT								MKI67 (312343 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130433811	130433811	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130433811delA								MKI67 (509343 upstream) : MGMT (831643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130605845	130605849	+	IGR	DEL	GTTAA	-	-	rs143664162		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130605845_130605849delGTTAA								MKI67 (681377 upstream) : MGMT (659605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	131584466	131584468	+	IGR	DEL	ATC	-	-	rs147423896		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131584466_131584468delATC								MGMT (18683 upstream) : EBF3 (49079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132201766	132201766	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132201766delA								GLRX3 (218982 upstream) : TCERG1L (688890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132589540	132589541	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132589540_132589541insC								GLRX3 (606756 upstream) : TCERG1L (301115 downstream)																																			---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	132908501	132908502	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132908501_132908502delAA	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597			transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	133031721	133031722	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133031721_133031722delAC	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597			transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	133281962	133281965	+	IGR	DEL	GATG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133281962_133281965delGATG								TCERG1L (171978 upstream) : PPP2R2D (465995 downstream)																																			---	---	---	---
JAKMIP3	282973	broad.mit.edu	37	10	133916826	133916828	+	5'Flank	DEL	CAT	-	-	rs67066716		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133916826_133916828delCAT	uc001lkx.3	+							NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)														---	---	---	---
STK32C	282974	broad.mit.edu	37	10	134021031	134021032	+	3'UTR	INS	-	TA	TA	rs139329266	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134021031_134021032insTA	uc001lle.1	-	12					STK32C_uc001lld.1_3'UTR|STK32C_uc010quu.1_3'UTR|STK32C_uc001llb.2_3'UTR|STK32C_uc001llc.1_RNA	NM_173575	NP_775846			serine/threonine kinase 32C								ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)														---	---	---	---
PAOX	196743	broad.mit.edu	37	10	135202325	135202359	+	Intron	DEL	GTCATCCCGGGGCTCTCTTTCTCCATGCAGGTCTG	-	-	rs144417516	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135202325_135202359delGTCATCCCGGGGCTCTCTTTCTCCATGCAGGTCTG	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)														---	---	---	---
LOC619207	619207	broad.mit.edu	37	10	135284458	135284458	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135284458delA	uc001lni.1	+											Homo sapiens cDNA FLJ41380 fis, clone BRCAN2011254.												0																		---	---	---	---
CYP2E1	1571	broad.mit.edu	37	10	135341282	135341283	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135341282_135341283insC	uc001lnj.1	+						CYP2E1_uc001lnk.1_Intron|CYP2E1_uc009ybl.1_Intron|CYP2E1_uc009ybm.1_Intron	NM_000773	NP_000764			cytochrome P450, family 2, subfamily E,						drug metabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding			central_nervous_system(3)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Dacarbazine(DB00851)|Dapsone(DB00250)|Enflurane(DB00228)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethosuximide(DB00593)|Fomepizole(DB01213)|Glutathione(DB00143)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Isoniazid(DB00951)|Menadione(DB00170)|Mephenytoin(DB00532)|Methoxyflurane(DB01028)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitrofurantoin(DB00698)|Orphenadrine(DB01173)|Phenelzine(DB00780)|Quinidine(DB00908)|S-Adenosylmethionine(DB00118)|Sevoflurane(DB01236)|Theophylline(DB00277)|Tolbutamide(DB01124)									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				---	---	---	---
FRG2B	441581	broad.mit.edu	37	10	135440780	135440781	+	5'Flank	INS	-	A	A	rs143239053	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135440780_135440781insA	uc010qvg.1	-							NM_001080998	NP_001074467			FSHD region gene 2 family, member B							nucleus					0		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	135457159	135457160	+	IGR	INS	-	AA	AA	rs140350571		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135457159_135457160insAA								FRG2B (16860 upstream) : LOC653544 (33119 downstream)																																			---	---	---	---
SIGIRR	59307	broad.mit.edu	37	11	413675	413676	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:413675_413676insT	uc001lpd.2	-						SIGIRR_uc001lpf.2_Intron|SIGIRR_uc001lpe.1_Intron	NM_001135054	NP_001128526			single Ig IL-1R-related molecule						acute-phase response|innate immune response|negative regulation of chemokine biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity	integral to membrane	protein binding|transmembrane receptor activity				0		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
RNH1	6050	broad.mit.edu	37	11	498992	498992	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:498992delC	uc001lpk.1	-						RNH1_uc001lpl.1_Intron|RNH1_uc001lpm.1_Intron|RNH1_uc001lpn.1_Intron|RNH1_uc001lpo.1_Intron|RNH1_uc009ybw.1_Splice_Site|RNH1_uc001lpp.1_Intron|RNH1_uc001lpt.1_Intron|RNH1_uc001lpq.1_Intron|RNH1_uc001lpr.1_Intron|RNH1_uc001lps.1_Intron	NM_203389	NP_976323			ribonuclease/angiogenin inhibitor						mRNA catabolic process|regulation of angiogenesis	angiogenin-PRI complex|cytoplasm	protein binding|ribonuclease inhibitor activity				0		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;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
CDHR5	53841	broad.mit.edu	37	11	622424	622427	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:622424_622427delTTTT	uc001lqj.2	-						CDHR5_uc001lqk.2_Intron|CDHR5_uc009ycc.2_Intron|CDHR5_uc009ycd.2_Intron|CDHR5_uc001lql.2_Intron|CDHR5_uc001lqm.2_Intron|CDHR5_uc009yce.1_Intron	NM_021924	NP_068743			mucin and cadherin-like isoform 1						calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	1933519	1933519	+	IGR	DEL	T	-	-	rs113143995		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1933519delT								LSP1 (20027 upstream) : TNNT3 (7280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	2050081	2050081	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2050081delG								H19 (31016 upstream) : IGF2 (100267 downstream)																																			---	---	---	---
SLC22A18	5002	broad.mit.edu	37	11	2920954	2920954	+	5'UTR	DEL	A	-	-	rs77164179		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2920954delA	uc001lwx.2	+	1					SLC22A18AS_uc001lwv.3_5'UTR|SLC22A18AS_uc001lww.3_Intron|SLC22A18_uc001lwy.2_5'Flank|SLC22A18_uc001lwz.2_5'Flank	NM_183233	NP_899056			tumor suppressing subtransferable candidate 5						excretion|organic cation transport	apical plasma membrane|cytoplasmic part|integral to membrane|nuclear envelope	drug:hydrogen antiporter activity|symporter activity|ubiquitin protein ligase binding			central_nervous_system(2)|ovary(1)	3		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)														---	---	---	---
NAP1L4	4676	broad.mit.edu	37	11	2976291	2976291	+	Intron	DEL	T	-	-	rs35712223		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2976291delT	uc001lxc.2	-						NAP1L4_uc001lxb.2_5'Flank|NAP1L4_uc009ydt.2_Intron|NAP1L4_uc010qxm.1_Intron|NAP1L4_uc010qxn.1_Intron	NM_005969	NP_005960			nucleosome assembly protein 1-like 4						nucleosome assembly	chromatin assembly complex|cytoplasm	unfolded protein binding			ovary(1)	1		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;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	3020838	3020839	+	IGR	INS	-	TC	TC	rs148251552	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3020838_3020839insTC								NAP1L4 (7231 upstream) : CARS (1321 downstream)																																			---	---	---	---
OSBPL5	114879	broad.mit.edu	37	11	3158336	3158336	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3158336delA	uc001lxk.2	-						OSBPL5_uc009ydw.2_Intron|OSBPL5_uc001lxl.2_Intron|OSBPL5_uc009ydx.2_Intron	NM_020896	NP_065947			oxysterol-binding protein-like protein 5 isoform						cholesterol metabolic process|cholesterol transport|Golgi to plasma membrane transport	cytosol	oxysterol binding|protein binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)														---	---	---	---
STIM1	6786	broad.mit.edu	37	11	3992765	3992765	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3992765delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	4236028	4236029	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4236028_4236029insT								RRM1 (12269 upstream) : OR52B4 (152554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	4932064	4932064	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4932064delA								OR51A7 (2528 upstream) : OR51G2 (3885 downstream)																																			---	---	---	---
OR52A4	390053	broad.mit.edu	37	11	5142960	5142960	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5142960delA	uc001lzz.1	-						OR52A4_uc001maa.2_RNA	NM_001005222	NP_001005222			olfactory receptor, family 52, subfamily A,											ovary(2)	2		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.7e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)														---	---	---	---
OR52H1	390067	broad.mit.edu	37	11	5565960	5565960	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5565960delA	uc010qzh.1	-	1	794	c.794delT	c.(793-795)TTCfs	p.F265fs	HBG2_uc001mak.1_Intron	NM_001005289	NP_001005289	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H,	265	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
TRIM22	10346	broad.mit.edu	37	11	5713519	5713519	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5713519delT	uc001mbr.2	+						TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Intron|TRIM22_uc009yes.2_Intron|TRIM22_uc010qzm.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	5775904	5775904	+	Intron	DEL	T	-	-	rs66975644		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5775904delT	uc009yet.1	+						TRIM5_uc001mbq.1_Intron|OR52N4_uc001mbu.2_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	6366592	6366593	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6366592_6366593delTC								PRKCDBP (24852 upstream) : SMPD1 (45062 downstream)																																			---	---	---	---
DNHD1	144132	broad.mit.edu	37	11	6585775	6585775	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6585775delC	uc001mdw.3	+	32	11061	c.10497delC	c.(10495-10497)AACfs	p.N3499fs	DNHD1_uc001mea.3_5'UTR|DNHD1_uc001meb.2_5'UTR|DNHD1_uc001mec.2_5'Flank|DNHD1_uc010rao.1_5'Flank	NM_144666	NP_653267	Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1 isoform 1	3499					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)														---	---	---	---
ZNF215	7762	broad.mit.edu	37	11	6976697	6976697	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6976697delT	uc001mey.2	+						ZNF215_uc010raw.1_Intron|ZNF215_uc010rax.1_Intron|ZNF215_uc001mez.1_Intron	NM_013250	NP_037382			zinc finger protein 215						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)														---	---	---	---
SYT9	143425	broad.mit.edu	37	11	7272330	7272331	+	5'Flank	INS	-	AC	AC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7272330_7272331insAC	uc001mfe.2	+						SYT9_uc001mfd.2_Intron|SYT9_uc009yfi.2_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	7765593	7765593	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7765593delT								OVCH2 (37652 upstream) : OR5P2 (51928 downstream)																																			---	---	---	---
LMO1	4004	broad.mit.edu	37	11	8278239	8278248	+	Intron	DEL	ATGGCCTGGA	-	-	rs5789571		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8278239_8278248delATGGCCTGGA	uc001mgg.1	-						LMO1_uc009yfo.1_Intron|LMO1_uc001mgh.1_Intron	NM_002315	NP_002306			LIM domain only 1						cell proliferation|multicellular organismal development|positive regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Epithelial(150;1.59e-07)|BRCA - Breast invasive adenocarcinoma(625;0.203)				T|A	TRD@	T-ALL|neuroblastoma	neuroblastoma							---	---	---	---
Unknown	0	broad.mit.edu	37	11	8398097	8398097	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8398097delT								LMO1 (107915 upstream) : STK33 (15321 downstream)																																			---	---	---	---
STK33	65975	broad.mit.edu	37	11	8519448	8519449	+	Intron	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8519448_8519449insCA	uc001mgj.1	-						STK33_uc001mgk.1_Intron|STK33_uc010rbn.1_Intron|STK33_uc001mgl.3_Intron|STK33_uc009yfp.2_Intron	NM_030906	NP_112168			serine/threonine kinase 33							Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|pancreas(1)|central_nervous_system(1)|skin(1)	7				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	8697782	8697782	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8697782delT	uc001mgo.2	-											Homo sapiens cDNA clone IMAGE:6266066, partial cds.																														---	---	---	---
DENND5A	23258	broad.mit.edu	37	11	9166336	9166336	+	Intron	DEL	A	-	-	rs112911509		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9166336delA	uc001mhl.2	-						DENND5A_uc001mhk.2_Intron|DENND5A_uc010rbw.1_Intron	NM_015213	NP_056028			RAB6 interacting protein 1											liver(1)	1																		---	---	---	---
ZNF143	7702	broad.mit.edu	37	11	9500908	9500908	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9500908delT	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	9754047	9754047	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9754047delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	9780927	9780927	+	Intron	DEL	T	-	-	rs34053083		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9780927delT	uc001mhz.1	+						uc001mhy.1_Intron|uc001mia.1_Intron					full-length cDNA clone CS0DK010YC18 of HeLa cells Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	10064542	10064542	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	10329610	10329611	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10329610_10329611delAA								ADM (687 upstream) : AMPD3 (142257 downstream)																																	OREG0020748	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	11	10433255	10433255	+	IGR	DEL	T	-	-	rs111390481		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10433255delT								ADM (104332 upstream) : AMPD3 (38613 downstream)																																			---	---	---	---
GALNTL4	374378	broad.mit.edu	37	11	11447164	11447164	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11447164delT	uc001mjo.2	-							NM_198516	NP_940918			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	11659544	11659544	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11659544delG								GALNTL4 (15983 upstream) : USP47 (203426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	11744482	11744482	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11744482delT								GALNTL4 (100921 upstream) : USP47 (118488 downstream)																																			---	---	---	---
MICALCL	84953	broad.mit.edu	37	11	12365469	12365469	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12365469delA	uc001mkg.1	+							NM_032867	NP_116256			MICAL C-terminal like						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding			skin(1)	1				Epithelial(150;0.00177)														---	---	---	---
PARVA	55742	broad.mit.edu	37	11	12485524	12485526	+	Intron	DEL	TTT	-	-	rs140855857		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12485524_12485526delTTT	uc001mki.2	+						PARVA_uc001mkh.2_Intron|PARVA_uc010rck.1_Intron	NM_018222	NP_060692			parvin, alpha						cell adhesion|cell junction assembly|cilium morphogenesis	actin cytoskeleton|cytosol|focal adhesion	actin binding			breast(3)	3				Epithelial(150;0.00624)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	12691466	12691467	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12691466_12691467delCA								PARVA (140056 upstream) : TEAD1 (4502 downstream)																																			---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12903079	12903079	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12903079delA	uc001mkj.3	+						TEAD1_uc001mkk.3_Intron|TEAD1_uc009ygl.2_Intron	NM_021961	NP_068780			TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12916747	12916747	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12916747delC	uc001mkj.3	+						TEAD1_uc001mkk.3_Intron|TEAD1_uc009ygl.2_Intron	NM_021961	NP_068780			TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12951569	12951569	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12951569delT	uc001mkj.3	+						TEAD1_uc001mkk.3_Intron|TEAD1_uc009ygl.2_Intron	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)														---	---	---	---
SPON1	10418	broad.mit.edu	37	11	14070818	14070818	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14070818delT	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)														---	---	---	---
COPB1	1315	broad.mit.edu	37	11	14480058	14480058	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14480058delA	uc001mli.2	-						COPB1_uc001mlg.2_Intron|COPB1_uc001mlh.2_Intron	NM_016451	NP_057535			coatomer protein complex, subunit beta 1						COPI coating of Golgi vesicle|interspecies interaction between organisms|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|ER-Golgi intermediate compartment|plasma membrane	protein binding|structural molecule activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	15344400	15344400	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15344400delT								INSC (75648 upstream) : SOX6 (643596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15560389	15560390	+	IGR	INS	-	A	A	rs147428944	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15560389_15560390insA								INSC (291637 upstream) : SOX6 (427606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15672626	15672626	+	IGR	DEL	A	-	-	rs113209425		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15672626delA								INSC (403874 upstream) : SOX6 (315370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15865691	15865691	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15865691delA								INSC (596939 upstream) : SOX6 (122305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15924599	15924606	+	IGR	DEL	TGTGTGTT	-	-	rs2099777		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15924599_15924606delTGTGTGTT								INSC (655847 upstream) : SOX6 (63390 downstream)																																			---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16197662	16197663	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16197662_16197663delAG	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	16395368	16395399	+	Intron	DEL	AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16395368_16395399delAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron|SOX6_uc001mmh.1_Intron|SOX6_uc009ygs.2_Intron|SOX6_uc001mmi.3_Intron|SOX6_uc001mmj.2_Intron	NM_001145819	NP_001139291			SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16506839	16506839	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16506839delA	uc001mmi.3	-						SOX6_uc001mmh.1_Intron|SOX6_uc001mmj.2_Intron					Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	17621735	17621735	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17621735delT	uc001mnh.1	+											SubName: Full=Putative uncharacterized protein OTOG;																												OREG0020813	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KCNC1	3746	broad.mit.edu	37	11	17799295	17799295	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17799295delT	uc001mnk.3	+	2					KCNC1_uc009yhc.1_Intron|KCNC1_uc001mnl.1_5'Flank	NM_004976	NP_004967			Shaw-related voltage-gated potassium channel							voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
KCNC1	3746	broad.mit.edu	37	11	17802413	17802414	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17802413_17802414insG	uc009yhc.1	+						KCNC1_uc001mnl.1_Intron	NM_001112741	NP_001106212			Shaw-related voltage-gated potassium channel							voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
SERGEF	26297	broad.mit.edu	37	11	17866774	17866774	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17866774delT	uc001mnm.2	-						SERGEF_uc009yhd.2_Intron|SERGEF_uc001mnn.2_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																		---	---	---	---
SERGEF	26297	broad.mit.edu	37	11	18027389	18027389	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18027389delA	uc001mnm.2	-						SERGEF_uc009yhd.2_Intron|SERGEF_uc001mnn.2_Intron|SERGEF_uc010rcz.1_Intron|SERGEF_uc001mno.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																		---	---	---	---
SAA3P	6290	broad.mit.edu	37	11	18136939	18136940	+	Intron	DEL	TG	-	-	rs71871691		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18136939_18136940delTG	uc001mnt.2	-							NR_026576				Homo sapiens truncated serum amyloid A3 precursor (SAA3) mRNA, complete cds.												0																OREG0020820	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
HPS5	11234	broad.mit.edu	37	11	18308089	18308090	+	Intron	DEL	AA	-	-	rs76467437		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18308089_18308090delAA	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				---	---	---	---
LDHA	3939	broad.mit.edu	37	11	18425971	18425971	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18425971delA	uc001mok.3	+						LDHA_uc010rdc.1_Intron|LDHA_uc009yhn.2_Intron|LDHA_uc009yho.2_Intron|LDHA_uc001mol.3_Intron|LDHA_uc010rdd.1_Intron	NM_005566	NP_005557			lactate dehydrogenase A isoform 1						glycolysis|pyruvate metabolic process	cytosol	L-lactate dehydrogenase activity|protein binding			central_nervous_system(3)	3					NADH(DB00157)													---	---	---	---
LDHC	3948	broad.mit.edu	37	11	18454946	18454948	+	Intron	DEL	AAA	-	-	rs12576249		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18454946_18454948delAAA	uc001mon.3	+						LDHC_uc001mom.3_Intron|LDHC_uc009yhp.2_Intron|LDHC_uc001moo.3_Intron|LDHC_uc009yhq.2_Intron|LDHC_uc009yhr.2_Intron	NM_017448	NP_059144			L-lactate dehydrogenase C						glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)													---	---	---	---
TSG101	7251	broad.mit.edu	37	11	18537746	18537746	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18537746delT	uc001mor.2	-						TSG101_uc001mos.1_Intron|TSG101_uc009yhs.1_Intron	NM_006292	NP_006283			tumor susceptibility gene 101						cell division|cellular membrane organization|endosome transport|interspecies interaction between organisms|non-lytic virus budding|protein transport|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	early endosome|late endosome membrane|multivesicular body|nucleolus|plasma membrane	calcium-dependent protein binding|DNA binding|transcription corepressor activity|ubiquitin binding|ubiquitin protein ligase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	18844572	18844572	+	IGR	DEL	T	-	-	rs111600529		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18844572delT								PTPN5 (31183 upstream) : MRGPRX1 (110789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	18944505	18944506	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18944505_18944506delAA								PTPN5 (131116 upstream) : MRGPRX1 (10855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	19120230	19120230	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19120230delA								MRGPRX2 (38002 upstream) : ZDHHC13 (18462 downstream)																																			---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19513501	19513504	+	Intron	DEL	AAAG	-	-	rs150403869	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19513501_19513504delAAAG	uc001mpp.2	+							NM_001111018	NP_001104488			neuron navigator 2 isoform 3							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19656831	19656831	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19656831delT	uc001mpp.2	+							NM_001111018	NP_001104488			neuron navigator 2 isoform 3							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	20041541	20041541	+	Intron	DEL	A	-	-	rs34418405		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20041541delA	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron|NAV2_uc001mpt.2_5'Flank	NM_145117	NP_660093			neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	20078331	20078332	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20078331_20078332insT	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron|NAV2_uc001mpt.2_Intron|NAV2_uc009yhx.2_Intron|NAV2_uc009yhy.1_Intron|NAV2_uc009yhz.2_Intron|NAV2_uc001mpu.2_Intron	NM_145117	NP_660093			neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	20168846	20168846	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20168846delA								NAV2 (25700 upstream) : DBX1 (8914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	20300611	20300611	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20300611delA								DBX1 (118741 upstream) : HTATIP2 (84620 downstream)																																			---	---	---	---
PRMT3	10196	broad.mit.edu	37	11	20419359	20419359	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20419359delT	uc001mqb.2	+						PRMT3_uc001mqc.2_Intron|PRMT3_uc010rdn.1_Intron	NM_005788	NP_005779			protein arginine methyltransferase 3 isoform 1								zinc ion binding				0																		---	---	---	---
SLC6A5	9152	broad.mit.edu	37	11	20658876	20658876	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20658876delG	uc001mqd.2	+						SLC6A5_uc009yic.2_Intron	NM_004211	NP_004202			solute carrier family 6 (neurotransmitter						synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)													---	---	---	---
ANO5	203859	broad.mit.edu	37	11	22233000	22233000	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22233000delA	uc001mqi.2	+						ANO5_uc001mqj.2_Intron	NM_213599	NP_998764			anoctamin 5 isoform a							chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	22851757	22851757	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22851757delT	uc001mqq.1	+						SVIP_uc001mqp.3_5'Flank					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	23740885	23740886	+	IGR	INS	-	TC	TC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23740885_23740886insTC								SVIP (889503 upstream) : LUZP2 (777670 downstream)																																			---	---	---	---
LUZP2	338645	broad.mit.edu	37	11	24637561	24637561	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24637561delT	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																		---	---	---	---
LUZP2	338645	broad.mit.edu	37	11	24671518	24671519	+	Intron	INS	-	AG	AG	rs146086509	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24671518_24671519insAG	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																		---	---	---	---
LUZP2	338645	broad.mit.edu	37	11	24892016	24892017	+	Intron	INS	-	AC	AC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24892016_24892017insAC	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																		---	---	---	---
LUZP2	338645	broad.mit.edu	37	11	24970371	24970386	+	Intron	DEL	ATCTATCTATCTATCT	-	-	rs10550731		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24970371_24970386delATCTATCTATCTATCT	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	25641348	25641350	+	IGR	DEL	TCT	-	-	rs149312821		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25641348_25641350delTCT								LUZP2 (537166 upstream) : ANO3 (569479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	25790164	25790164	+	IGR	DEL	G	-	-	rs138201934	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25790164delG								LUZP2 (685982 upstream) : ANO3 (420665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	26104399	26104399	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26104399delT								None (None upstream) : ANO3 (106430 downstream)																																			---	---	---	---
SLC5A12	159963	broad.mit.edu	37	11	26747702	26747709	+	5'Flank	DEL	TTCTTCCT	-	-	rs4259786		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26747702_26747709delTTCTTCCT	uc001mrb.2	-											Homo sapiens mRNA; cDNA DKFZp564G223 (from clone DKFZp564G223).						sodium ion transport	apical plasma membrane|integral to membrane	symporter activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	27354537	27354537	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27354537delA								BBOX1 (205183 upstream) : CCDC34 (5524 downstream)																																			---	---	---	---
CCDC34	91057	broad.mit.edu	37	11	27367942	27367942	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27367942delA	uc001mrh.1	-							NM_030771	NP_110398			coiled-coil domain containing 34 isoform 1												0																		---	---	---	---
BDNFOS	497258	broad.mit.edu	37	11	27610409	27610409	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27610409delA	uc001mrm.2	+						BDNFOS_uc009yij.2_Intron|BDNFOS_uc009yik.2_Intron|BDNFOS_uc009yil.2_Intron|BDNFOS_uc001mrp.2_Intron|BDNFOS_uc009yim.2_Intron|BDNFOS_uc009yin.2_Intron|BDNFOS_uc009yio.2_Intron|BDNFOS_uc009yip.2_Intron|BDNFOS_uc001mrn.2_Intron|BDNFOS_uc009yiq.2_Intron|BDNFOS_uc001mro.2_Intron|BDNFOS_uc009yir.2_Intron|BDNFOS_uc009yis.2_Intron|BDNFOS_uc009yit.2_Intron|BDNFOS_uc009yiu.2_Intron|BDNFOS_uc009yiv.2_Intron|BDNFOS_uc009yiw.2_Intron|BDNFOS_uc009yix.2_Intron|BDNFOS_uc009yiy.2_Intron|BDNFOS_uc009yiz.2_Intron|BDNFOS_uc001mrq.3_Intron|BDNFOS_uc001mrr.3_Intron|BDNFOS_uc009yja.2_Intron|BDNFOS_uc009yjb.2_Intron	NR_002832				Homo sapiens non-coding transcript BT2C (BDNF) mRNA, complete sequence; alternatively spliced.												0																		---	---	---	---
METT5D1	196074	broad.mit.edu	37	11	28318565	28318566	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28318565_28318566delTG	uc001msh.2	+						METT5D1_uc001msg.2_Intron|METT5D1_uc001mse.2_Intron|METT5D1_uc001msi.2_Intron	NM_001113528	NP_001107000			methyltransferase 5 domain containing 1 isoform								methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	28866158	28866159	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28866158_28866159insT								METT5D1 (511104 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	29188529	29188529	+	IGR	DEL	T	-	-	rs143593377		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29188529delT								METT5D1 (833475 upstream) : KCNA4 (843237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30023432	30023432	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30023432delA								None (None upstream) : KCNA4 (8334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30119082	30119082	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30119082delC								KCNA4 (80594 upstream) : FSHB (133481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30208149	30208149	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30208149delA								KCNA4 (169661 upstream) : FSHB (44414 downstream)																																			---	---	---	---
MPPED2	744	broad.mit.edu	37	11	30602049	30602049	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30602049delA	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	30797314	30797314	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30797314delC								MPPED2 (189384 upstream) : DCDC1 (167435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30925317	30925317	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30925317delA	uc001mss.1	-						uc009yjk.1_Intron|uc009yjj.1_Intron					Homo sapiens mRNA for KIAA1493 protein, partial cds.																														---	---	---	---
IMMP1L	196294	broad.mit.edu	37	11	31454958	31454959	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31454958_31454959delTT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	32242267	32242268	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32242267_32242268delAA								RCN1 (114996 upstream) : WT1 (167057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	32528136	32528136	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32528136delT								WIT1 (59875 upstream) : EIF3M (77255 downstream)																																			---	---	---	---
CCDC73	493860	broad.mit.edu	37	11	32676507	32676507	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32676507delT	uc001mtv.2	-	10	701	c.657delA	c.(655-657)AAAfs	p.K219fs	CCDC73_uc001mtw.1_Frame_Shift_Del_p.K219fs	NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79	219										ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)																	---	---	---	---
CCDC73	493860	broad.mit.edu	37	11	32718543	32718543	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32718543delT	uc001mtv.2	-						CCDC73_uc001mtw.1_Intron|CCDC73_uc009yjt.2_Intron	NM_001008391	NP_001008392			sarcoma antigen NY-SAR-79											ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	32902552	32902553	+	IGR	DEL	AG	-	-	rs116765422		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32902552_32902553delAG								PRRG4 (26449 upstream) : QSER1 (12239 downstream)																																			---	---	---	---
TCP11L1	55346	broad.mit.edu	37	11	33094800	33094800	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33094800delT	uc001mud.2	+	10					TCP11L1_uc009yju.2_3'UTR|TCP11L1_uc010rei.1_3'UTR|TCP11L1_uc001mue.2_3'UTR|TCP11L1_uc001muf.1_Intron|LOC283267_uc001mug.3_5'Flank	NM_018393	NP_060863			t-complex 11 (mouse) like 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	33484319	33484319	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33484319delT								HIPK3 (108380 upstream) : C11orf41 (79558 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	33511871	33511871	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33511871delT								HIPK3 (135932 upstream) : C11orf41 (52006 downstream)																																			---	---	---	---
CD59	966	broad.mit.edu	37	11	33737153	33737153	+	Intron	DEL	A	-	-	rs77791064		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33737153delA	uc001mus.3	-						CD59_uc009yjx.2_Intron|CD59_uc009yjy.2_Intron|CD59_uc009yjz.2_Intron|CD59_uc001mut.3_Intron|CD59_uc009yka.2_Intron|CD59_uc001muu.3_Intron|CD59_uc001muv.3_Intron|CD59_uc001mux.3_Intron	NM_001127223	NP_001120695			CD59 antigen preproprotein						blood coagulation|cell surface receptor linked signaling pathway	anchored to external side of plasma membrane|extracellular region|membrane fraction					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	34014618	34014618	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34014618delA								LMO2 (100782 upstream) : CAPRIN1 (58612 downstream)																																			---	---	---	---
NAT10	55226	broad.mit.edu	37	11	34162954	34162955	+	Intron	INS	-	TC	TC	rs141705432		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34162954_34162955insTC	uc001mvk.2	+						NAT10_uc010ren.1_Intron	NM_024662	NP_078938			N-acetyltransferase 10 isoform a							nucleolus	ATP binding|N-acetyltransferase activity|protein binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)																---	---	---	---
ABTB2	25841	broad.mit.edu	37	11	34188528	34188529	+	Intron	INS	-	GA	GA	rs150838892	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34188528_34188529insGA	uc001mvl.1	-							NM_145804	NP_665803			ankyrin repeat and BTB (POZ) domain containing								DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)																---	---	---	---
ABTB2	25841	broad.mit.edu	37	11	34315274	34315274	+	Intron	DEL	T	-	-	rs12223270	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34315274delT	uc001mvl.1	-							NM_145804	NP_665803			ankyrin repeat and BTB (POZ) domain containing								DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)																---	---	---	---
CAT	847	broad.mit.edu	37	11	34490058	34490059	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34490058_34490059delAA	uc001mvm.2	+						CAT_uc001mvn.2_Intron	NM_001752	NP_001743			catalase						hydrogen peroxide catabolic process|negative regulation of apoptosis|positive regulation of cell division|protein tetramerization|purine base metabolic process|purine nucleotide catabolic process|UV protection	peroxisomal matrix|peroxisomal membrane	catalase activity|heme binding|NADP binding|protein homodimerization activity			ovary(2)|pancreas(1)	3		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	34850989	34850989	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34850989delC								EHF (167908 upstream) : APIP (45725 downstream)																																			---	---	---	---
PDHX	8050	broad.mit.edu	37	11	34979161	34979161	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34979161delA	uc001mvt.2	+						PDHX_uc010rep.1_Intron|PDHX_uc010req.1_Intron	NM_003477	NP_003468			pyruvate dehydrogenase complex, component X						pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	acyltransferase activity			kidney(1)	1	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)															---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35457302	35457302	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35457302delA	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991			regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	35599496	35599496	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35599496delA								PAMR1 (47648 upstream) : FJX1 (40239 downstream)																																			---	---	---	---
LDLRAD3	143458	broad.mit.edu	37	11	36011976	36011976	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36011976delT	uc001mwk.1	+						LDLRAD3_uc010rey.1_Intron|LDLRAD3_uc010rez.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)																---	---	---	---
TRAF6	7189	broad.mit.edu	37	11	36514055	36514055	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36514055delT	uc001mwr.1	-						TRAF6_uc001mws.1_Intron	NM_145803	NP_665802			TNF receptor-associated factor 6						activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|membrane protein intracellular domain proteolysis|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|ossification|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 osteoclast differentiation|positive regulation of T cell cytokine production|protein autoubiquitination|protein K63-linked ubiquitination|response to interleukin-1|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	CD40 receptor complex|cell cortex|cytosol|endosome membrane|internal side of plasma membrane|nuclear membrane	histone deacetylase binding|mitogen-activated protein kinase kinase kinase binding|protein kinase B binding|protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1	all_lung(20;0.211)	all_hematologic(20;0.107)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	36986876	36986876	+	IGR	DEL	T	-	-	rs146219740		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36986876delT								C11orf74 (290486 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38424113	38424114	+	IGR	INS	-	TT	TT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38424113_38424114insTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38517134	38517135	+	IGR	INS	-	GT	GT	rs11034799	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38517134_38517135insGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38626513	38626513	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38626513delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39032345	39032345	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39032345delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39441580	39441580	+	IGR	DEL	A	-	-	rs66939145		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39441580delA								None (None upstream) : LRRC4C (694173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39973579	39973580	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39973579_39973580insT								None (None upstream) : LRRC4C (162173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	40099211	40099211	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40099211delA								None (None upstream) : LRRC4C (36542 downstream)																																			---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40313482	40313482	+	Intron	DEL	T	-	-	rs76770016		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40313482delT	uc001mxa.1	-						LRRC4C_uc001mxc.1_Intron|LRRC4C_uc001mxd.1_Intron|LRRC4C_uc001mxb.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)																---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40398271	40398272	+	Intron	INS	-	TGTG	TGTG	rs72450159		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40398271_40398272insTGTG	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)																---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40620842	40620843	+	Intron	DEL	TA	-	-	rs140548469	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40620842_40620843delTA	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)																---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40959153	40959154	+	Intron	INS	-	TG	TG	rs71948000		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40959153_40959154insTG	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	41526613	41526615	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41526613_41526615delTTT								LRRC4C (45290 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	41857523	41857524	+	IGR	INS	-	TGTG	TGTG	rs147483492	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41857523_41857524insTGTG								LRRC4C (376200 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	41921495	41921495	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41921495delA								LRRC4C (440172 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42091205	42091206	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42091205_42091206delGA								LRRC4C (609882 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42275262	42275262	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42275262delA								LRRC4C (793939 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42719912	42719912	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42719912delT								None (None upstream) : API5 (613593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43003990	43003991	+	IGR	INS	-	ACAC	ACAC	rs139565276	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43003990_43003991insACAC								None (None upstream) : API5 (329514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43004048	43004048	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43004048delA								None (None upstream) : API5 (329457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43012073	43012073	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43012073delA								None (None upstream) : API5 (321432 downstream)																																			---	---	---	---
MIR670	100313777	broad.mit.edu	37	11	43580799	43580799	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43580799delA	hsa-mir-670|MI0003933	+																							0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	43617389	43617390	+	IGR	INS	-	GA	GA	rs149648117	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43617389_43617390insGA								MIR129-2 (14356 upstream) : HSD17B12 (84753 downstream)																																			---	---	---	---
ALKBH3	221120	broad.mit.edu	37	11	43936453	43936453	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43936453delA	uc001mxs.2	+						ALKBH3_uc009ykp.2_Intron|ALKBH3_uc001mxt.2_Intron|ALKBH3_uc009ykq.2_Intron|uc001mxu.1_Intron	NM_139178	NP_631917			AlkB homolog 3						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation	mitochondrion|nucleoplasm	damaged DNA binding|DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0					Vitamin C(DB00126)								Direct_reversal_of_damage					---	---	---	---
Unknown	0	broad.mit.edu	37	11	44002404	44002406	+	IGR	DEL	ATC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44002404_44002406delATC								AG2 (36972 upstream) : ACCSL (67125 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44039377	44039378	+	IGR	DEL	GA	-	-	rs66608647		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44039377_44039378delGA								AG2 (73945 upstream) : ACCSL (30153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44055516	44055516	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44055516delA								AG2 (90084 upstream) : ACCSL (14015 downstream)																																			---	---	---	---
ALX4	60529	broad.mit.edu	37	11	44286624	44286624	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44286624delG	uc001myb.2	-	4	1120	c.1016delC	c.(1015-1017)CCTfs	p.P339fs		NM_021926	NP_068745	Q9H161	ALX4_HUMAN	aristaless-like homeobox 4	339					hair follicle development						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	44429516	44429517	+	IGR	INS	-	TGAA	TGAA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44429516_44429517insTGAA								ALX4 (97800 upstream) : CD82 (157624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44736394	44736394	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44736394delA								CD82 (95081 upstream) : TSPAN18 (145485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44761348	44761349	+	IGR	DEL	TT	-	-	rs72320647		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44761348_44761349delTT								CD82 (120035 upstream) : TSPAN18 (120530 downstream)																																			---	---	---	---
TSPAN18	90139	broad.mit.edu	37	11	44932307	44932308	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44932307_44932308insG	uc001mye.3	+						TP53I11_uc001myf.1_Intron|TSPAN18_uc001myg.2_Intron	NM_130783	NP_570139			tetraspanin 18 isoform 2							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	45099535	45099535	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45099535delA								LOC221122 (99959 upstream) : PRDM11 (16029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45512793	45512793	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45512793delC								SYT13 (204909 upstream) : CHST1 (157634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45764950	45764965	+	IGR	DEL	AAGGAAGGAAGGAAGA	-	-	rs56170165	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45764950_45764965delAAGGAAGGAAGGAAGA								CHST1 (77778 upstream) : DKFZp779M0652 (28018 downstream)																																			---	---	---	---
PHF21A	51317	broad.mit.edu	37	11	46059705	46059705	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46059705delT	uc001ncc.3	-						PHF21A_uc001ncb.3_Intron|PHF21A_uc009ykx.2_Intron|PHF21A_uc001nce.2_Intron	NM_001101802	NP_001095272			BRAF35/HDAC2 complex isoform a						blood coagulation|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|transcription, DNA-dependent	histone deacetylase complex	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
F2	2147	broad.mit.edu	37	11	46742602	46742602	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)													---	---	---	---
CKAP5	9793	broad.mit.edu	37	11	46775145	46775145	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46775145delT	uc001ndi.1	-						CKAP5_uc009ylg.1_Intron|CKAP5_uc001ndj.1_Intron|CKAP5_uc001ndh.1_Intron	NM_001008938	NP_001008938			colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
LRP4	4038	broad.mit.edu	37	11	46881784	46881785	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46881784_46881785delAA	uc001ndn.3	-						uc001ndl.2_Intron|LRP4_uc001ndm.3_Intron	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	47162148	47162150	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47162148_47162150delTTT	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																		---	---	---	---
ARFGAP2	84364	broad.mit.edu	37	11	47189417	47189417	+	Intron	DEL	A	-	-	rs34204386		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47189417delA	uc001ndt.2	-						ARFGAP2_uc010rha.1_Intron|ARFGAP2_uc010rhb.1_Intron|ARFGAP2_uc001ndu.2_Intron|ARFGAP2_uc010rhc.1_Intron	NM_032389	NP_115765			ADP-ribosylation factor GTPase activating						protein transport|regulation of ARF GTPase activity|vesicle-mediated transport	Golgi membrane|nucleolus|plasma membrane	ARF GTPase activator activity|zinc ion binding			ovary(1)	1																		---	---	---	---
DDB2	1643	broad.mit.edu	37	11	47249818	47249819	+	Intron	DEL	AA	-	-	rs78615445		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47249818_47249819delAA	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				---	---	---	---
MADD	8567	broad.mit.edu	37	11	47311225	47311225	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47311225delG	uc001ner.1	+						MADD_uc001neq.2_Intron|MADD_uc001nev.1_Intron|MADD_uc001nes.1_Intron|MADD_uc001net.1_Intron|MADD_uc009yln.1_Intron|MADD_uc001neu.1_Intron|MADD_uc001nex.2_Intron|MADD_uc001nez.2_Intron|MADD_uc001new.2_Intron|MADD_uc009ylo.2_5'Flank	NM_003682	NP_003673			MAP-kinase activating death domain-containing						activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)														---	---	---	---
PSMC3	5702	broad.mit.edu	37	11	47443239	47443240	+	Intron	DEL	TG	-	-	rs139948403		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47443239_47443240delTG	uc001nfh.2	-						PSMC3_uc009ylr.1_Intron	NM_002804	NP_002795			proteasome 26S ATPase subunit 3						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|nucleoside-triphosphatase activity|protein binding|transcription coactivator activity|transcription corepressor activity			ovary(4)	4				Lung(87;0.0932)|BRCA - Breast invasive adenocarcinoma(625;0.13)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	47455125	47455125	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47455125delT								PSMC3 (7101 upstream) : RAPSN (4190 downstream)																																			---	---	---	---
AGBL2	79841	broad.mit.edu	37	11	47724428	47724428	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47724428delA	uc001ngg.2	-						AGBL2_uc010rhq.1_Intron|AGBL2_uc001ngh.1_Intron	NM_024783	NP_079059			carboxypeptidase 2, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
AGBL2	79841	broad.mit.edu	37	11	47731449	47731449	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47731449delT	uc001ngg.2	-						AGBL2_uc010rhq.1_Intron|AGBL2_uc001ngh.1_Intron	NM_024783	NP_079059			carboxypeptidase 2, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
FNBP4	23360	broad.mit.edu	37	11	47739767	47739767	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47739767delT	uc009ylv.2	-						FNBP4_uc001ngi.2_Intron|FNBP4_uc001ngj.2_Intron	NM_015308	NP_056123			formin binding protein 4											ovary(1)	1																		---	---	---	---
NUP160	23279	broad.mit.edu	37	11	47843813	47843814	+	Intron	DEL	AT	-	-	rs76943871		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47843813_47843814delAT	uc001ngm.2	-						NUP160_uc009ylw.2_Intron	NM_015231	NP_056046			nucleoporin 160kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	48342971	48342972	+	IGR	INS	-	A	A	rs143296079	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48342971_48342972insA								OR4S1 (14268 upstream) : OR4C3 (3521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48355893	48355893	+	IGR	DEL	A	-	-	rs67880258		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48355893delA								OR4C3 (8413 upstream) : OR4C45 (11009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48377559	48377559	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48377559delA								OR4C45 (3560 upstream) : OR4A47 (132786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48503367	48503367	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48503367delT								OR4C45 (129368 upstream) : OR4A47 (6978 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48895492	48895493	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48895492_48895493insG								OR4A47 (384220 upstream) : FOLH1 (272695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49428742	49428743	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49428742_49428743delTG								FOLH1 (198520 upstream) : LOC440040 (151337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49465303	49465303	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49465303delC								FOLH1 (235081 upstream) : LOC440040 (114777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	50074319	50074319	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50074319delA								OR4C12 (70282 upstream) : LOC441601 (164681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	50690220	50690220	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50690220delT								LOC646813 (310417 upstream) : OR4A5 (721228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	50699243	50699243	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50699243delG								LOC646813 (319440 upstream) : OR4A5 (712205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	50741545	50741546	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50741545_50741546delAG								LOC646813 (361742 upstream) : OR4A5 (669902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	51245153	51245153	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51245153delA								LOC646813 (865350 upstream) : OR4A5 (166295 downstream)																																			---	---	---	---
OR4A16	81327	broad.mit.edu	37	11	55111418	55111419	+	Frame_Shift_Ins	INS	-	T	T	rs141537673		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55111418_55111419insT	uc010rie.1	+	1	742_743	c.742_743insT	c.(742-744)GTTfs	p.V248fs		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	248	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	55984490	55984490	+	IGR	DEL	T	-	-	rs143834359		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55984490delT								OR5J2 (39460 upstream) : OR5T2 (15097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	56524184	56524185	+	IGR	INS	-	AG	AG	rs143565690	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56524184_56524185insAG								OR9G4 (12897 upstream) : OR5AK2 (232204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	56859245	56859245	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56859245delA								OR5AK2 (101929 upstream) : LRRC55 (89976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	57065878	57065880	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57065878_57065880delTTT								APLNR (60951 upstream) : TNKS1BP1 (1224 downstream)																																			---	---	---	---
SLC43A3	29015	broad.mit.edu	37	11	57185812	57185812	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57185812delA	uc001nkg.2	-						PRG2_uc001nke.2_Intron|SLC43A3_uc001nkh.2_Intron|SLC43A3_uc010rjr.1_Intron|SLC43A3_uc009yme.2_Intron|SLC43A3_uc001nki.2_Intron|SLC43A3_uc009ymf.1_Intron|SLC43A3_uc010rjs.1_Intron|SLC43A3_uc009ymg.1_Intron	NM_014096	NP_054815			solute carrier family 43, member 3						transmembrane transport	integral to membrane				central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	57405414	57405415	+	5'Flank	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57405414_57405415insC	uc001nkt.1	+											Homo sapiens cDNA FLJ34998 fis, clone OCBBF2011706.																														---	---	---	---
CLP1	10978	broad.mit.edu	37	11	57428126	57428126	+	Intron	DEL	A	-	-	rs74496835		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57428126delA	uc001nkw.2	+						CLP1_uc010rjw.1_Intron|CLP1_uc009yml.2_Intron	NM_006831	NP_006822			ATP/GTP-binding protein isoform 1						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	57628953	57628954	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57628953_57628954delTT								CTNND1 (42302 upstream) : OR9Q1 (162399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	57681827	57681828	+	IGR	INS	-	T	T	rs641325	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57681827_57681828insT								CTNND1 (95176 upstream) : OR9Q1 (109525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	57712901	57712901	+	IGR	DEL	T	-	-	rs141683940	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57712901delT								CTNND1 (126250 upstream) : OR9Q1 (78452 downstream)																																			---	---	---	---
ZFP91	80829	broad.mit.edu	37	11	58374522	58374522	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58374522delT	uc001nmx.3	+						ZFP91_uc001nmy.3_Intron|ZFP91-CNTF_uc010rkm.1_Intron	NM_053023	NP_444251			zinc finger protein 91						activation of NF-kappaB-inducing kinase activity|protein K63-linked ubiquitination	nucleus	nucleic acid binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	58399979	58399979	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58399979delT								ZFP91-CNTF (6776 upstream) : GLYAT (76252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	58767822	58767822	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58767822delA	uc001nng.1	-											Homo sapiens cDNA FLJ34127 fis, clone FCBBF3010124.																														---	---	---	---
FAM111A	63901	broad.mit.edu	37	11	58920101	58920101	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58920101delA	uc010rkp.1	+	5	1187	c.960delA	c.(958-960)GTAfs	p.V320fs	FAM111A_uc010rkq.1_Frame_Shift_Del_p.V320fs|FAM111A_uc010rkr.1_Frame_Shift_Del_p.V320fs|FAM111A_uc001nno.2_Frame_Shift_Del_p.V320fs|FAM111A_uc001nnp.2_Frame_Shift_Del_p.V320fs|FAM111A_uc001nnq.2_Frame_Shift_Del_p.V320fs	NM_001142521	NP_001135993	Q96PZ2	F111A_HUMAN	hypothetical protein LOC63901	320					proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_epithelial(135;0.139)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	58923270	58923272	+	IGR	DEL	AAA	-	-	rs2507938		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58923270_58923272delAAA								FAM111A (761 upstream) : DTX4 (15631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59186519	59186519	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59186519delA								OR5AN1 (53653 upstream) : OR5A2 (2935 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59195350	59195351	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59195350_59195351delAA								OR5A2 (4924 upstream) : OR5A1 (15291 downstream)																																			---	---	---	---
MS4A2	2206	broad.mit.edu	37	11	59860241	59860241	+	Intron	DEL	T	-	-	rs74337069		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59860241delT	uc001nop.2	+						MS4A2_uc009ymu.2_Intron	NM_000139	NP_000130			membrane-spanning 4-domains, subfamily A, member						cell proliferation|humoral immune response	integral to plasma membrane	calcium channel activity			ovary(1)	1		all_epithelial(135;0.245)			Omalizumab(DB00043)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	60010336	60010336	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60010336delT								MS4A6A (58197 upstream) : MS4A4A (37803 downstream)																																			---	---	---	---
MS4A12	54860	broad.mit.edu	37	11	60260549	60260549	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60260549delA	uc001npr.2	+						MS4A12_uc009ynb.2_Intron	NM_017716	NP_060186			membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity				0																		---	---	---	---
TMEM109	79073	broad.mit.edu	37	11	60685140	60685140	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60685140delT	uc001nqg.2	+							NM_024092	NP_076997			transmembrane protein 109 precursor							integral to membrane|nuclear outer membrane|sarcoplasmic reticulum membrane					0																		---	---	---	---
CD6	923	broad.mit.edu	37	11	60783054	60783054	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60783054delA	uc001nqq.2	+						CD6_uc001nqp.2_Intron|CD6_uc001nqr.2_Intron|CD6_uc001nqs.2_Intron|CD6_uc001nqt.2_Intron	NM_006725	NP_006716			CD6 molecule precursor						cell adhesion	cell surface|integral to plasma membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	60951710	60951711	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60951710_60951711delTT								VPS37C (22794 upstream) : PGA3 (19273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	61022660	61022661	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61022660_61022661delTT								PGA5 (3747 upstream) : VWCE (3098 downstream)																																			---	---	---	---
SDHAF2	54949	broad.mit.edu	37	11	61206516	61206516	+	Intron	DEL	A	-	-	rs3019190		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61206516delA	uc001nrt.2	+							NM_017841	NP_060311			succinate dehydrogenase complex assembly factor						mitochondrial electron transport, succinate to ubiquinone|protein-FAD linkage	mitochondrion	protein binding			ovary(2)	2														Familial_Paragangliomas				---	---	---	---
Unknown	0	broad.mit.edu	37	11	61225037	61225037	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61225037delA								SDHAF2 (10810 upstream) : C11orf66 (23555 downstream)																																			---	---	---	---
C11orf66	220004	broad.mit.edu	37	11	61247839	61247840	+	5'Flank	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61247839_61247840delAA	uc001nru.1	+						C11orf66_uc009ynq.1_5'Flank	NM_145017	NP_659454			IIIG9 protein											ovary(1)	1																		---	---	---	---
FADS3	3995	broad.mit.edu	37	11	61643074	61643074	+	Intron	DEL	C	-	-	rs6591666	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61643074delC	uc001nsm.2	-						FADS3_uc001nsn.2_Intron	NM_021727	NP_068373			fatty acid desaturase 3						electron transport chain|transport|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|membrane fraction	heme binding|oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water			ovary(1)|pancreas(1)	2																		---	---	---	---
BEST1	7439	broad.mit.edu	37	11	61716307	61716307	+	5'Flank	DEL	G	-	-	rs974121	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61716307delG	uc001nss.2	+						BEST1_uc010rlp.1_5'Flank|BEST1_uc001nsq.2_5'Flank|BEST1_uc010rlq.1_5'Flank|BEST1_uc010rlr.1_5'Flank|BEST1_uc010rls.1_5'Flank|BEST1_uc001nsr.2_5'Flank|BEST1_uc009ynt.2_5'Flank|BEST1_uc010rlt.1_5'Flank|BEST1_uc001nst.2_5'Flank	NM_004183	NP_004174			bestrophin 1 isoform 1						response to stimulus|transepithelial chloride transport|visual perception	basolateral plasma membrane|chloride channel complex|cytosol|membrane fraction	chloride channel activity			central_nervous_system(1)	1																		---	---	---	---
INCENP	3619	broad.mit.edu	37	11	61912525	61912527	+	In_Frame_Del	DEL	GGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61912525_61912527delGGA	uc001nsw.1	+	12	1879_1881	c.1677_1679delGGA	c.(1675-1680)GTGGAG>GTG	p.E561del	INCENP_uc009ynw.1_In_Frame_Del_p.E561del|INCENP_uc001nsx.1_In_Frame_Del_p.E557del|INCENP_uc001nsy.1_5'UTR	NM_001040694	NP_001035784	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	561	Potential.				chromosome segregation|cytokinesis|mitotic prometaphase	centromeric heterochromatin|condensed chromosome kinetochore|cytosol|microtubule|spindle	protein binding			lung(1)	1																		---	---	---	---
SLC3A2	6520	broad.mit.edu	37	11	62649529	62649529	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	62799908	62799909	+	IGR	DEL	TT	-	-	rs114064409	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62799908_62799909delTT								SLC22A8 (16597 upstream) : SLC22A24 (47505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	63212633	63212633	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63212633delT								SLC22A9 (34923 upstream) : HRASLS5 (16243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	63702257	63702257	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63702257delT								RCOR2 (17941 upstream) : NAA40 (4185 downstream)																																			---	---	---	---
MACROD1	28992	broad.mit.edu	37	11	63815370	63815376	+	Intron	DEL	AAAAAAA	-	-	rs72071311		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63815370_63815376delAAAAAAA	uc001nyh.2	-							NM_014067	NP_054786			MACRO domain containing 1												0																		---	---	---	---
MACROD1	28992	broad.mit.edu	37	11	63889443	63889445	+	Intron	DEL	AAA	-	-	rs11411184		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63889443_63889445delAAA	uc001nyh.2	-							NM_014067	NP_054786			MACRO domain containing 1												0																		---	---	---	---
PPP1R14B	26472	broad.mit.edu	37	11	64012791	64012792	+	Intron	DEL	AT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64012791_64012792delAT	uc001nza.2	-							NM_138689	NP_619634			protein phosphatase 1 regulatory subunit 14B						regulation of phosphorylation	cytoplasm	protein phosphatase inhibitor activity				0																		---	---	---	---
PLCB3	5331	broad.mit.edu	37	11	64025626	64025628	+	Intron	DEL	AAA	-	-	rs34969821		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64025626_64025628delAAA	uc001nzb.2	+						PLCB3_uc009ypg.1_Intron|PLCB3_uc009yph.1_Intron|PLCB3_uc009ypi.2_Intron	NM_000932	NP_000923			phospholipase C beta 3						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	64235584	64235584	+	IGR	DEL	A	-	-	rs10897506		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64235584delA								RPS6KA4 (95898 upstream) : SLC22A11 (87514 downstream)																																			---	---	---	---
SLC22A11	55867	broad.mit.edu	37	11	64320619	64320620	+	5'Flank	INS	-	A	A	rs142063841		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64320619_64320620insA	uc001oai.2	+						SLC22A11_uc001oah.1_5'Flank|SLC22A11_uc001oaj.2_5'Flank|SLC22A11_uc009ypq.2_5'Flank	NM_018484	NP_060954			solute carrier family 22 member 11						urate metabolic process	apical plasma membrane|external side of plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium-independent organic anion transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2					Probenecid(DB01032)													---	---	---	---
CDC42BPG	55561	broad.mit.edu	37	11	64592215	64592215	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64592215delT	uc001obs.3	-							NM_017525	NP_059995			CDC42 binding protein kinase gamma (DMPK-like)						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																		---	---	---	---
C11orf85	283129	broad.mit.edu	37	11	64740928	64740928	+	5'Flank	DEL	A	-	-	rs113705383		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64740928delA	uc001ocd.1	-						C11orf85_uc001occ.1_5'Flank					SubName: Full=cDNA FLJ35811 fis, clone TESTI2006045;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	65252869	65252869	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65252869delA								MIR612 (40841 upstream) : MALAT1 (12364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	65465793	65465794	+	IGR	DEL	AC	-	-	rs4014097		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65465793_65465794delAC								RELA (35350 upstream) : KAT5 (13695 downstream)																																			---	---	---	---
BANF1	8815	broad.mit.edu	37	11	65770687	65770687	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65770687delT	uc001ogo.2	+						EIF1AD_uc001ogm.1_5'Flank|EIF1AD_uc001ogn.1_5'Flank|BANF1_uc001ogp.2_Intron	NM_003860	NP_003851			barrier to autointegration factor 1						initiation of viral infection|interspecies interaction between organisms|provirus integration|response to virus	chromosome|cytosol|nucleoplasm	DNA binding				0																		---	---	---	---
BBS1	582	broad.mit.edu	37	11	66278428	66278428	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66278428delT	uc001oij.1	+						BBS1_uc001oii.1_Intron|BBS1_uc010rpf.1_Intron|BBS1_uc010rpg.1_Intron|BBS1_uc001oik.1_Intron|BBS1_uc001oil.1_Intron	NM_024649	NP_078925			Bardet-Biedl syndrome 1						nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1														Bardet-Biedl_syndrome				---	---	---	---
RBM14	10432	broad.mit.edu	37	11	66391646	66391646	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66391646delC	uc001oit.2	+						RBM14_uc009yrh.2_Intron|RBM14_uc009yri.2_Intron|RBM4_uc009yrj.2_Intron|RBM4_uc009yrk.2_Intron	NM_006328	NP_006319			RNA binding motif protein 14						DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|histone deacetylation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus	mediator complex|ribonucleoprotein complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|protein binding, bridging|RNA binding|RNA polymerase II transcription cofactor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	66729729	66729729	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66729729delT								PC (3882 upstream) : C11orf86 (13025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	66786294	66786294	+	IGR	DEL	A	-	-	rs79379737		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66786294delA								C11orf86 (41816 upstream) : SYT12 (3896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	66843320	66843322	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66843320_66843322delAAA								RHOD (3833 upstream) : KDM2A (43418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	66874972	66874973	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66874972_66874973delAC								RHOD (35485 upstream) : KDM2A (11767 downstream)																																			---	---	---	---
LOC100130987	100130987	broad.mit.edu	37	11	67151026	67151027	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67151026_67151027delAA	uc010rpo.1	+							NR_024469				Homo sapiens cDNA FLJ38836 fis, clone MESAN2002519, weakly similar to Mus musculus cell cycle checkpoint control protein Mrad9 gene.												0																		---	---	---	---
RPS6KB2	6199	broad.mit.edu	37	11	67202044	67202044	+	Intron	DEL	G	-	-	rs1790752	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67202044delG	uc001old.2	+						RPS6KB2_uc001olf.2_Intron|RPS6KB2_uc001olg.2_Intron|RPS6KB2_uc009yrq.2_Intron|RPS6KB2_uc001ole.2_Intron|RPS6KB2_uc001olh.2_Intron|RPS6KB2_uc009yrr.2_Intron	NM_003952	NP_003943			ribosomal protein S6 kinase, 70kDa, polypeptide						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of translational initiation|translation	nucleoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|stomach(1)|lung(1)|salivary_gland(1)	7			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)															---	---	---	---
ALDH3B2	222	broad.mit.edu	37	11	67451366	67451366	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67451366delT	uc001oms.2	-							NM_001031615	NP_001026786			aldehyde dehydrogenase 3B2						alcohol metabolic process|cellular aldehyde metabolic process|lipid metabolic process		3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase			lung(1)|kidney(1)	2					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	67518764	67518799	+	IGR	DEL	GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAA	-	-	rs56306942	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67518764_67518799delGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAA								ALDH3B2 (70079 upstream) : LOC645332 (40441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	67707033	67707033	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67707033delT								LOC645332 (134226 upstream) : UNC93B1 (51542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	67753938	67753938	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67753938delG								LOC645332 (181131 upstream) : UNC93B1 (4637 downstream)																																			---	---	---	---
CHKA	1119	broad.mit.edu	37	11	67832102	67832102	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67832102delA	uc001onj.2	-						CHKA_uc001onk.2_Intron	NM_001277	NP_001268			choline kinase alpha isoform a						lipid transport|phosphatidylethanolamine biosynthetic process	cytoplasm	ATP binding|choline kinase activity|drug binding|ethanolamine kinase activity|signal transducer activity			ovary(1)|central_nervous_system(1)	2					Choline(DB00122)													---	---	---	---
LRP5	4041	broad.mit.edu	37	11	68123317	68123317	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68123317delT	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	68267755	68267755	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68267755delT	uc001onw.2	+						SAPS3_uc010rqb.1_Intron|SAPS3_uc001onv.2_Intron|SAPS3_uc001ony.3_Intron|SAPS3_uc001onx.2_Intron|SAPS3_uc009ysh.2_Intron|SAPS3_uc001onu.2_Intron|SAPS3_uc010rqc.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	68467587	68467587	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68467587delT								GAL (8945 upstream) : MTL5 (7323 downstream)																																			---	---	---	---
CPT1A	1374	broad.mit.edu	37	11	68546164	68546164	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68546164delA	uc001oog.3	-						CPT1A_uc001oof.3_Intron|CPT1A_uc009ysj.2_Intron	NM_001876	NP_001867			carnitine palmitoyltransferase 1A liver isoform						carnitine shuttle|fatty acid beta-oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			skin(2)	2	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		L-Carnitine(DB00583)|Perhexiline(DB01074)													---	---	---	---
TPCN2	219931	broad.mit.edu	37	11	68839275	68839275	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68839275delC	uc001oos.2	+						TPCN2_uc009ysk.1_Intron|TPCN2_uc001oor.2_Intron|TPCN2_uc010rqg.1_Intron|TPCN2_uc001oot.2_5'Flank	NM_139075	NP_620714			two pore segment channel 2						cellular calcium ion homeostasis|smooth muscle contraction	endosome membrane|integral to membrane|lysosomal membrane	NAADP-sensitive calcium-release channel activity|voltage-gated calcium channel activity				0			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)															---	---	---	---
ORAOV1	220064	broad.mit.edu	37	11	69487294	69487295	+	Intron	DEL	AA	-	-	rs112417405		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69487294_69487295delAA	uc001opc.2	-						ORAOV1_uc010rqi.1_Intron|ORAOV1_uc009ysm.2_Intron|ORAOV1_uc001opd.2_Intron|ORAOV1_uc001ope.1_Intron	NM_153451	NP_703152			oral cancer overexpressed 1												0	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;5.64e-57)|all cancers(3;5.98e-51)|BRCA - Breast invasive adenocarcinoma(2;5.49e-48)|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)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	69605296	69605296	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69605296delA								FGF4 (15125 upstream) : FGF3 (19441 downstream)																																			---	---	---	---
ANO1	55107	broad.mit.edu	37	11	69971955	69971959	+	Intron	DEL	AAAAC	-	-	rs10792912		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69971955_69971959delAAAAC	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron	NM_018043	NP_060513			anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2																		---	---	---	---
ANO1	55107	broad.mit.edu	37	11	69995756	69995761	+	Intron	DEL	AAAAAA	-	-	rs72410022		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69995756_69995761delAAAAAA	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron	NM_018043	NP_060513			anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	70113693	70113696	+	IGR	DEL	AGGA	-	-	rs71974523		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70113693_70113696delAGGA								FADD (60185 upstream) : PPFIA1 (3127 downstream)																																			---	---	---	---
PPFIA1	8500	broad.mit.edu	37	11	70176201	70176201	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70176201delT	uc001opo.2	+						PPFIA1_uc001opn.1_Intron|PPFIA1_uc001opp.2_Intron|PPFIA1_uc001opq.1_Intron	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)															---	---	---	---
CTTN	2017	broad.mit.edu	37	11	70281531	70281531	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70281531delT	uc001opv.3	+	18					CTTN_uc001opu.2_Intron|CTTN_uc001opw.3_3'UTR|CTTN_uc010rqm.1_Intron|CTTN_uc001opx.2_3'UTR	NM_005231	NP_005222			cortactin isoform a							cell cortex|cytoskeleton|lamellipodium|ruffle|soluble fraction	protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)														---	---	---	---
NADSYN1	55191	broad.mit.edu	37	11	71173242	71173242	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71173242delT	uc001oqn.2	+						NADSYN1_uc001oqm.2_Intron|NADSYN1_uc001oqo.2_Intron	NM_018161	NP_060631			NAD synthetase 1						NAD biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds|NAD+ synthase (glutamine-hydrolyzing) activity|protein binding			ovary(2)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
NADSYN1	55191	broad.mit.edu	37	11	71177281	71177281	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71177281delA	uc001oqn.2	+						NADSYN1_uc001oqm.2_Intron|NADSYN1_uc001oqo.2_Intron	NM_018161	NP_060631			NAD synthetase 1						NAD biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds|NAD+ synthase (glutamine-hydrolyzing) activity|protein binding			ovary(2)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	71223315	71223315	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71223315delC								NADSYN1 (10736 upstream) : KRTAP5-7 (14998 downstream)																																			---	---	---	---
RNF121	55298	broad.mit.edu	37	11	71705621	71705621	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71705621delA	uc001ora.2	+						RNF121_uc001ord.2_Intron|RNF121_uc001orb.2_Intron|RNF121_uc009yst.2_Intron	NM_018320	NP_060790			ring finger protein 121							integral to membrane	zinc ion binding				0																		---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71728560	71728560	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71728560delA	uc001orl.1	-						NUMA1_uc009ysw.1_5'Flank|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc001orn.2_5'Flank|NUMA1_uc009ysx.1_Intron|NUMA1_uc001oro.1_Intron|NUMA1_uc009ysy.1_3'UTR|NUMA1_uc001orp.2_3'UTR|NUMA1_uc001orq.2_3'UTR	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								---	---	---	---
CLPB	81570	broad.mit.edu	37	11	72113304	72113305	+	Intron	INS	-	A	A	rs144479896	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72113304_72113305insA	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	72294641	72294641	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72294641delA	uc010rrc.1	-						PDE2A_uc001oso.2_Intron|PDE2A_uc010rra.1_Intron|PDE2A_uc001osn.2_Intron|PDE2A_uc010rrb.1_Intron|PDE2A_uc010rrd.1_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	72399053	72399053	+	Intron	DEL	T	-	-	rs34505326		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72399053delT	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	72424414	72424414	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72424414delA	uc001osu.2	-						ARAP1_uc001osv.2_Intron|ARAP1_uc001osr.2_5'Flank|ARAP1_uc001oss.2_Intron|ARAP1_uc009yth.2_Intron|ARAP1_uc010rre.1_Intron	NM_001040118	NP_001035207			ArfGAP with RhoGAP domain, ankyrin repeat and PH						actin filament reorganization involved in cell cycle|negative regulation of stress fiber assembly|positive regulation of Cdc42 GTPase activity|positive regulation of filopodium assembly|regulation of ARF GTPase activity|regulation of cell shape|regulation of cellular component movement|small GTPase mediated signal transduction	cytosol|Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|Rho GTPase activator activity|zinc ion binding			skin(1)	1																		---	---	---	---
FCHSD2	9873	broad.mit.edu	37	11	72709586	72709586	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72709586delA	uc009ytl.2	-						FCHSD2_uc010rrg.1_Intron|FCHSD2_uc001oth.3_Intron|FCHSD2_uc001oti.2_Intron	NM_014824	NP_055639			FCH and double SH3 domains 2								protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	72960484	72960485	+	IGR	DEL	GA	-	-	rs113662913		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72960484_72960485delGA								P2RY2 (13091 upstream) : P2RY6 (15085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	73682889	73682889	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73682889delT								DNAJB13 (1558 upstream) : UCP2 (2827 downstream)																																			---	---	---	---
UCP3	7352	broad.mit.edu	37	11	73714711	73714711	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73714711delT	uc001our.2	-						UCP3_uc001ous.2_3'UTR	NM_003356	NP_003347			uncoupling protein 3 isoform UCP3L						mitochondrial transport|respiratory electron transport chain|respiratory gaseous exchange	integral to membrane|mitochondrial inner membrane	binding			pancreas(1)	1	Breast(11;2.08e-05)																	---	---	---	---
UCP3	7352	broad.mit.edu	37	11	73717786	73717786	+	Intron	DEL	T	-	-	rs17132562	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73717786delT	uc001our.2	-						UCP3_uc001ous.2_Intron	NM_003356	NP_003347			uncoupling protein 3 isoform UCP3L						mitochondrial transport|respiratory electron transport chain|respiratory gaseous exchange	integral to membrane|mitochondrial inner membrane	binding			pancreas(1)	1	Breast(11;2.08e-05)																	---	---	---	---
C2CD3	26005	broad.mit.edu	37	11	73865062	73865062	+	Intron	DEL	A	-	-	rs76190461		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73865062delA	uc001ouu.2	-						C2CD3_uc001ouv.2_Intron	NM_015531	NP_056346			C2 calcium-dependent domain containing 3							centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	74267625	74267625	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74267625delA								LIPT2 (62870 upstream) : POLD3 (36004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	74287434	74287435	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74287434_74287435insT								LIPT2 (82679 upstream) : POLD3 (16194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	74405040	74405040	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74405040delT								POLD3 (51275 upstream) : CHRDL2 (2435 downstream)																																			---	---	---	---
CHRDL2	25884	broad.mit.edu	37	11	74420087	74420087	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74420087delG	uc001ovi.2	-						CHRDL2_uc001ovg.2_Intron|CHRDL2_uc001ovh.2_Intron|CHRDL2_uc001ovk.1_Intron					RecName: Full=Chordin-like protein 2; AltName: Full=Chordin-related protein 2; AltName: Full=Breast tumor novel factor 1;          Short=BNF-1; Flags: Precursor;						cartilage development|cell differentiation|ossification	extracellular region|mitochondrion					0	Hepatocellular(1;0.098)																	---	---	---	---
XRRA1	143570	broad.mit.edu	37	11	74645032	74645033	+	Intron	INS	-	TTCA	TTCA	rs140602440	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74645032_74645033insTTCA	uc009yub.2	-						XRRA1_uc001ovm.2_Intron|XRRA1_uc001ovo.2_Intron|XRRA1_uc001ovq.3_Intron|XRRA1_uc001ovp.3_Intron|XRRA1_uc001ovr.2_Intron	NM_182969	NP_892014			X-ray radiation resistance associated 1						response to X-ray	cytoplasm|nucleus				central_nervous_system(1)	1																		---	---	---	---
SPCS2	9789	broad.mit.edu	37	11	74683118	74683118	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74683118delT	uc001ovu.2	+							NM_014752	NP_055567			signal peptidase complex subunit 2 homolog						energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	integral to membrane|microsome|signal peptidase complex	peptidase activity			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	74753118	74753118	+	IGR	DEL	A	-	-	rs72992610	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74753118delA								NEU3 (34377 upstream) : OR2AT4 (46679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	76140824	76140824	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76140824delT								PRKRIR (48944 upstream) : C11orf30 (15245 downstream)																																			---	---	---	---
C11orf30	56946	broad.mit.edu	37	11	76157923	76157923	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76157923delT	uc001oxl.2	+						C11orf30_uc001oxj.2_Intron|C11orf30_uc001oxk.2_Intron|C11orf30_uc009yuj.1_Intron|C11orf30_uc010rsa.1_Intron|C11orf30_uc001oxm.2_Intron|C11orf30_uc010rsb.1_5'Flank|C11orf30_uc010rsc.1_5'Flank|C11orf30_uc001oxn.2_5'Flank|C11orf30_uc010rsd.1_5'Flank	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	76205743	76205744	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76205743_76205744insT	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	76246914	76246914	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76246914delT	uc001oxl.2	+						C11orf30_uc001oxm.2_Intron|C11orf30_uc010rsb.1_Intron|C11orf30_uc010rsc.1_Intron|C11orf30_uc001oxn.2_Intron|C11orf30_uc010rsd.1_Intron|C11orf30_uc001oxo.1_Intron|C11orf30_uc010rse.1_Intron	NM_020193	NP_064578			EMSY protein						chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	76471393	76471393	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76471393delA								GUCY2E (38560 upstream) : TSKU (22892 downstream)																																			---	---	---	---
PAK1	5058	broad.mit.edu	37	11	77084703	77084704	+	Intron	DEL	CT	-	-	rs139023477		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77084703_77084704delCT	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)																	---	---	---	---
PAK1	5058	broad.mit.edu	37	11	77165566	77165566	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77165566delT	uc001oyh.3	-						PAK1_uc001oyg.3_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	77296801	77296801	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77296801delA								PAK1 (111693 upstream) : AQP11 (3635 downstream)																																			---	---	---	---
INTS4	92105	broad.mit.edu	37	11	77639340	77639340	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	78150395	78150395	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78150395delT	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	78378032	78378032	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78378032delT	uc001ozl.3	-						ODZ4_uc001ozk.3_Intron|ODZ4_uc009yvb.1_Intron	NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78402777	78402777	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78402777delA	uc001ozl.3	-						ODZ4_uc009yvb.1_Intron	NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78769589	78769591	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78769589_78769591delAAA	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	79593692	79593692	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79593692delT								ODZ4 (441997 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	79867021	79867021	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79867021delT								ODZ4 (715326 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	79891311	79891312	+	IGR	DEL	TT	-	-	rs112695634		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79891311_79891312delTT								ODZ4 (739616 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80439239	80439239	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80439239delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80495154	80495155	+	IGR	INS	-	A	A	rs149947469	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80495154_80495155insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80520489	80520490	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80520489_80520490insC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80728914	80728914	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80728914delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80740798	80740799	+	IGR	INS	-	GG	GG	rs147863960	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80740798_80740799insGG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81168977	81168977	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81168977delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81488199	81488199	+	IGR	DEL	T	-	-	rs79518160	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81488199delT								None (None upstream) : FAM181B (954854 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81557217	81557218	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81557217_81557218delAA								None (None upstream) : FAM181B (885835 downstream)																																			---	---	---	---
ANKRD42	338699	broad.mit.edu	37	11	82966931	82966931	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	83088575	83088575	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83088575delT	uc001pag.2	+											Homo sapiens cDNA clone IMAGE:5296561.																														---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84412235	84412235	+	Intron	DEL	T	-	-	rs112132617		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84412235delT	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	84758875	84758876	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84758875_84758876insA	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)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	85330878	85330878	+	Intron	DEL	A	-	-	rs2511792		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85330878delA	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)																---	---	---	---
PICALM	8301	broad.mit.edu	37	11	85717954	85717955	+	Intron	DEL	TT	-	-	rs147153790	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85717954_85717955delTT	uc001pbm.2	-						PICALM_uc001pbl.2_Intron|PICALM_uc001pbn.2_Intron|PICALM_uc010rtl.1_Intron|PICALM_uc001pbo.1_Intron	NM_007166	NP_009097			phosphatidylinositol-binding clathrin assembly						clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)						T	MLLT10|MLL	TALL|AML|								---	---	---	---
EED	8726	broad.mit.edu	37	11	85956063	85956064	+	5'UTR	DEL	GC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85956063_85956064delGC	uc001pbp.2	+	1					EED_uc010rtm.1_5'UTR|EED_uc001pbq.2_5'UTR|EED_uc001pbr.2_5'UTR|EED_uc001pbs.2_5'UTR	NM_003797	NP_003788			embryonic ectoderm development isoform a						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|identical protein binding			skin(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	86405834	86405834	+	IGR	DEL	G	-	-	rs5793210		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86405834delG								ME3 (22156 upstream) : PRSS23 (105657 downstream)																																			---	---	---	---
TMEM135	65084	broad.mit.edu	37	11	86855752	86855753	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86855752_86855753delGT	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)																---	---	---	---
TMEM135	65084	broad.mit.edu	37	11	86909750	86909750	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86909750delT	uc001pch.2	+						TMEM135_uc010rtt.1_Intron|TMEM135_uc001pci.2_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	87671277	87671280	+	IGR	DEL	AAAG	-	-	rs67529624		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87671277_87671280delAAAG								TMEM135 (636709 upstream) : RAB38 (175151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	88840056	88840056	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88840056delT								GRM5 (40943 upstream) : TYR (70984 downstream)																																			---	---	---	---
TYR	7299	broad.mit.edu	37	11	88979089	88979090	+	Intron	DEL	AA	-	-	rs112370459		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88979089_88979090delAA	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	89106467	89106467	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89106467delC	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	89832233	89832234	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89832233_89832234insA								UBTFL1 (11935 upstream) : NAALAD2 (35584 downstream)																																			---	---	---	---
NAALAD2	10003	broad.mit.edu	37	11	89919697	89919698	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89919697_89919698insA	uc001pdf.3	+						NAALAD2_uc009yvx.2_Intron|NAALAD2_uc009yvy.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	90004312	90004312	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90004312delA								CHORDC1 (47780 upstream) : MIR1261 (597977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90329895	90329895	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90329895delT								CHORDC1 (373363 upstream) : MIR1261 (272394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90350473	90350474	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90350473_90350474delAC								CHORDC1 (393941 upstream) : MIR1261 (251815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90865810	90865811	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90865810_90865811insC								MIR1261 (263440 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91848471	91848471	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91848471delT								None (None upstream) : FAT3 (236791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	92827573	92827573	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92827573delT								MTNR1B (111625 upstream) : SLC36A4 (53279 downstream)																																			---	---	---	---
MED17	9440	broad.mit.edu	37	11	93527948	93527948	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93527948delA	uc001pem.3	+							NM_004268	NP_004259			mediator complex subunit 17						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	93732181	93732182	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93732181_93732182insC								C11orf90 (148513 upstream) : HEPHL1 (22196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	94072474	94072474	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94072474delT								FOLR4 (31617 upstream) : GPR83 (38003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	94373327	94373327	+	IGR	DEL	T	-	-	rs35643333		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94373327delT								PIWIL4 (18741 upstream) : AMOTL1 (128181 downstream)																																			---	---	---	---
KDM4D	55693	broad.mit.edu	37	11	94730458	94730458	+	5'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94730458delT	uc001pfe.2	+	3						NM_018039	NP_060509			jumonji domain containing 2D						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				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	94817951	94817952	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94817951_94817952insA								SFRS2B (13564 upstream) : ENDOD1 (5065 downstream)																																			---	---	---	---
ENDOD1	23052	broad.mit.edu	37	11	94828468	94828470	+	Intron	DEL	CTC	-	-	rs140996219		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94828468_94828470delCTC	uc001pfh.2	+							NM_015036	NP_055851			endonuclease domain containing 1 precursor							extracellular region	endonuclease activity|metal ion binding|nucleic acid binding				0		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	94894411	94894412	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94894411_94894412delAA								ENDOD1 (28596 upstream) : SESN3 (11721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	95002582	95002583	+	IGR	INS	-	A	A	rs35048075		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95002582_95002583insA								SESN3 (36877 upstream) : FAM76B (499523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	95059227	95059228	+	IGR	INS	-	TGTAA	TGTAA	rs139537032	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95059227_95059228insTGTAA								SESN3 (93522 upstream) : FAM76B (442878 downstream)																																			---	---	---	---
MAML2	84441	broad.mit.edu	37	11	95921807	95921807	+	Intron	DEL	T	-	-	rs112854219		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95921807delT	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								---	---	---	---
MAML2	84441	broad.mit.edu	37	11	96011397	96011397	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96011397delA	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	96159832	96159833	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96159832_96159833delCA								JRKL (33105 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	96557995	96557995	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96557995delA								JRKL (431268 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	96724360	96724360	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96724360delT								JRKL (597633 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	97624610	97624611	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97624610_97624611delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98431174	98431174	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98431174delA								None (None upstream) : CNTN5 (460697 downstream)																																			---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99033007	99033008	+	Intron	INS	-	T	T	rs144436271	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99033007_99033008insT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	100234630	100234630	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100234630delA								CNTN5 (7158 upstream) : ARHGAP42 (323777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	101166839	101166839	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101166839delT								PGR (166295 upstream) : TRPC6 (155457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	101473674	101473675	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101473674_101473675delTG								TRPC6 (19015 upstream) : ANGPTL5 (287731 downstream)																																			---	---	---	---
ANGPTL5	253935	broad.mit.edu	37	11	101778725	101778725	+	5'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101778725delA	uc001pgl.2	-	2						NM_178127	NP_835228			angiopoietin-like 5 precursor						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)														---	---	---	---
KIAA1377	57562	broad.mit.edu	37	11	101817589	101817589	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101817589delA	uc001pgm.2	+						KIAA1377_uc001pgn.2_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	101832459	101832459	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
MMP20	9313	broad.mit.edu	37	11	102489863	102489864	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102489863_102489864insT	uc001phc.2	-							NM_004771	NP_004762			matrix metalloproteinase 20 preproprotein						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)														---	---	---	---
MMP27	64066	broad.mit.edu	37	11	102578214	102578214	+	5'Flank	DEL	T	-	-	rs1300202	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102578214delT	uc001phd.1	-							NM_022122	NP_071405			matrix metalloproteinase 27 precursor						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	102625643	102625651	+	5'Flank	DEL	AAAAAAAAA	-	-	rs7952598		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102625643_102625651delAAAAAAAAA	uc001phf.2	-											Homo sapiens mRNA for hypothetical protein, partial cds, clone:Hsa11-digit16-11-10-F.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	102928450	102928450	+	IGR	DEL	A	-	-	rs2509111		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102928450delA								MMP13 (101988 upstream) : DCUN1D5 (4372 downstream)																																			---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103124000	103124000	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103124000delT	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	103243663	103243664	+	Intron	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103243663_103243664insTG	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	103263495	103263495	+	Intron	DEL	A	-	-	rs4315038		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103263495delA	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932			dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	103544492	103544493	+	IGR	INS	-	A	A	rs142199104	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103544492_103544493insA								DYNC2H1 (193901 upstream) : PDGFD (233422 downstream)																																			---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	103899166	103899167	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103899166_103899167delTT	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)														---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	103899600	103899600	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103899600delA	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)														---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	103920253	103920254	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103920253_103920254insT	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)														---	---	---	---
CASP5	838	broad.mit.edu	37	11	104872625	104872626	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104872625_104872626delAC	uc010rva.1	-						CASP5_uc010ruz.1_Intron|CASP5_uc010rvb.1_Intron|CASP5_uc010rvc.1_Intron|CASP5_uc009yxh.2_Intron|CASP5_uc010rvd.1_Intron	NM_004347	NP_004338			caspase 5 isoform a precursor						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)														---	---	---	---
CASP5	838	broad.mit.edu	37	11	104894076	104894076	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104894076delA	uc010rva.1	-						CASP5_uc010ruz.1_5'Flank|CASP5_uc010rvb.1_5'Flank|CASP5_uc010rvc.1_5'Flank|CASP5_uc009yxh.2_5'Flank|CASP5_uc010rvd.1_5'Flank	NM_004347	NP_004338			caspase 5 isoform a precursor						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)														---	---	---	---
GRIA4	2893	broad.mit.edu	37	11	105505081	105505083	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105505081_105505083delAAA	uc001pix.2	+						GRIA4_uc001piu.1_Intron|GRIA4_uc001piw.2_Intron|GRIA4_uc001piv.2_Intron|GRIA4_uc009yxk.1_Intron	NM_000829	NP_000820			glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)													---	---	---	---
KBTBD3	143879	broad.mit.edu	37	11	105929470	105929472	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105929470_105929472delTTT	uc001pja.2	-						KBTBD3_uc001pjb.2_Intron|KBTBD3_uc009yxm.2_Intron	NM_198439	NP_940841			BTB and kelch domain containing 3											ovary(1)|central_nervous_system(1)	2		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)														---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106786700	106786701	+	Intron	INS	-	A	A	rs142281325	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106786700_106786701insA	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)														---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106883667	106883667	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106883667delT	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	106913511	106913511	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106913511delT								GUCY1A2 (24340 upstream) : CWF19L2 (283563 downstream)																																			---	---	---	---
ALKBH8	91801	broad.mit.edu	37	11	107414061	107414061	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107414061delA	uc010rvr.1	-						ALKBH8_uc001pjk.2_Intron|ALKBH8_uc010rvq.1_Intron|ALKBH8_uc009yxp.2_Intron|ALKBH8_uc001pjl.2_Intron	NM_138775	NP_620130			alkB, alkylation repair homolog 8						response to DNA damage stimulus	cytosol|nucleus	metal ion binding|nucleotide 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|protein binding|RNA binding|tRNA (uracil) methyltransferase activity				0		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00512)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.53e-05)|Epithelial(105;0.00029)|all cancers(92;0.00518)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	107571804	107571804	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107571804delA								ELMOD1 (34300 upstream) : SLN (6305 downstream)																																			---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107904513	107904513	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107904513delT	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	108031565	108031565	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108031565delA	uc001pjz.3	-						NPAT_uc010rvv.1_Intron	NM_002519	NP_002510			nuclear protein,  ataxia-telangiectasia locus						positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)														---	---	---	---
EXPH5	23086	broad.mit.edu	37	11	108435012	108435012	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108435012delA	uc001pkk.2	-							NM_015065	NP_055880			exophilin 5 isoform a						intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	109529578	109529578	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109529578delT								C11orf87 (229740 upstream) : ZC3H12C (434348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109575307	109575308	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109575307_109575308delAC								C11orf87 (275469 upstream) : ZC3H12C (388618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109602679	109602679	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109602679delA								C11orf87 (302841 upstream) : ZC3H12C (361247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	110901240	110901240	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110901240delA								ARHGAP20 (317328 upstream) : C11orf53 (225467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	111094195	111094195	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111094195delA								ARHGAP20 (510283 upstream) : C11orf53 (32512 downstream)																																			---	---	---	---
C11orf53	341032	broad.mit.edu	37	11	111132012	111132019	+	Intron	DEL	ACACACAT	-	-	rs58464008		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111132012_111132019delACACACAT	uc001plc.2	+							NM_198498	NP_940900			hypothetical protein LOC341032												0		all_cancers(61;2.05e-09)|Melanoma(852;4.04e-05)|all_epithelial(67;6.15e-05)|all_hematologic(158;0.000826)|Acute lymphoblastic leukemia(157;0.000966)|all_neural(223;0.0332)|Medulloblastoma(222;0.0425)|Breast(348;0.147)		Epithelial(105;1.7e-06)|BRCA - Breast invasive adenocarcinoma(274;3.16e-06)|all cancers(92;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0507)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	111319210	111319210	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111319210delC	uc001pli.1	+											Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit04-11-01-F.																														---	---	---	---
LAYN	143903	broad.mit.edu	37	11	111420297	111420297	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111420297delG	uc001plr.1	+						LAYN_uc001plp.1_Intron|LAYN_uc001plq.1_Intron|LAYN_uc001pls.1_Intron|LAYN_uc010rwg.1_Intron|LAYN_uc010rwh.1_Intron	NM_178834	NP_849156			layilin							cell surface|integral to membrane|ruffle	hyaluronic acid binding|sugar binding				0		all_cancers(61;9.06e-10)|all_epithelial(67;1.34e-05)|Melanoma(852;1.74e-05)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.086)		Epithelial(105;1.5e-06)|BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|all cancers(92;2.45e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0476)														---	---	---	---
SIK2	23235	broad.mit.edu	37	11	111520537	111520538	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111520537_111520538insT	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																		---	---	---	---
DLAT	1737	broad.mit.edu	37	11	111916412	111916413	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111916412_111916413delAA	uc001pmo.2	+						DLAT_uc009yyk.1_Intron|DLAT_uc010rwr.1_Intron	NM_001931	NP_001922			dihydrolipoamide S-acetyltransferase precursor						glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)													---	---	---	---
IL18	3606	broad.mit.edu	37	11	112024223	112024223	+	Intron	DEL	T	-	-	rs78854082		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112024223delT	uc001pnb.1	-						IL18_uc001pna.1_5'Flank|IL18_uc009yym.1_Intron	NM_001562	NP_001553			interleukin 18 proprotein						angiogenesis|cell-cell signaling|chemokine biosynthetic process|granulocyte macrophage colony-stimulating factor biosynthetic process|interferon-gamma biosynthetic process|interleukin-13 biosynthetic process|interleukin-2 biosynthetic process|positive regulation of activated T cell proliferation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of interferon-gamma production|positive regulation of interleukin-17 production|positive regulation of natural killer cell proliferation|positive regulation of NK T cell proliferation|regulation of cell adhesion|sleep|T-helper 1 type immune response|type 2 immune response	cytosol|extracellular space	cytokine activity|signal transducer activity				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)														---	---	---	---
BCO2	83875	broad.mit.edu	37	11	112092503	112092503	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112092503delT	uc001pni.2	+							NM_001037290	NP_001032367			beta-carotene dioxygenase 2 isoform b						carotene metabolic process|retinal metabolic process|retinoic acid metabolic process		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
PTS	5805	broad.mit.edu	37	11	112100900	112100901	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112100900_112100901insT	uc001pnj.3	+						PTS_uc009yyo.2_Intron	NM_000317	NP_000308			6-pyruvoyltetrahydropterin synthase						cellular amino acid metabolic process|central nervous system development|tetrahydrobiopterin biosynthetic process	mitochondrion	6-pyruvoyltetrahydropterin synthase activity|metal ion binding				0		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-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)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	112233258	112233258	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112233258delA								PTS (92581 upstream) : NCAM1 (598737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	112756113	112756113	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112756113delT								PTS (615436 upstream) : NCAM1 (75882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	112763793	112763794	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112763793_112763794delTT								PTS (623116 upstream) : NCAM1 (68201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	113170092	113170093	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113170092_113170093delAA								NCAM1 (20935 upstream) : TTC12 (15158 downstream)																																			---	---	---	---
TTC12	54970	broad.mit.edu	37	11	113196066	113196066	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113196066delA	uc001pnu.2	+						TTC12_uc001pnv.2_Intron|TTC12_uc001pnw.2_Intron|TTC12_uc001pnx.2_Intron	NM_017868	NP_060338			tetratricopeptide repeat domain 12								binding			pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)														---	---	---	---
DRD2	1813	broad.mit.edu	37	11	113323158	113323159	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113323158_113323159delGT	uc001poa.3	-						DRD2_uc001pob.3_Intron|DRD2_uc009yyr.1_Intron|hsa-mir-4301|MI0015828_5'Flank	NM_000795	NP_000786			dopamine receptor D2 isoform long						activation of phospholipase C activity by dopamine receptor signaling pathway|adenohypophysis development|adult walking behavior|arachidonic acid secretion|axonogenesis|behavioral response to cocaine|behavioral response to ethanol|branching morphogenesis of a nerve|cerebral cortex GABAergic interneuron migration|circadian regulation of gene expression|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|intracellular protein kinase cascade|negative regulation of blood pressure|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of dopamine receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|negative regulation of synaptic transmission, glutamatergic|neurological system process involved in regulation of systemic arterial blood pressure|peristalsis|phosphatidylinositol metabolic process|positive regulation of dopamine uptake|positive regulation of growth hormone secretion|positive regulation of neuroblast proliferation|prepulse inhibition|protein localization|regulation of heart rate|regulation of long-term neuronal synaptic plasticity|regulation of potassium ion transport|regulation of sodium ion transport|regulation of synaptic transmission, GABAergic|release of sequestered calcium ion into cytosol|response to amphetamine|response to drug|response to histamine|response to morphine|sensory perception of smell|synapse assembly|temperature homeostasis|visual learning	integral to plasma membrane	dopamine D2 receptor activity|dopamine receptor activity, coupled via Gi/Go|drug binding|potassium channel regulator activity|protein binding			pancreas(1)|skin(1)	2		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Carphenazine(DB01038)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Domperidone(DB01184)|Droperidol(DB00450)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Mesoridazine(DB00933)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Sulpiride(DB00391)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Ziprasidone(DB00246)|Zuclopenthixol(DB01624)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	113498174	113498177	+	IGR	DEL	AGGA	-	-	rs142026132	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113498174_113498177delAGGA								DRD2 (151761 upstream) : TMPRSS5 (60092 downstream)																																			---	---	---	---
ZW10	9183	broad.mit.edu	37	11	113608928	113608928	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113608928delA	uc001poe.2	-						ZW10_uc009yyv.2_Intron	NM_004724	NP_004715			centromere/kinetochore protein zw10						cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)														---	---	---	---
ZW10	9183	broad.mit.edu	37	11	113633630	113633630	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113633630delA	uc001poe.2	-						ZW10_uc009yyv.2_Intron	NM_004724	NP_004715			centromere/kinetochore protein zw10						cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)														---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	114002782	114002783	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114002782_114002783delAA	uc001pop.2	+						ZBTB16_uc001poo.1_Intron|ZBTB16_uc001poq.2_Intron	NM_006006	NP_005997			promyelocytic leukemia zinc finger protein						apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)														---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	114085313	114085313	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114085313delT	uc001pop.2	+						ZBTB16_uc001poq.2_Intron	NM_006006	NP_005997			promyelocytic leukemia zinc finger protein						apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)														---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	114104354	114104354	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114104354delT	uc001pop.2	+						ZBTB16_uc001poq.2_Intron	NM_006006	NP_005997			promyelocytic leukemia zinc finger protein						apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)														---	---	---	---
NNMT	4837	broad.mit.edu	37	11	114149334	114149335	+	Intron	INS	-	TG	TG	rs138088817	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114149334_114149335insTG	uc001por.1	+							NM_006169	NP_006160			nicotinamide N-methyltransferase						xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	115566670	115566670	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115566670delC								CADM1 (191429 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116100118	116100120	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116100118_116100120delTTT								CADM1 (724877 upstream) : BUD13 (518768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116437872	116437872	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116437872delG								None (None upstream) : BUD13 (181016 downstream)																																			---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116911353	116911355	+	Intron	DEL	GAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116911353_116911355delGAG	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440			serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12																		---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116939021	116939021	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116939021delA	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440			serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12																		---	---	---	---
CEP164	22897	broad.mit.edu	37	11	117209549	117209549	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117209549delT	uc001prc.2	+						CEP164_uc001prb.2_Intron|CEP164_uc001prd.2_Intron|CEP164_uc010rxj.1_Intron|CEP164_uc010rxk.1_Intron	NM_014956	NP_055771			centrosomal protein 164kDa						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	117306294	117306295	+	Intron	INS	-	G	G	rs146782057	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117306294_117306295insG	uc001prh.1	-							NM_020693	NP_065744			Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117506425	117506425	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117506425delA	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744			Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117625221	117625221	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117625221delG	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744			Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
TMPRSS13	84000	broad.mit.edu	37	11	117791092	117791092	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117791092delC	uc001prs.1	-						TMPRSS13_uc009yzr.1_5'Flank|TMPRSS13_uc001prt.1_5'Flank|TMPRSS13_uc001pru.1_Intron	NM_001077263	NP_001070731			transmembrane protease, serine 13						proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			pancreas(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	117853469	117853471	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117853469_117853471delAAA								TMPRSS13 (53354 upstream) : IL10RA (3635 downstream)																																			---	---	---	---
SCN2B	6327	broad.mit.edu	37	11	118041678	118041678	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118041678delT	uc001psf.2	-							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)														---	---	---	---
UBE4A	9354	broad.mit.edu	37	11	118241338	118241339	+	Intron	DEL	AA	-	-	rs142959441		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118241338_118241339delAA	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)														---	---	---	---
TREH	11181	broad.mit.edu	37	11	118539761	118539761	+	Intron	DEL	A	-	-	rs12801676		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118539761delA	uc001pty.1	-						TREH_uc009zaj.1_Intron|TREH_uc001ptz.1_Intron|TREH_uc009zak.2_Intron	NM_007180	NP_009111			trehalase precursor						polysaccharide digestion|trehalose catabolic process	anchored to plasma membrane	alpha,alpha-trehalase activity			pancreas(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.16e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	118558614	118558614	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118558614delC								TREH (8233 upstream) : DDX6 (59859 downstream)																																			---	---	---	---
DDX6	1656	broad.mit.edu	37	11	118629614	118629614	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118629614delG	uc001pub.2	-						DDX6_uc001pua.2_5'UTR|DDX6_uc001puc.2_Intron	NM_004397	NP_004388			DEAD (Asp-Glu-Ala-Asp) box polypeptide 6						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|RNA-induced silencing complex|stress granule	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|RNA helicase activity			ovary(1)	1	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)				T	IGH@	B-NHL								---	---	---	---
Unknown	0	broad.mit.edu	37	11	118852938	118852938	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118852938delT								FOXR1 (944 upstream) : CCDC84 (15914 downstream)																																			---	---	---	---
CCDC84	338657	broad.mit.edu	37	11	118876356	118876356	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118876356delT	uc001pul.2	+						CCDC84_uc010ryk.1_Intron|CCDC84_uc010ryl.1_Intron|CCDC84_uc010rym.1_Intron|RPL23AP64_uc001pum.2_5'Flank	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)														---	---	---	---
PDZD3	79849	broad.mit.edu	37	11	119058254	119058254	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119058254delT	uc001pwb.2	+						PDZD3_uc001pvy.2_Intron|PDZD3_uc001pvz.2_Intron|PDZD3_uc010rzd.1_Intron|PDZD3_uc001pwa.2_Intron					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;						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	119225313	119225313	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119225313delA								MFRP (7930 upstream) : USP2 (613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	119255293	119255293	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119255293delT	uc001pwo.2	+						uc001pwp.1_Intron|USP2_uc001pwm.3_5'Flank|USP2_uc001pwn.3_5'Flank					Homo sapiens cDNA FLJ40501 fis, clone TESTI2045171.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	119363684	119363684	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119363684delT	uc001pwo.2	+						uc001pwp.1_Intron					Homo sapiens cDNA FLJ40501 fis, clone TESTI2045171.																														---	---	---	---
PVRL1	5818	broad.mit.edu	37	11	119535451	119535451	+	3'UTR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119535451delG	uc001pwv.2	-	6					PVRL1_uc001pwu.1_Intron	NM_002855	NP_002846			poliovirus receptor-related 1 isoform 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	119689682	119689687	+	IGR	DEL	CACACG	-	-	rs111364837		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119689682_119689687delCACACG								PVRL1 (90247 upstream) : TRIM29 (292308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	119929294	119929295	+	IGR	INS	-	AA	AA	rs149207689	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119929294_119929295insAA								PVRL1 (329859 upstream) : TRIM29 (52700 downstream)																																			---	---	---	---
POU2F3	25833	broad.mit.edu	37	11	120129529	120129529	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120129529delG	uc001pxc.2	+						POU2F3_uc010rzk.1_Intron|POU2F3_uc010rzl.1_Intron|uc001pxd.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)														---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120266470	120266470	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120266470delC	uc001pxl.1	+						ARHGEF12_uc009zat.2_Intron|ARHGEF12_uc010rzn.1_Intron|ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128			Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120418304	120418305	+	Intron	DEL	TT	-	-	rs111357927		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120418304_120418305delTT	uc001pxn.2	+							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	120456562	120456562	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120456562delG	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	120547777	120547777	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120547777delT	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)													---	---	---	---
TECTA	7007	broad.mit.edu	37	11	120973343	120973343	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120973343delT	uc010rzo.1	+							NM_005422	NP_005413			tectorin alpha precursor						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	121344604	121344604	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121344604delA	uc001pxx.2	+							NM_003105	NP_003096			sortilin-related receptor containing LDLR class						cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	121549505	121549505	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121549505delT								SORL1 (45034 upstream) : LOC399959 (410306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	121775080	121775081	+	IGR	DEL	TT	-	-	rs35984902		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121775080_121775081delTT								SORL1 (270609 upstream) : LOC399959 (184730 downstream)																																			---	---	---	---
LOC399959	399959	broad.mit.edu	37	11	121992582	121992582	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121992582delT	uc009zba.2	-							NR_024430				Homo sapiens cDNA FLJ34394 fis, clone HCHON2000676.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	122455459	122455459	+	IGR	DEL	A	-	-	rs112806101		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122455459delA								LOC399959 (216992 upstream) : UBASH3B (70939 downstream)																																			---	---	---	---
C11orf63	79864	broad.mit.edu	37	11	122775729	122775729	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122775729delT	uc001pym.2	+						C11orf63_uc001pyl.1_Intron	NM_024806	NP_079082			hypothetical protein LOC79864 isoform 1											ovary(3)	3		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	122893102	122893102	+	IGR	DEL	A	-	-	rs77174704		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122893102delA								LOC341056 (2784 upstream) : HSPA8 (35099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	123080697	123080697	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123080697delT								ASAM (14690 upstream) : GRAMD1B (315831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	123192552	123192552	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123192552delT								ASAM (126545 upstream) : GRAMD1B (203976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	123704376	123704376	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123704376delA								OR6M1 (27319 upstream) : TMEM225 (49259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124330292	124330292	+	IGR	DEL	A	-	-	rs116268854	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124330292delA								OR8B8 (19311 upstream) : OR8B12 (82328 downstream)																																			---	---	---	---
SIAE	54414	broad.mit.edu	37	11	124519316	124519316	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
PKNOX2	63876	broad.mit.edu	37	11	125204670	125204670	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125204670delT	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	125264855	125264856	+	Intron	INS	-	GT	GT	rs149774655	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125264855_125264856insGT	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)														---	---	---	---
EI24	9538	broad.mit.edu	37	11	125452222	125452224	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125452222_125452224delTTT	uc001qca.2	+						EI24_uc001qcb.2_Intron|EI24_uc010sbd.1_Intron|EI24_uc009zbl.2_Intron|EI24_uc001qcc.2_Intron|EI24_uc010sbe.1_Intron|EI24_uc010sbf.1_Intron	NM_004879	NP_004870			etoposide induced 2.4 isoform 1						apoptosis|autophagy|induction of apoptosis|negative regulation of cell growth	endoplasmic reticulum membrane|integral to membrane|nuclear membrane				ovary(1)	1	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)														---	---	---	---
STT3A	3703	broad.mit.edu	37	11	125472348	125472349	+	Intron	INS	-	A	A	rs74685340		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125472348_125472349insA	uc001qcd.2	+						STT3A_uc009zbm.2_Intron|STT3A_uc001qce.2_Intron|STT3A_uc010sbg.1_Intron	NM_152713	NP_689926			integral membrane protein 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	125711778	125711779	+	IGR	INS	-	AAAC	AAAC	rs141218616	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125711778_125711779insAAAC								PATE4 (1812 upstream) : HYLS1 (41730 downstream)																																			---	---	---	---
ST3GAL4	6484	broad.mit.edu	37	11	126229193	126229195	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126229193_126229195delAAA	uc001qds.2	+						ST3GAL4_uc001qdt.2_Intron|ST3GAL4_uc009zcc.2_Intron|ST3GAL4_uc009zcd.2_Intron|ST3GAL4_uc001qdu.2_Intron|ST3GAL4_uc001qdv.2_Intron	NM_006278	NP_006269			ST3 beta-galactoside alpha-2,3-sialyltransferase						post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)														---	---	---	---
KIRREL3	84623	broad.mit.edu	37	11	126736885	126736885	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126736885delC	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	127630697	127630697	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127630697delA								KIRREL3 (757342 upstream) : ETS1 (697959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	127763887	127763887	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127763887delA								KIRREL3 (890532 upstream) : ETS1 (564769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	128303279	128303279	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128303279delC								None (None upstream) : ETS1 (25377 downstream)																																			---	---	---	---
ETS1	2113	broad.mit.edu	37	11	128385147	128385148	+	Intron	INS	-	CA	CA	rs144501511	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128385147_128385148insCA	uc010sbs.1	-						ETS1_uc001qej.2_Intron|ETS1_uc009zch.2_Intron|ETS1_uc009zcg.2_Intron	NM_005238	NP_005229			v-ets erythroblastosis virus E26 oncogene						cell motility|immune response|induction of apoptosis|negative regulation of cell cycle|negative regulation of cell cycle|negative regulation of cell proliferation|PML body organization|positive regulation of cellular component movement|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|response to antibiotic|transcription from RNA polymerase II promoter	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			lung(4)|central_nervous_system(1)|pleura(1)	6	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	128479911	128479911	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128479911delA								ETS1 (22458 upstream) : FLI1 (76519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	128552682	128552683	+	Intron	INS	-	AC	AC	rs147701021	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128552682_128552683insAC	uc001qek.2	-											Homo sapiens cDNA FLJ35701 fis, clone SPLEN2020007.																														---	---	---	---
FLI1	2313	broad.mit.edu	37	11	128557164	128557164	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128557164delT	uc010sbt.1	+						uc001qek.2_5'Flank					SubName: Full=cDNA FLJ52260, highly similar to Friend leukemia integration 1 transcription factor;						hemostasis|organ morphogenesis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2266)	bone(2210)|soft_tissue(48)|autonomic_ganglia(4)|central_nervous_system(4)|lung(3)|ovary(2)|pancreas(2)	2273	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)				T	EWSR1	Ewing sarcoma								---	---	---	---
Unknown	0	broad.mit.edu	37	11	128689663	128689668	+	IGR	DEL	CACACG	-	-	rs72126306		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128689663_128689668delCACACG								FLI1 (6502 upstream) : KCNJ1 (18247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	128800696	128800697	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128800696_128800697insA								KCNJ5 (12747 upstream) : TP53AIP1 (4575 downstream)																																			---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	129004107	129004107	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129004107delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	129511348	129511348	+	IGR	DEL	C	-	-	rs66471032		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129511348delC								BARX2 (189175 upstream) : TMEM45B (174393 downstream)																																			---	---	---	---
NFRKB	4798	broad.mit.edu	37	11	129752688	129752688	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129752688delT	uc001qfi.2	-						NFRKB_uc001qfg.2_Intron|NFRKB_uc001qfh.2_Intron|NFRKB_uc010sbw.1_Intron	NM_001143835	NP_001137307			nuclear factor related to kappaB binding protein						DNA recombination|DNA repair|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Ino80 complex	DNA binding|protease binding			ovary(3)	3	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)														---	---	---	---
PRDM10	56980	broad.mit.edu	37	11	129798461	129798461	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129798461delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	129902698	129902699	+	IGR	DEL	TT	-	-	rs71985644		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129902698_129902699delTT								NCRNA00167 (27317 upstream) : APLP2 (37017 downstream)																																			---	---	---	---
APLP2	334	broad.mit.edu	37	11	129981280	129981280	+	Intron	DEL	A	-	-	rs3216113		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129981280delA	uc010sby.1	+						APLP2_uc001qfp.2_Intron|APLP2_uc001qfq.2_Intron|APLP2_uc010sbz.1_Intron|APLP2_uc001qfr.2_Intron|APLP2_uc001qfs.2_Intron|APLP2_uc001qfv.2_Intron	NM_001642	NP_001633			amyloid beta (A4) precursor-like protein 2						G-protein coupled receptor protein signaling pathway	integral to membrane|nucleus|plasma membrane	DNA binding|identical protein binding|serine-type endopeptidase inhibitor activity			ovary(3)	3	all_hematologic(175;0.0429)	Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0197)|Lung(977;0.24)														---	---	---	---
ZBTB44	29068	broad.mit.edu	37	11	130135129	130135129	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130135129delT	uc001qga.2	-						ZBTB44_uc001qgb.3_Intron|ZBTB44_uc001qfx.2_Intron|ZBTB44_uc001qgc.1_Intron	NM_014155	NP_054874			zinc finger and BTB domain containing 44						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0192)|Lung(977;0.235)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	130302614	130302617	+	IGR	DEL	TTTT	-	-	rs34619459		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130302614_130302617delTTTT								ADAMTS8 (4075 upstream) : ADAMTS15 (16252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	130569206	130569206	+	IGR	DEL	A	-	-	rs142397713	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130569206delA								ADAMTS15 (225491 upstream) : SNX19 (176561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	130714223	130714223	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130714223delT	uc001qgj.2	-	6										Homo sapiens cDNA clone IMAGE:4838987.																														---	---	---	---
SNX19	399979	broad.mit.edu	37	11	130763889	130763889	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130763889delA	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	130923643	130923643	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130923643delA								SNX19 (137261 upstream) : NTM (316728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	131195518	131195519	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131195518_131195519delCT								SNX19 (409136 upstream) : NTM (44852 downstream)																																			---	---	---	---
NTM	50863	broad.mit.edu	37	11	131295700	131295700	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131295700delT	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530			neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
NTM	50863	broad.mit.edu	37	11	131433227	131433227	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131433227delA	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530			neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
NTM	50863	broad.mit.edu	37	11	131523121	131523121	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131523121delT	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530			neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
NTM	50863	broad.mit.edu	37	11	131531655	131531655	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131531655delT	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530			neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
NTM	50863	broad.mit.edu	37	11	131775525	131775525	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131775525delT	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530			neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
NTM	50863	broad.mit.edu	37	11	132197709	132197712	+	Intron	DEL	CTCC	-	-	rs71958910		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132197709_132197712delCTCC	uc001qgp.2	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgq.2_Intron|NTM_uc001qgr.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	132654482	132654482	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132654482delC	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	132794022	132794023	+	Intron	INS	-	TGTG	TGTG	rs139501971	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132794022_132794023insTGTG	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	133010658	133010659	+	Intron	INS	-	GAA	GAA	rs138549636	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133010658_133010659insGAA	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	133448817	133448818	+	IGR	INS	-	GG	GG	rs149101666	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133448817_133448818insGG								OPCML (46414 upstream) : SPATA19 (261699 downstream)																																			---	---	---	---
JAM3	83700	broad.mit.edu	37	11	133965523	133965523	+	Intron	DEL	A	-	-	rs71479590		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133965523delA	uc001qhb.1	+						JAM3_uc009zcz.1_Intron	NM_032801	NP_116190			junctional adhesion molecule 3 precursor						angiogenesis|blood coagulation|regulation of neutrophil chemotaxis	cell-cell contact zone|desmosome|extracellular space|integral to membrane	integrin binding			ovary(1)	1	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)														---	---	---	---
NCAPD3	23310	broad.mit.edu	37	11	134029714	134029717	+	Intron	DEL	CAGA	-	-	rs151072505		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134029714_134029717delCAGA	uc001qhd.1	-						NCAPD3_uc010scm.1_Intron|NCAPD3_uc009zda.1_Intron|NCAPD3_uc001qhc.1_Intron	NM_015261	NP_056076			non-SMC condensin II complex, subunit D3						cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	5	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)														---	---	---	---
GLB1L3	112937	broad.mit.edu	37	11	134155130	134155130	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134155130delT	uc009zdf.2	+						GLB1L3_uc010scs.1_Intron|GLB1L3_uc010sct.1_Intron	NM_001080407	NP_001073876			galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)														---	---	---	---
GLB1L3	112937	broad.mit.edu	37	11	134178366	134178369	+	Intron	DEL	AAAT	-	-	rs5795876		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134178366_134178369delAAAT	uc009zdf.2	+						GLB1L3_uc010scu.1_Intron|GLB1L3_uc001qho.3_Intron	NM_001080407	NP_001073876			galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	134435504	134435505	+	IGR	INS	-	CGA	CGA	rs61908899		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134435504_134435505insCGA								B3GAT1 (153692 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	134671646	134671646	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134671646delA								B3GAT1 (389834 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93003	93003	+	5'UTR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93003delG	uc010sdi.1	-	1					uc010sdj.1_RNA					SubName: Full=DEAD/H box polypeptide 11 like 11;																														---	---	---	---
B4GALNT3	283358	broad.mit.edu	37	12	620769	620775	+	Intron	DEL	ACCTTCG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:620769_620775delACCTTCG	uc001qii.1	+							NM_173593	NP_775864			beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)															---	---	---	---
B4GALNT3	283358	broad.mit.edu	37	12	664364	664364	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:664364delA	uc001qii.1	+						B4GALNT3_uc001qij.1_Intron|B4GALNT3_uc001qik.1_Intron	NM_173593	NP_775864			beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)															---	---	---	---
NINJ2	4815	broad.mit.edu	37	12	697356	697364	+	Intron	DEL	GGGACGGAG	-	-	rs74475206		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:697356_697364delGGGACGGAG	uc001qil.2	-						NINJ2_uc010sdr.1_Intron|NINJ2_uc010sds.1_Intron	NM_016533	NP_057617			ninjurin 2						nervous system development|neuron cell-cell adhesion|tissue regeneration	integral to plasma membrane				ovary(2)	2	all_cancers(10;0.0101)|all_epithelial(11;0.0174)|Ovarian(42;0.0512)|all_lung(10;0.103)|Lung NSC(10;0.185)		OV - Ovarian serous cystadenocarcinoma(31;3.26e-05)|BRCA - Breast invasive adenocarcinoma(9;0.0508)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	848100	848100	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:848100delA								NINJ2 (75345 upstream) : WNK1 (14125 downstream)																																			---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1137798	1137798	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1137798delT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron	NM_178040	NP_829884			RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1513551	1513553	+	Intron	DEL	AAA	-	-	rs35010065		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1513551_1513553delAAA	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_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)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1582796	1582801	+	Intron	DEL	AAAAAA	-	-	rs141729042		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1582796_1582801delAAAAAA	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.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)															---	---	---	---
WNT5B	81029	broad.mit.edu	37	12	1741793	1741793	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1741793delT	uc009zdq.2	+						WNT5B_uc001qjj.2_Intron|WNT5B_uc001qjk.2_Intron|WNT5B_uc001qjl.2_Intron	NM_032642	NP_116031			wingless-type MMTV integration site family,						angiogenesis|anterior/posterior pattern formation|cell migration involved in gastrulation|cellular response to retinoic acid|chondrocyte differentiation|convergent extension involved in axis elongation|convergent extension involved in gastrulation|dorsal/ventral axis specification|endocrine pancreas development|fat cell differentiation|lens fiber cell development|negative regulation of canonical Wnt receptor signaling pathway|neuron differentiation|positive regulation of cell migration|positive regulation of fat cell differentiation|respiratory system development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)															---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2622162	2622164	+	Intron	DEL	TCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2622162_2622164delTCT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	2887034	2887034	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2887034delT								CACNA1C (79919 upstream) : FKBP4 (17074 downstream)																																			---	---	---	---
TULP3	7289	broad.mit.edu	37	12	3046966	3046966	+	Intron	DEL	A	-	-	rs3742080	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3046966delA	uc010seh.1	+						TULP3_uc009zec.1_Intron|TULP3_uc010seg.1_Intron|TULP3_uc001qlj.2_Intron|TULP3_uc010sei.1_Intron	NM_003324	NP_003315			tubby like protein 3 isoform 1						G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
EFCAB4B	84766	broad.mit.edu	37	12	3739013	3739013	+	Intron	DEL	A	-	-	rs150187051	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3739013delA	uc010sen.1	-						EFCAB4B_uc001qmi.1_Intron	NM_001144958	NP_001138430			EF-hand calcium binding domain 4B isoform a						activation of store-operated calcium channel activity|store-operated calcium entry	cytoplasm	calcium ion binding|protein binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	4418964	4418965	+	IGR	INS	-	CT	CT	rs142543210	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4418964_4418965insCT								CCND2 (4443 upstream) : C12orf5 (11394 downstream)																																			---	---	---	---
FGF23	8074	broad.mit.edu	37	12	4488831	4488831	+	5'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4488831delT	uc001qmq.1	-	1						NM_020638	NP_065689			fibroblast growth factor 23 precursor						cell differentiation|insulin receptor signaling pathway|negative regulation of bone mineralization|negative regulation of hormone secretion|negative regulation of osteoblast differentiation|positive regulation of vitamin D 24-hydroxylase activity|regulation of phosphate transport|vitamin D catabolic process	extracellular space	growth factor activity			ovary(2)|breast(1)|skin(1)	4			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)|STAD - Stomach adenocarcinoma(119;0.206)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	4531404	4531404	+	IGR	DEL	T	-	-	rs112373636		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4531404delT								FGF23 (42510 upstream) : FGF6 (11904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	4581127	4581127	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4581127delA								FGF6 (26347 upstream) : C12orf4 (15784 downstream)																																			---	---	---	---
RAD51AP1	10635	broad.mit.edu	37	12	4667939	4667939	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4667939delT	uc001qmw.2	+						RAD51AP1_uc001qmu.2_Intron|RAD51AP1_uc001qmv.2_Intron|RAD51AP1_uc010sep.1_Intron|RAD51AP1_uc010seq.1_Intron|RAD51AP1_uc009zeg.2_Intron	NM_001130862	NP_001124334			RAD51 associated protein 1 isoform a						double-strand break repair via homologous recombination		double-stranded DNA binding|protein binding|protein binding|RNA binding|single-stranded DNA binding				0			Colorectal(7;0.00306)|COAD - Colon adenocarcinoma(12;0.0389)															---	---	---	---
DYRK4	8798	broad.mit.edu	37	12	4719362	4719362	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4719362delA	uc001qmx.2	+	11	1217	c.1057delA	c.(1057-1059)AAAfs	p.K353fs	DYRK4_uc009zeh.1_Frame_Shift_Del_p.K468fs|DYRK4_uc001qmy.1_Frame_Shift_Del_p.K353fs|DYRK4_uc001qmz.1_Frame_Shift_Del_p.K67fs|DYRK4_uc001qna.1_5'UTR|DYRK4_uc010ser.1_5'UTR	NM_003845	NP_003836	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	353	Protein kinase.					Golgi apparatus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|skin(1)	3			Colorectal(7;0.103)															---	---	---	---
GALNT8	26290	broad.mit.edu	37	12	4848291	4848291	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4848291delA	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	5210808	5210808	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5210808delT								KCNA5 (54860 upstream) : NTF3 (330472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	5475204	5475204	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5475204delT								KCNA5 (319256 upstream) : NTF3 (66076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	5629426	5629427	+	IGR	INS	-	GATC	GATC	rs139841019	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5629426_5629427insGATC								NTF3 (24963 upstream) : ANO2 (42390 downstream)																																			---	---	---	---
VWF	7450	broad.mit.edu	37	12	6185235	6185235	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6185235delA	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	6266013	6266013	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6266013delT								VWF (32177 upstream) : CD9 (42860 downstream)																																			---	---	---	---
VAMP1	6843	broad.mit.edu	37	12	6579673	6579673	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6579673delC	uc001qok.2	-						VAMP1_uc001qoj.2_Intron|VAMP1_uc001qol.2_Intron	NM_014231	NP_055046			vesicle-associated membrane protein 1 isoform 1						neurotransmitter secretion|vesicle-mediated transport	cell junction|endocytic vesicle membrane|integral to plasma membrane|mitochondrial outer membrane|synaptic vesicle membrane|synaptosome	protein binding				0					Botulinum Toxin Type B(DB00042)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	6583982	6583982	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6583982delT								VAMP1 (4139 upstream) : MRPL51 (17334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	6593250	6593250	+	IGR	DEL	A	-	-	rs74499427		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6593250delA								VAMP1 (13407 upstream) : MRPL51 (8066 downstream)																																			---	---	---	---
NCAPD2	9918	broad.mit.edu	37	12	6606466	6606466	+	Intron	DEL	T	-	-	rs11445549		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6606466delT	uc001qoo.2	+						NCAPD2_uc009zen.1_Intron|NCAPD2_uc010sfd.1_Intron	NM_014865	NP_055680			non-SMC condensin I complex, subunit D2						cell division|mitotic chromosome condensation	condensin core heterodimer|cytoplasm	histone binding			ovary(2)|lung(1)|breast(1)|kidney(1)	5																		---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6690187	6690187	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6690187delA	uc001qpo.2	-						CHD4_uc001qpn.2_Intron|CHD4_uc001qpp.2_Intron|uc001qpq.1_Intron	NM_001273	NP_001264			chromodomain helicase DNA binding protein 4						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
LPAR5	57121	broad.mit.edu	37	12	6741136	6741136	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6741136delT	uc009zer.2	-						LPAR5_uc001qps.2_Intron|LPAR5_uc010sff.1_Intron	NM_001142961	NP_001136433			lysophosphatidic acid receptor 5							integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)|skin(1)	2																		---	---	---	---
ZNF384	171017	broad.mit.edu	37	12	6780021	6780021	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6780021delA	uc010sfh.1	-						ZNF384_uc001qpz.2_Intron|ZNF384_uc001qqa.2_Intron|ZNF384_uc001qqb.2_Intron|ZNF384_uc001qqc.2_Intron|ZNF384_uc001qqd.2_Intron|ZNF384_uc001qqe.2_Intron	NM_001135734	NP_001129206			nuclear matrix transcription factor 4 isoform d						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/ZNF384(4)	haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1)	8								T	EWSR1|TAF15 	ALL								---	---	---	---
ATN1	1822	broad.mit.edu	37	12	7035645	7035645	+	Intron	DEL	T	-	-	rs67968349		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7035645delT	uc001qrw.1	+						ATN1_uc001qrx.1_5'Flank	NM_001007026	NP_001007027			atrophin-1						cell death|central nervous system development	cytoplasm|nucleus	protein domain specific binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																		---	---	---	---
RBP5	83758	broad.mit.edu	37	12	7277514	7277514	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7277514delT	uc001qsq.2	-							NM_031491	NP_113679			retinol binding protein 5, cellular							cytoplasm	retinal binding|retinol binding|transporter activity			ovary(1)	1					Vitamin A(DB00162)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	7686774	7686774	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7686774delA								CD163 (30360 upstream) : APOBEC1 (115223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	7765109	7765144	+	IGR	DEL	GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7765109_7765144delGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG								CD163 (108695 upstream) : APOBEC1 (36853 downstream)																																			---	---	---	---
SLC2A14	144195	broad.mit.edu	37	12	8028573	8028574	+	Intron	INS	-	AA	AA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8028573_8028574insAA	uc010sgh.1	-						SLC2A14_uc001qto.2_5'Flank|uc001qtp.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	8095541	8095541	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8095541delT								SLC2A3 (6649 upstream) : FOXJ2 (89818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	8141523	8141523	+	IGR	DEL	T	-	-	rs11056780	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8141523delT								SLC2A3 (52631 upstream) : FOXJ2 (43836 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	8467577	8467578	+	IGR	DEL	GT	-	-	rs59992207		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8467577_8467578delGT								LOC653113 (72035 upstream) : LOC389634 (41984 downstream)																																			---	---	---	---
CLEC6A	93978	broad.mit.edu	37	12	8622021	8622021	+	Intron	DEL	A	-	-	rs140414120		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8622021delA	uc001qum.1	+							NM_001007033	NP_001007034			dectin-2						defense response to fungus|innate immune response|positive regulation of cytokine secretion|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	sugar binding			breast(1)	1	Lung SC(5;0.184)																	---	---	---	---
CLEC6A	93978	broad.mit.edu	37	12	8630103	8630103	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8630103delT	uc001qum.1	+	6						NM_001007033	NP_001007034			dectin-2						defense response to fungus|innate immune response|positive regulation of cytokine secretion|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	sugar binding			breast(1)	1	Lung SC(5;0.184)																	---	---	---	---
CLEC4D	338339	broad.mit.edu	37	12	8666083	8666083	+	5'Flank	DEL	T	-	-	rs112268689		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8666083delT	uc001qun.2	+							NM_080387	NP_525126			C-type lectin domain family 4, member D						innate immune response	integral to membrane	sugar binding				0	Lung SC(5;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	8725334	8725334	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8725334delA								CLEC4E (31776 upstream) : AICDA (29428 downstream)																																			---	---	---	---
KLRG1	10219	broad.mit.edu	37	12	9148757	9148758	+	Intron	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9148757_9148758insTG	uc001qvh.2	+						KLRG1_uc001qvg.2_Intron	NM_005810	NP_005801			killer cell lectin-like receptor subfamily G,						cell surface receptor linked signaling pathway|cellular defense response|inflammatory response|regulation of immune response	integral to membrane	receptor activity|sugar binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	9213234	9213234	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9213234delA	uc009zgh.1	-						uc009zgi.1_Intron					Homo sapiens cDNA FLJ41814 fis, clone NT2RI2011683.																														---	---	---	---
A2M	2	broad.mit.edu	37	12	9242623	9242623	+	Intron	DEL	A	-	-	rs11609582	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9242623delA	uc001qvk.1	-						A2M_uc009zgk.1_Intron	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	9511708	9511708	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9511708delT								LOC642846 (45024 upstream) : DDX12 (58580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	9772129	9772129	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9772129delT								KLRB1 (11632 upstream) : LOC374443 (13886 downstream)																																			---	---	---	---
OLR1	4973	broad.mit.edu	37	12	10313272	10313272	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10313272delA	uc001qxo.1	-						OLR1_uc010sgz.1_Intron|OLR1_uc010sha.1_Intron	NM_002543	NP_002534			oxidized low density lipoprotein (lectin-like)						blood circulation|blood coagulation|inflammatory response|leukocyte migration|proteolysis	extracellular region|integral to plasma membrane|membrane fraction	sugar binding			ovary(1)	1																		---	---	---	---
OLR1	4973	broad.mit.edu	37	12	10322523	10322524	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10322523_10322524delAA	uc001qxo.1	-						OLR1_uc010sgz.1_5'Flank|OLR1_uc010sha.1_Intron	NM_002543	NP_002534			oxidized low density lipoprotein (lectin-like)						blood circulation|blood coagulation|inflammatory response|leukocyte migration|proteolysis	extracellular region|integral to plasma membrane|membrane fraction	sugar binding			ovary(1)	1																		---	---	---	---
C12orf59	120939	broad.mit.edu	37	12	10336260	10336260	+	Intron	DEL	T	-	-	rs72216168		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10336260delT	uc001qxr.2	+						C12orf59_uc001qxq.2_Intron					RecName: Full=Uncharacterized protein C12orf59; Flags: Precursor;							integral to membrane				ovary(1)	1																		---	---	---	---
KLRD1	3824	broad.mit.edu	37	12	10467143	10467143	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10467143delA	uc001qxw.3	+						KLRD1_uc001qxx.3_Intron|KLRD1_uc001qxy.3_Intron|KLRD1_uc009zhh.2_Intron|KLRD1_uc009zhi.2_Intron|KLRD1_uc001qxz.3_Intron	NM_001114396	NP_001107868			killer cell lectin-like receptor subfamily D,						cell surface receptor linked signaling pathway|regulation of immune response	integral to membrane|plasma membrane	sugar binding|transmembrane receptor activity				0																		---	---	---	---
PRB4	5545	broad.mit.edu	37	12	11225475	11225475	+	Intron	DEL	G	-	-	rs66889442		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11225475delG	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)			---	---	---	---
ETV6	2120	broad.mit.edu	37	12	12264842	12264842	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12264842delA	uc001raa.1	+						BCL2L14_uc001raf.1_Intron	NM_001987	NP_001978			ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)						T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								---	---	---	---
LRP6	4040	broad.mit.edu	37	12	12346434	12346435	+	Intron	INS	-	A	A	rs141958720	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12346434_12346435insA	uc001rah.3	-						BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Intron	NM_002336	NP_002327			low density lipoprotein receptor-related protein						cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)																---	---	---	---
MANSC1	54682	broad.mit.edu	37	12	12482821	12482822	+	3'UTR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12482821_12482822delAA	uc001rai.1	-	4					MANSC1_uc010shm.1_3'UTR|MANSC1_uc001raj.1_3'UTR|MANSC1_uc009zht.1_3'UTR	NM_018050	NP_060520			MANSC domain containing 1 precursor							integral to membrane					0		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)														---	---	---	---
LOH12CR1	118426	broad.mit.edu	37	12	12510571	12510571	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
LOH12CR1	118426	broad.mit.edu	37	12	12517542	12517542	+	Intron	DEL	T	-	-	rs75763875		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12517542delT	uc001ral.2	+						LOH12CR1_uc009zhu.2_Intron	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	12704014	12704014	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12704014delT	uc001rao.1	-							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	14242136	14242136	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14242136delA								GRIN2B (109114 upstream) : ATF7IP (276475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	14357883	14357886	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14357883_14357886delTTTT								GRIN2B (224861 upstream) : ATF7IP (160725 downstream)																																			---	---	---	---
ATF7IP	55729	broad.mit.edu	37	12	14540949	14540949	+	Intron	DEL	T	-	-	rs34633217		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14540949delT	uc001rbw.2	+						ATF7IP_uc010shs.1_Intron|ATF7IP_uc001rbu.2_Intron|ATF7IP_uc001rbv.1_Intron|ATF7IP_uc001rbx.2_Intron|ATF7IP_uc010sht.1_Intron|ATF7IP_uc001rby.3_Intron	NM_018179	NP_060649			activating transcription factor 7 interacting						DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5																		---	---	---	---
ATF7IP	55729	broad.mit.edu	37	12	14608694	14608694	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14608694delT	uc001rbw.2	+						ATF7IP_uc010shs.1_Intron|ATF7IP_uc001rbu.2_Intron|ATF7IP_uc001rbv.1_Intron|ATF7IP_uc001rbx.2_Intron|ATF7IP_uc010sht.1_Intron|ATF7IP_uc001rby.3_Intron|ATF7IP_uc001rca.2_Intron	NM_018179	NP_060649			activating transcription factor 7 interacting						DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5																		---	---	---	---
ATF7IP	55729	broad.mit.edu	37	12	14609430	14609430	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14609430delT	uc001rbw.2	+						ATF7IP_uc010shs.1_Intron|ATF7IP_uc001rbu.2_Intron|ATF7IP_uc001rbv.1_Intron|ATF7IP_uc001rbx.2_Intron|ATF7IP_uc010sht.1_Intron|ATF7IP_uc001rby.3_Intron|ATF7IP_uc001rca.2_Intron	NM_018179	NP_060649			activating transcription factor 7 interacting						DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5																		---	---	---	---
ERP27	121506	broad.mit.edu	37	12	15067493	15067494	+	3'UTR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15067493_15067494delTG	uc001rco.2	-	7						NM_152321	NP_689534			endoplasmic reticulum protein 27 kDa precursor							endoplasmic reticulum lumen				breast(1)	1																		---	---	---	---
ARHGDIB	397	broad.mit.edu	37	12	15105517	15105517	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15105517delA	uc001rcq.1	-							NM_001175	NP_001166			Rho GDP dissociation inhibitor (GDI) beta						actin cytoskeleton organization|cellular component movement|immune response|multicellular organismal development|negative regulation of cell adhesion|regulation of small GTPase mediated signal transduction|Rho protein signal transduction	cytoplasmic membrane-bounded vesicle|cytoskeleton|cytosol	GTPase activator activity|Rho GDP-dissociation inhibitor activity				0																		---	---	---	---
PTPRO	5800	broad.mit.edu	37	12	15708178	15708178	+	Intron	DEL	A	-	-	rs80244888		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15708178delA	uc001rcv.1	+						PTPRO_uc001rcw.1_Intron|PTPRO_uc001rcx.1_Intron|PTPRO_uc001rcy.1_Intron|PTPRO_uc001rcz.1_Intron|PTPRO_uc001rda.1_Intron	NM_030667	NP_109592			receptor-type protein tyrosine phosphatase O							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)																---	---	---	---
MGST1	4257	broad.mit.edu	37	12	16518678	16518679	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16518678_16518679delCA	uc009zih.1	+											Homo sapiens cDNA FLJ76401 complete cds, highly similar to Homo sapiens microsomal glutathione S-transferase 1 (MGST1), transcript variant 1b, mRNA.						protein homotrimerization|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane	glutathione transferase activity				0		Hepatocellular(102;0.121)			Glutathione(DB00143)													---	---	---	---
LMO3	55885	broad.mit.edu	37	12	16737520	16737520	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16737520delG	uc001rdk.1	-						LMO3_uc001rdj.1_Intron|LMO3_uc010shy.1_Intron|LMO3_uc001rdl.1_Intron|LMO3_uc009zii.1_Intron|LMO3_uc010shz.1_Intron|LMO3_uc001rdm.1_Intron|LMO3_uc001rdo.1_Intron|LMO3_uc001rdp.1_Intron|LMO3_uc001rdn.1_Intron|LMO3_uc009zij.1_Intron|LMO3_uc009zik.1_Intron	NM_018640	NP_061110			LIM domain only 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent		zinc ion binding				0		Hepatocellular(102;0.244)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	17665134	17665135	+	IGR	INS	-	TG	TG	rs148287919	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17665134_17665135insTG								LMO3 (902376 upstream) : RERGL (568669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	17686237	17686237	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17686237delA								LMO3 (923479 upstream) : RERGL (547567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	17755878	17755878	+	IGR	DEL	G	-	-	rs111945034		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17755878delG								LMO3 (993120 upstream) : RERGL (477926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	18122042	18122042	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18122042delA								None (None upstream) : RERGL (111762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	18222782	18222782	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18222782delG								None (None upstream) : RERGL (11022 downstream)																																			---	---	---	---
PIK3C2G	5288	broad.mit.edu	37	12	18514908	18514908	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18514908delT	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)																---	---	---	---
PIK3C2G	5288	broad.mit.edu	37	12	18787803	18787803	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18787803delT	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)																---	---	---	---
PLCZ1	89869	broad.mit.edu	37	12	18889158	18889158	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18889158delA	uc010sid.1	-	3	323	c.132delT	c.(130-132)TTTfs	p.F44fs	PLCZ1_uc001rdv.3_5'UTR|PLCZ1_uc001rdw.3_5'UTR|CAPZA3_uc001rdy.2_5'Flank	NM_033123	NP_149114	Q86YW0	PLCZ1_HUMAN	phospholipase C, zeta 1	44	EF-hand.				intracellular signal transduction|lipid catabolic process|multicellular organismal development	nucleus|perinuclear region of cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	18902424	18902425	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18902424_18902425delGT								CAPZA3 (10303 upstream) : PLEKHA5 (380223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	19042438	19042439	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19042438_19042439delAC								CAPZA3 (150317 upstream) : PLEKHA5 (240209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	19055435	19055435	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19055435delA								CAPZA3 (163314 upstream) : PLEKHA5 (227213 downstream)																																			---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19494670	19494670	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19494670delT	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron|PLEKHA5_uc001rec.1_Intron|PLEKHA5_uc009zio.2_Intron	NM_019012	NP_061885			pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)																	---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19503694	19503695	+	Intron	INS	-	AA	AA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19503694_19503695insAA	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron|PLEKHA5_uc001rec.1_Intron|PLEKHA5_uc009zio.2_Intron	NM_019012	NP_061885			pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)																	---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19507078	19507088	+	Intron	DEL	TTTTTTTTTTT	-	-	rs67731032		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19507078_19507088delTTTTTTTTTTT	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron|PLEKHA5_uc001rec.1_Intron|PLEKHA5_uc009zio.2_Intron	NM_019012	NP_061885			pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	19693150	19693151	+	IGR	INS	-	T	T	rs149788601	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19693150_19693151insT								AEBP2 (17977 upstream) : PDE3A (829046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	20001194	20001194	+	IGR	DEL	A	-	-	rs11464383		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20001194delA								AEBP2 (326021 upstream) : PDE3A (521003 downstream)																																			---	---	---	---
PDE3A	5139	broad.mit.edu	37	12	20602591	20602591	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20602591delC	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)													---	---	---	---
PDE3A	5139	broad.mit.edu	37	12	20615730	20615730	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20615730delT	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	20997962	20997970	+	Intron	DEL	AAAAAAAAA	-	-	rs36120748		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20997962_20997970delAAAAAAAAA	uc001rek.2	+						SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron	NM_019844	NP_062818			solute carrier organic anion transporter family,						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)																	---	---	---	---
SLCO1B3	28234	broad.mit.edu	37	12	21235690	21235691	+	Intron	INS	-	TG	TG	rs139634000	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21235690_21235691insTG	uc010sil.1	+						LST-3TM12_uc010sim.1_Intron|LST-3TM12_uc010sin.1_Intron					SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	21569419	21569419	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21569419delT								SLCO1A2 (21048 upstream) : PYROXD1 (21119 downstream)																																			---	---	---	---
PYROXD1	79912	broad.mit.edu	37	12	21623285	21623290	+	3'UTR	DEL	AAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21623285_21623290delAAAAAA	uc001rew.2	+	12					RECQL_uc001rex.2_Intron|RECQL_uc001rey.2_Intron|PYROXD1_uc009ziq.2_3'UTR|PYROXD1_uc009zir.2_3'UTR	NM_024854	NP_079130			pyridine nucleotide-disulphide oxidoreductase								oxidoreductase activity			ovary(1)	1																		---	---	---	---
GOLT1B	51026	broad.mit.edu	37	12	21665210	21665210	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21665210delT	uc001rez.2	+						GOLT1B_uc009zis.2_Intron|GOLT1B_uc009zit.2_Intron|GOLT1B_uc009ziu.2_Intron	NM_016072	NP_057156			golgi transport 1 homolog B						positive regulation of I-kappaB kinase/NF-kappaB cascade|protein transport|vesicle-mediated transport	endoplasmic reticulum|Golgi membrane|integral to membrane	signal transducer activity				0																		---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	21967555	21967555	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21967555delA	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	21972623	21972623	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21972623delT	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	22035948	22035949	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22035948_22035949insA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	22745992	22745992	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22745992delT								KIAA0528 (48540 upstream) : ETNK1 (32084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	23038748	23038750	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23038748_23038750delTTT								ETNK1 (195141 upstream) : SOX5 (646482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	23667087	23667087	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23667087delA								ETNK1 (823480 upstream) : SOX5 (18145 downstream)																																			---	---	---	---
SOX5	6660	broad.mit.edu	37	12	24323127	24323127	+	Intron	DEL	A	-	-	rs74707951		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24323127delA	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																		---	---	---	---
LRMP	4033	broad.mit.edu	37	12	25259856	25259856	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25259856delA	uc001rgh.2	+						LRMP_uc010sja.1_Intron|LRMP_uc010sjb.1_Intron|LRMP_uc001rgi.2_Intron|LRMP_uc010sjc.1_Intron|LRMP_uc010sjd.1_Intron	NM_006152	NP_006143			lymphoid-restricted membrane protein						vesicle fusion|vesicle targeting	endoplasmic reticulum membrane|integral to plasma membrane				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)																	---	---	---	---
KRAS	3845	broad.mit.edu	37	12	25368594	25368595	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25368594_25368595delTT	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	26055226	26055226	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26055226delA								IFLTD1 (253738 upstream) : RASSF8 (56743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	26077046	26077046	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26077046delT								IFLTD1 (275558 upstream) : RASSF8 (34923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	26095369	26095369	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26095369delT								IFLTD1 (293881 upstream) : RASSF8 (16600 downstream)																																			---	---	---	---
SSPN	8082	broad.mit.edu	37	12	26351606	26351607	+	Intron	INS	-	AT	AT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26351606_26351607insAT	uc001rhe.2	+						SSPN_uc001rhd.2_Intron|SSPN_uc009zjf.2_Intron|SSPN_uc001rhf.3_Intron	NM_005086	NP_005077			sarcospan isoform 1						cell adhesion|muscle contraction	cell junction|dystrophin-associated glycoprotein complex|integral to plasma membrane|postsynaptic membrane|sarcolemma|transport vesicle					0	Colorectal(261;0.0847)																	---	---	---	---
TM7SF3	51768	broad.mit.edu	37	12	27152717	27152717	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27152717delA	uc010sjl.1	-							NM_016551	NP_057635			transmembrane 7 superfamily member 3 precursor							integral to membrane|plasma membrane				upper_aerodigestive_tract(2)	2	Colorectal(261;0.0847)																	---	---	---	---
STK38L	23012	broad.mit.edu	37	12	27467937	27467937	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27467937delT	uc001rhr.2	+						STK38L_uc001rhs.2_Intron|STK38L_uc010sjm.1_Intron|STK38L_uc010sjn.1_Intron|STK38L_uc010sjo.1_5'Flank	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)																	---	---	---	---
PPFIBP1	8496	broad.mit.edu	37	12	27816772	27816773	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27816772_27816773insA	uc001ric.1	+						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)																	---	---	---	---
FAR2	55711	broad.mit.edu	37	12	29385755	29385756	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29385755_29385756delCA	uc001ris.3	+						FAR2_uc001rit.2_Intron|FAR2_uc009zjm.2_Intron	NM_018099	NP_060569			fatty acyl CoA reductase 2						ether lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	30022124	30022124	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30022124delT								TMTC1 (84432 upstream) : IPO8 (759799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30484642	30484642	+	IGR	DEL	T	-	-	rs1506376	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30484642delT								TMTC1 (546950 upstream) : IPO8 (297281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30489349	30489349	+	IGR	DEL	A	-	-	rs61921962		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30489349delA								TMTC1 (551657 upstream) : IPO8 (292574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	31056313	31056316	+	IGR	DEL	TGGA	-	-	rs144741100		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31056313_31056316delTGGA								CAPRIN2 (148865 upstream) : TSPAN11 (23046 downstream)																																			---	---	---	---
TSPAN11	441631	broad.mit.edu	37	12	31148720	31148723	+	3'UTR	DEL	ACAA	-	-	rs143654637	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31148720_31148723delACAA	uc010sju.1	+	8					TSPAN11_uc001rjp.2_3'UTR|TSPAN11_uc010sjv.1_3'UTR	NM_001080509	NP_001073978			tetraspanin 11							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)																	---	---	---	---
FAM60A	58516	broad.mit.edu	37	12	31480838	31480838	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31480838delT	uc001rkd.2	-						FAM60A_uc010ska.1_5'Flank|FAM60A_uc001rke.2_5'Flank|FAM60A_uc010skb.1_5'Flank	NM_001135811	NP_001129283			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	31562360	31562364	+	Intron	DEL	AAAAA	-	-	rs111670680		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31562360_31562364delAAAAA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31585222	31585222	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31585222delA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	31965320	31965320	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31965320delT								H3F3C (20145 upstream) : C12orf35 (147033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	32215699	32215700	+	IGR	DEL	TT	-	-	rs67756690		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32215699_32215700delTT								C12orf35 (69668 upstream) : BICD1 (44485 downstream)																																			---	---	---	---
BICD1	636	broad.mit.edu	37	12	32520417	32520418	+	Intron	DEL	AA	-	-	rs63514564		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32520417_32520418delAA	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	33452341	33452341	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33452341delA								PKP2 (402561 upstream) : SYT10 (76007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	33897416	33897416	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33897416delA								SYT10 (304662 upstream) : ALG10 (277800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34016916	34016916	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34016916delT								SYT10 (424162 upstream) : ALG10 (158300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34066285	34066285	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34066285delT								SYT10 (473531 upstream) : ALG10 (108931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34469883	34469883	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34469883delT								ALG10 (288649 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34757348	34757348	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34757348delC								ALG10 (576114 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	37903806	37903806	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:37903806delT								None (None upstream) : ALG10B (806751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38025842	38025842	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38025842delC								None (None upstream) : ALG10B (684715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38366296	38366297	+	IGR	INS	-	G	G	rs150643385	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38366296_38366297insG								None (None upstream) : ALG10B (344260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38528364	38528365	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38528364_38528365insT								None (None upstream) : ALG10B (182192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38667550	38667550	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38667550delA								None (None upstream) : ALG10B (43007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	39505373	39505373	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39505373delA								CPNE8 (205953 upstream) : KIF21A (181658 downstream)																																			---	---	---	---
KIF21A	55605	broad.mit.edu	37	12	39750759	39750759	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39750759delA	uc001rly.2	-						KIF21A_uc001rlx.2_Intron|KIF21A_uc001rlz.2_Intron|KIF21A_uc010skl.1_Intron|KIF21A_uc001rma.1_Intron	NM_017641	NP_060111			kinesin family member 21A						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|pancreas(1)|lung(1)|skin(1)	7		Lung NSC(34;0.179)|all_lung(34;0.213)																---	---	---	---
C12orf40	283461	broad.mit.edu	37	12	40037146	40037146	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40037146delT	uc001rmc.2	+						C12orf40_uc009zjv.1_Intron	NM_001031748	NP_001026918			hypothetical protein LOC283461											ovary(6)	6																		---	---	---	---
SLC2A13	114134	broad.mit.edu	37	12	40271198	40271198	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40271198delC	uc010skm.1	-						C12orf40_uc009zjv.1_Intron	NM_052885	NP_443117			solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)													HNSCC(50;0.14)			---	---	---	---
Unknown	0	broad.mit.edu	37	12	40917533	40917533	+	Intron	DEL	A	-	-	rs79341017		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40917533delA	uc001rmj.1	+											Homo sapiens mRNA; cDNA DKFZp686N11246 (from clone DKFZp686N11246).																														---	---	---	---
CNTN1	1272	broad.mit.edu	37	12	41358320	41358323	+	Intron	DEL	GTAA	-	-	rs4768326		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41358320_41358323delGTAA	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	41522652	41522652	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41522652delT								CNTN1 (58558 upstream) : PDZRN4 (60135 downstream)																																			---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41768774	41768775	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41768774_41768775delTC	uc010skn.1	+							NM_013377	NP_037509			PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41840653	41840655	+	Intron	DEL	TTT	-	-	rs36011837		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41840653_41840655delTTT	uc010skn.1	+						PDZRN4_uc001rmq.3_Intron|PDZRN4_uc009zjz.2_Intron	NM_013377	NP_037509			PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41949205	41949205	+	Intron	DEL	A	-	-	rs145186833		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41949205delA	uc010skn.1	+						PDZRN4_uc001rmq.3_Intron|PDZRN4_uc009zjz.2_Intron|PDZRN4_uc001rmr.2_Intron	NM_013377	NP_037509			PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	41990066	41990066	+	IGR	DEL	A	-	-	rs11300017		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41990066delA								PDZRN4 (21682 upstream) : GXYLT1 (485584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	42123708	42123709	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42123708_42123709delAA								PDZRN4 (155324 upstream) : GXYLT1 (351941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	42271762	42271762	+	IGR	DEL	A	-	-	rs113507360		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42271762delA								PDZRN4 (303378 upstream) : GXYLT1 (203888 downstream)																																			---	---	---	---
GXYLT1	283464	broad.mit.edu	37	12	42477781	42477781	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42477781delA	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																		---	---	---	---
PPHLN1	51535	broad.mit.edu	37	12	42717961	42717961	+	5'Flank	DEL	G	-	-	rs3747557	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42717961delG	uc001rng.1	+						PPHLN1_uc001rmy.2_Intron|PPHLN1_uc001rna.2_5'Flank|PPHLN1_uc001rne.2_5'Flank|PPHLN1_uc001rnb.2_5'Flank|PPHLN1_uc001rnd.2_5'Flank|PPHLN1_uc001rnc.2_5'Flank|PPHLN1_uc001rnf.2_5'Flank|PPHLN1_uc010skq.1_5'Flank|PPHLN1_uc010skr.1_5'Flank|PPHLN1_uc010sks.1_5'Flank|PPHLN1_uc010skt.1_5'Flank|PPHLN1_uc001rni.1_5'Flank|PPHLN1_uc001rnh.1_5'Flank|PPHLN1_uc010sku.1_5'Flank|ZCRB1_uc001rmz.2_Intron	NM_016488	NP_057572			periphilin 1 isoform 1						keratinization	cytoplasm|nucleus				ovary(1)|breast(1)	2	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)														---	---	---	---
PRICKLE1	144165	broad.mit.edu	37	12	42878622	42878622	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42878622delA	uc010skv.1	-						PRICKLE1_uc001rnl.2_5'Flank|PRICKLE1_uc010skw.1_5'Flank|PRICKLE1_uc001rnm.2_Intron|PRICKLE1_uc009zka.2_Intron	NM_001144881	NP_001138353			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)														---	---	---	---
PRICKLE1	144165	broad.mit.edu	37	12	42982317	42982319	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42982317_42982319delTTT	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	43064528	+	IGR	DEL	AA	-	-	rs77046005		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43064527_43064528delAA								PRICKLE1 (80955 upstream) : ADAMTS20 (683485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	43152972	43152972	+	IGR	DEL	C	-	-	rs34380675		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43152972delC								PRICKLE1 (169400 upstream) : ADAMTS20 (595041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	43166771	43166772	+	IGR	DEL	AA	-	-	rs80291418		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43166771_43166772delAA								PRICKLE1 (183199 upstream) : ADAMTS20 (581241 downstream)																																			---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43813543	43813544	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43813543_43813544delAC	uc010skx.1	-							NM_025003	NP_079279			a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	43971065	43971066	+	IGR	INS	-	GT	GT	rs150765743	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43971065_43971066insGT								ADAMTS20 (25341 upstream) : PUS7L (151348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	44035682	44035682	+	IGR	DEL	T	-	-	rs141880065		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44035682delT								ADAMTS20 (89958 upstream) : PUS7L (86732 downstream)																																			---	---	---	---
TMEM117	84216	broad.mit.edu	37	12	44417764	44417764	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44417764delA	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632			transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)														---	---	---	---
TMEM117	84216	broad.mit.edu	37	12	44756617	44756618	+	Intron	DEL	TT	-	-	rs11301034		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44756617_44756618delTT	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632			transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	45480393	45480393	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45480393delT								RACGAP1P (21199 upstream) : PLEKHA9 (86454 downstream)																																			---	---	---	---
PLEKHA9	51054	broad.mit.edu	37	12	45581422	45581424	+	Intron	DEL	ATC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45581422_45581424delATC	uc001rom.1	-						PLEKHA9_uc009zke.2_Intron|RNY5_uc010slc.1_5'Flank	NM_015899	NP_056983			pleckstrin homology domain containing, family A												0	Lung SC(27;0.192)|Renal(347;0.236)			GBM - Glioblastoma multiforme(48;0.173)														---	---	---	---
PLEKHA9	51054	broad.mit.edu	37	12	45607864	45607864	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45607864delA	uc001rom.1	-						ANO6_uc001roo.2_5'Flank|ANO6_uc010sld.1_5'Flank|ANO6_uc010sle.1_5'Flank|ANO6_uc010slf.1_5'Flank|PLEKHA9_uc009zke.2_Intron	NM_015899	NP_056983			pleckstrin homology domain containing, family A												0	Lung SC(27;0.192)|Renal(347;0.236)			GBM - Glioblastoma multiforme(48;0.173)														---	---	---	---
ARID2	196528	broad.mit.edu	37	12	46275603	46275603	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46275603delT	uc001ros.1	+						ARID2_uc001ror.2_Intron|ARID2_uc009zkg.1_Intron|ARID2_uc009zkh.1_Intron|ARID2_uc001rou.1_Intron	NM_152641	NP_689854			AT rich interactive domain 2 (ARID, RFX-like)						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)														---	---	---	---
SFRS2IP	9169	broad.mit.edu	37	12	46358030	46358030	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46358030delA	uc001rox.2	-						SFRS2IP_uc001roy.1_Intron|SFRS2IP_uc009zki.1_Intron|SFRS2IP_uc001roz.2_Intron	NM_004719	NP_004710			splicing factor, arginine/serine-rich 2,						spliceosome assembly	nucleus	protein binding|zinc ion binding				0	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.209)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.1)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	46525221	46525222	+	IGR	DEL	AA	-	-	rs140670987		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46525221_46525222delAA								SFRS2IP (139318 upstream) : SLC38A1 (51621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	46839110	46839110	+	IGR	DEL	T	-	-	rs5797984		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46839110delT								SLC38A2 (72465 upstream) : SLC38A4 (319434 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47435398	47435398	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47435398delT								SLC38A4 (215618 upstream) : AMIGO2 (34093 downstream)																																			---	---	---	---
FAM113B	91523	broad.mit.edu	37	12	47525457	47525458	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47525457_47525458delTT	uc001rpn.2	+							NM_138371	NP_612380			hypothetical protein LOC91523								hydrolase activity			skin(3)|ovary(2)	5	Renal(347;0.138)|Lung SC(27;0.192)																	---	---	---	---
FAM113B	91523	broad.mit.edu	37	12	47599556	47599556	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47599556delA	uc001rpn.2	+							NM_138371	NP_612380			hypothetical protein LOC91523								hydrolase activity			skin(3)|ovary(2)	5	Renal(347;0.138)|Lung SC(27;0.192)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	47788086	47788086	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47788086delA								FAM113B (157645 upstream) : RPAP3 (267630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47788605	47788605	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47788605delA								FAM113B (158164 upstream) : RPAP3 (267111 downstream)																																			---	---	---	---
RAPGEF3	10411	broad.mit.edu	37	12	48146461	48146461	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48146461delA	uc009zkp.2	-						RAPGEF3_uc009zkq.2_Intron|RAPGEF3_uc001rpz.3_Intron|RAPGEF3_uc009zkr.2_Intron|RAPGEF3_uc009zks.2_Intron|RAPGEF3_uc001rqb.3_Intron	NM_001098532	NP_001092002			Rap guanine nucleotide exchange factor 3 isoform						regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex	cAMP-dependent protein kinase regulator activity|guanyl-nucleotide exchange factor activity			lung(2)|skin(1)|pancreas(1)	4	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)														---	---	---	---
SLC48A1	55652	broad.mit.edu	37	12	48167592	48167593	+	Intron	INS	-	AC	AC	rs150100667	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48167592_48167593insAC	uc001rqd.2	+						RAPGEF3_uc009zks.2_5'Flank|SLC48A1_uc001rqc.2_Intron	NM_017842	NP_060312			heme-responsive gene 1						transport	endosome membrane|integral to membrane|lysosomal membrane					0																		---	---	---	---
SENP1	29843	broad.mit.edu	37	12	48490244	48490245	+	Intron	DEL	TT	-	-	rs63235460		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48490244_48490245delTT	uc001rqx.2	-						SENP1_uc001rqw.2_Intron|SENP1_uc001rqy.2_Intron|SENP1_uc001rqz.2_Intron|SENP1_uc009zkx.2_Intron	NM_014554	NP_055369			sentrin/SUMO-specific protease 1						activation of caspase activity|induction of apoptosis by extracellular signals|protein desumoylation|proteolysis	cytoplasm|nucleus	endopeptidase activity|SUMO-specific protease activity			pancreas(2)|lung(1)	3		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	48751410	48751412	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48751410_48751412delTTT								ZNF641 (6389 upstream) : ANP32D (115036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	48837519	48837521	+	IGR	DEL	TCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48837519_48837521delTCT								ZNF641 (92498 upstream) : ANP32D (28927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	48995642	48995642	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48995642delA								LALBA (31813 upstream) : C12orf41 (51353 downstream)																																			---	---	---	---
RHEBL1	121268	broad.mit.edu	37	12	49459415	49459415	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49459415delA	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	49708866	49708866	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49708866delA								PRPH (16386 upstream) : TROAP (8105 downstream)																																			---	---	---	---
SPATS2	65244	broad.mit.edu	37	12	49892629	49892630	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49892629_49892630insG	uc001rud.2	+						SPATS2_uc001rue.2_Intron|SPATS2_uc009zli.1_Intron|SPATS2_uc001ruf.2_Intron|SPATS2_uc001rug.2_Intron	NM_023071	NP_075559			spermatogenesis associated, serine-rich 2							cytoplasm				breast(1)	1																		---	---	---	---
KCNH3	23416	broad.mit.edu	37	12	49943832	49943832	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49943832delC	uc001ruh.1	+						KCNH3_uc010smj.1_Intron	NM_012284	NP_036416			potassium voltage-gated channel, subfamily H						regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity|voltage-gated potassium channel activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	49974143	49974143	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49974143delA								MCRS1 (12232 upstream) : FAM186B (2516 downstream)																																	OREG0021796	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM186B	84070	broad.mit.edu	37	12	49987416	49987416	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49987416delA	uc001ruo.2	-						FAM186B_uc010smk.1_Intron	NM_032130	NP_115506			hypothetical protein LOC84070							protein complex				ovary(1)	1																		---	---	---	---
LIMA1	51474	broad.mit.edu	37	12	50636145	50636145	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50636145delT	uc001rwj.3	-						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																		---	---	---	---
LIMA1	51474	broad.mit.edu	37	12	50673928	50673942	+	Intron	DEL	TTTTTTTTTTTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50673928_50673942delTTTTTTTTTTTTTTT	uc001rwj.3	-						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	50867693	50867693	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50867693delA	uc001rwp.1	+						LARP4_uc001rwo.1_Intron|LARP4_uc001rwq.1_Intron|LARP4_uc001rwr.1_Intron|LARP4_uc001rws.1_Intron|LARP4_uc009zlr.1_Intron|LARP4_uc001rwt.1_Intron	NM_052879	NP_443111			c-Mpl binding protein isoform a								nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	51008202	51008202	+	Intron	DEL	T	-	-	rs11365705		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51008202delT	uc001rwv.2	+						DIP2B_uc001rwu.2_Intron	NM_173602	NP_775873			DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6																		---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	51034721	51034721	+	Intron	DEL	C	-	-	rs2731436	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51034721delC	uc001rwv.2	+						DIP2B_uc001rwu.2_Intron|DIP2B_uc009zls.1_Intron	NM_173602	NP_775873			DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6																		---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	51092009	51092009	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51092009delT	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																		---	---	---	---
ATF1	466	broad.mit.edu	37	12	51171178	51171178	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51171178delA	uc001rww.3	+						ATF1_uc010smu.1_Intron	NM_005171	NP_005162			activating transcription factor 1						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|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				EWSR1/ATF1(323)|FUS/ATF1(4)	soft_tissue(321)|ovary(2)|NS(2)|bone(2)|skin(2)	329								T	EWSR1|FUS	malignant melanoma of soft parts |angiomatoid fibrous histiocytoma 								---	---	---	---
CELA1	1990	broad.mit.edu	37	12	51736568	51736568	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51736568delT	uc001ryi.1	-							NM_001971	NP_001962			chymotrypsin-like elastase family, member 1						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			breast(1)	1																		---	---	---	---
SLC4A8	9498	broad.mit.edu	37	12	51844775	51844775	+	Frame_Shift_Del	DEL	G	-	-	rs139949142		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51844775delG	uc001rys.1	+	3	424	c.246delG	c.(244-246)CAGfs	p.Q82fs	SLC4A8_uc010sni.1_Frame_Shift_Del_p.Q29fs|SLC4A8_uc001rym.2_Frame_Shift_Del_p.Q29fs|SLC4A8_uc001ryn.2_Frame_Shift_Del_p.Q29fs|SLC4A8_uc001ryo.2_Frame_Shift_Del_p.Q29fs|SLC4A8_uc001ryp.1_Frame_Shift_Del_p.Q29fs|SLC4A8_uc010snj.1_Frame_Shift_Del_p.Q109fs|SLC4A8_uc001ryq.3_Frame_Shift_Del_p.Q82fs|SLC4A8_uc001ryr.2_Frame_Shift_Del_p.Q82fs|SLC4A8_uc010snk.1_Frame_Shift_Del_p.Q29fs	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate	82	Extracellular (Potential).				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	51945143	51945143	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51945143delA								SLC4A8 (35596 upstream) : SCN8A (39877 downstream)																																			---	---	---	---
KRT81	3887	broad.mit.edu	37	12	52700832	52700833	+	5'UTR	DEL	TT	-	-	rs67766873		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52700832_52700833delTT	uc001sac.2	-	2					KRT86_uc010snq.1_Intron|KRT86_uc009zmg.2_Intron|KRT86_uc001sad.2_Intron	NM_002281	NP_002272			keratin, hair, basic, 1							keratin filament	protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
KRT6B	3854	broad.mit.edu	37	12	52842584	52842584	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52842584delA	uc001sak.2	-							NM_005555	NP_005546			keratin 6B						ectoderm development	keratin filament	structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.083)														---	---	---	---
KRT6B	3854	broad.mit.edu	37	12	52847626	52847626	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52847626delT	uc001sak.2	-							NM_005555	NP_005546			keratin 6B						ectoderm development	keratin filament	structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.083)														---	---	---	---
TENC1	23371	broad.mit.edu	37	12	53449246	53449246	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53449246delC	uc001sbp.2	+						uc001sbk.1_5'Flank|TENC1_uc001sbl.2_Intron|TENC1_uc001sbm.2_Intron|TENC1_uc001sbn.2_Intron|TENC1_uc001sbo.1_Intron|TENC1_uc001sbq.2_5'Flank	NM_170754	NP_736610			tensin like C1 domain containing phosphatase						intracellular signal transduction|negative regulation of cell proliferation	focal adhesion	metal ion binding|phosphoprotein phosphatase activity|protein binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	53649881	53649882	+	IGR	INS	-	A	A	rs143746166	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53649881_53649882insA								MFSD5 (1693 upstream) : ESPL1 (12201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	53740688	53740688	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53740688delT								SP7 (10522 upstream) : SP1 (33291 downstream)																																			---	---	---	---
SP1	6667	broad.mit.edu	37	12	53797304	53797306	+	Intron	DEL	TTT	-	-	rs34078240		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53797304_53797306delTTT	uc001scw.2	+						SP1_uc010sog.1_Intron	NM_138473	NP_612482			Sp1 transcription factor isoform a						positive regulation by host of viral transcription|positive regulation of transcription from RNA polymerase II promoter	cytoplasm	double-stranded DNA binding|histone deacetylase binding|HMG box domain binding|protein C-terminus binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(357;0.00527)														---	---	---	---
AMHR2	269	broad.mit.edu	37	12	53818452	53818452	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53818452delC	uc001scx.1	+						AMHR2_uc009zmy.1_Intron	NM_020547	NP_065434			anti-Mullerian hormone receptor, type II isoform						Mullerian duct regression		ATP binding|hormone binding|metal ion binding			ovary(1)|skin(1)	2					Adenosine triphosphate(DB00171)									Persistant_Mullerian_Duct_Syndrome_(type_I_and_II)				---	---	---	---
ATF7	11016	broad.mit.edu	37	12	53926424	53926426	+	Intron	DEL	AAA	-	-	rs111391259		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53926424_53926426delAAA	uc001sdy.2	-						ATF7_uc010sok.1_Intron|ATF7_uc001sdz.2_Intron|ATF7_uc010sol.1_Intron	NM_001130059	NP_001123531			activating transcription factor 7 isoform 1						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	54137151	54137151	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54137151delC								CALCOCO1 (15844 upstream) : HOXC13 (195425 downstream)																																	OREG0021878	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
HOXC12	3228	broad.mit.edu	37	12	54349900	54349901	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54349900_54349901insA	uc010soq.1	+							NM_173860	NP_776272			homeobox C12						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
HOXC4	3221	broad.mit.edu	37	12	54422130	54422130	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54422130delT	uc001seu.2	+						HOXC6_uc001ses.2_Intron|HOXC5_uc001set.2_Intron|HOXC6_uc001sev.2_5'Flank	NM_014620	NP_055435			homeobox C4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	54613047	54613047	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54613047delA								SMUG1 (30290 upstream) : CBX5 (11685 downstream)																																			---	---	---	---
CBX5	23468	broad.mit.edu	37	12	54627090	54627090	+	3'UTR	DEL	C	-	-	rs2272470	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54627090delC	uc001sfh.3	-	5					CBX5_uc001sfk.3_3'UTR|CBX5_uc001sfi.3_3'UTR|CBX5_uc001sfj.3_3'UTR	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	54753725	54753727	+	IGR	DEL	TTC	-	-	rs148085822	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54753725_54753727delTTC								COPZ1 (8092 upstream) : GPR84 (2504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	54875601	54875601	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54875601delT								GTSF1 (8215 upstream) : NCKAP1L (15894 downstream)																																			---	---	---	---
NCKAP1L	3071	broad.mit.edu	37	12	54910235	54910236	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54910235_54910236delTT	uc001sgc.3	+						NCKAP1L_uc010sox.1_Intron|NCKAP1L_uc010soy.1_Intron	NM_005337	NP_005328			NCK-associated protein 1-like						actin polymerization-dependent cell motility|B cell homeostasis|B cell receptor signaling pathway|cortical actin cytoskeleton organization|erythrocyte development|maintenance of cell polarity|myeloid cell homeostasis|negative regulation of apoptosis|negative regulation of interleukin-17 production|negative regulation of interleukin-6 production|negative regulation of myosin-light-chain-phosphatase activity|neutrophil chemotaxis|positive regulation of actin filament polymerization|positive regulation of B cell differentiation|positive regulation of B cell proliferation|positive regulation of CD4-positive, alpha-beta T cell differentiation|positive regulation of CD8-positive, alpha-beta T cell differentiation|positive regulation of cell adhesion mediated by integrin|positive regulation of erythrocyte differentiation|positive regulation of gamma-delta T cell differentiation|positive regulation of neutrophil chemotaxis|positive regulation of phagocytosis, engulfment|positive regulation of T cell proliferation|protein complex assembly|response to drug|T cell homeostasis	cytosol|integral to plasma membrane|membrane fraction|SCAR complex	protein complex binding|protein kinase activator activity|Rac GTPase activator activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
NCKAP1L	3071	broad.mit.edu	37	12	54925872	54925876	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54925872_54925876delTTTTT	uc001sgc.3	+						NCKAP1L_uc010sox.1_Intron|NCKAP1L_uc010soy.1_Intron	NM_005337	NP_005328			NCK-associated protein 1-like						actin polymerization-dependent cell motility|B cell homeostasis|B cell receptor signaling pathway|cortical actin cytoskeleton organization|erythrocyte development|maintenance of cell polarity|myeloid cell homeostasis|negative regulation of apoptosis|negative regulation of interleukin-17 production|negative regulation of interleukin-6 production|negative regulation of myosin-light-chain-phosphatase activity|neutrophil chemotaxis|positive regulation of actin filament polymerization|positive regulation of B cell differentiation|positive regulation of B cell proliferation|positive regulation of CD4-positive, alpha-beta T cell differentiation|positive regulation of CD8-positive, alpha-beta T cell differentiation|positive regulation of cell adhesion mediated by integrin|positive regulation of erythrocyte differentiation|positive regulation of gamma-delta T cell differentiation|positive regulation of neutrophil chemotaxis|positive regulation of phagocytosis, engulfment|positive regulation of T cell proliferation|protein complex assembly|response to drug|T cell homeostasis	cytosol|integral to plasma membrane|membrane fraction|SCAR complex	protein complex binding|protein kinase activator activity|Rac GTPase activator activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
DCD	117159	broad.mit.edu	37	12	55038760	55038760	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55038760delA	uc001sgj.2	-						DCD_uc009znt.2_Intron|DCD_uc009znu.2_Intron	NM_053283	NP_444513			dermcidin preproprotein						defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular region	protein binding			ovary(1)	1		Myeloproliferative disorder(1001;0.0255)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	55262244	55262244	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55262244delT								MUCL1 (10072 upstream) : KIAA0748 (81621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55481224	55481224	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55481224delT								NEUROD4 (57424 upstream) : OR9K2 (42329 downstream)																																			---	---	---	---
OR6C75	390323	broad.mit.edu	37	12	55759486	55759486	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55759486delT	uc010spk.1	+	1	592	c.592delT	c.(592-594)TTTfs	p.F198fs		NM_001005497	NP_001005497	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C,	198	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
DNAJC14	85406	broad.mit.edu	37	12	56219847	56219847	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56219847delA	uc001shx.1	-						DNAJC14_uc001shu.1_Intron|DNAJC14_uc009zob.1_Intron	NM_032364	NP_115740			dopamine receptor interacting protein						protein folding|protein transport	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|unfolded protein binding			ovary(3)|large_intestine(1)	4																		---	---	---	---
SILV	6490	broad.mit.edu	37	12	56352573	56352573	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56352573delT	uc001sip.2	-						SILV_uc001siq.2_Intron|SILV_uc010spx.1_Intron|SILV_uc001sir.2_Intron	NM_006928	NP_008859			silver homolog						melanin biosynthetic process|melanosome organization	endoplasmic reticulum membrane|extracellular region|Golgi apparatus|integral to membrane|melanosome|multivesicular body membrane|plasma membrane	protein binding				0																		---	---	---	---
CDK2	1017	broad.mit.edu	37	12	56362650	56362650	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56362650delT	uc001sit.3	+	4	641	c.404delT	c.(403-405)ATTfs	p.I135fs	CDK2_uc001siu.3_Frame_Shift_Del_p.I135fs|CDK2_uc010spy.1_Frame_Shift_Del_p.I109fs	NM_001798	NP_001789	P24941	CDK2_HUMAN	cyclin-dependent kinase 2 isoform 1	135	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|blood coagulation|cell division|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA replication|G1/S transition of mitotic cell cycle|G2 phase of mitotic cell cycle|G2/M transition of mitotic cell cycle|histone phosphorylation|M/G1 transition of mitotic cell cycle|mitosis|positive regulation of cell proliferation|Ras protein signal transduction|regulation of DNA replication|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|traversing start control point of mitotic cell cycle	cyclin-dependent protein kinase holoenzyme complex|cytosol	ATP binding|cyclin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2			UCEC - Uterine corpus endometrioid carcinoma (6;0.123)|OV - Ovarian serous cystadenocarcinoma(18;0.235)															---	---	---	---
SMARCC2	6601	broad.mit.edu	37	12	56559113	56559113	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56559113delG	uc001skb.2	-	26	3234	c.3128delC	c.(3127-3129)CCTfs	p.P1043fs	SMARCC2_uc001skd.2_Frame_Shift_Del_p.P1074fs|SMARCC2_uc001ska.2_Frame_Shift_Del_p.P1074fs|SMARCC2_uc001skc.2_Frame_Shift_Del_p.P1073fs|SMARCC2_uc010sqf.1_Frame_Shift_Del_p.P963fs	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	1043	Pro-rich.				chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)															---	---	---	---
SMARCC2	6601	broad.mit.edu	37	12	56564203	56564203	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56564203delT	uc001skb.2	-						SMARCC2_uc001skd.2_Intron|SMARCC2_uc001ska.2_Intron|SMARCC2_uc001skc.2_Intron|SMARCC2_uc010sqf.1_Intron	NM_003075	NP_003066			SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)															---	---	---	---
BAZ2A	11176	broad.mit.edu	37	12	56999550	56999552	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
BAZ2A	11176	broad.mit.edu	37	12	57026345	57026345	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57026345delC	uc001slq.1	-						BAZ2A_uc001slp.1_5'Flank|BAZ2A_uc010sqr.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	57088336	57088338	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57088336_57088338delTTT								PTGES3 (6258 upstream) : NACA (17873 downstream)																																			---	---	---	---
PRIM1	5557	broad.mit.edu	37	12	57144805	57144805	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57144805delA	uc001smd.2	-						PRIM1_uc001sme.1_Intron|PRIM1_uc009zoz.1_Intron|PRIM1_uc001smf.2_Intron	NM_000946	NP_000937			DNA primase polypeptide 1						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	DNA primase activity|metal ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	57255300	57255300	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57255300delA								HSD17B6 (73726 upstream) : SDR9C7 (62319 downstream)																																			---	---	---	---
RDH16	8608	broad.mit.edu	37	12	57371271	57371271	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57371271delA	uc010sqx.1	-											Synthetic construct DNA, clone: pF1KSDA0352, Homo sapiens ZBTB39 gene for zinc finger and BTB domain-containing protein 39, complete cds, without stop codon, in Flexi system.						lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	binding|electron carrier activity|retinol dehydrogenase activity				0																		---	---	---	---
MYO1A	4640	broad.mit.edu	37	12	57426474	57426474	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57426474delA	uc001smw.3	-						MYO1A_uc010sqz.1_Intron|MYO1A_uc009zpd.2_Intron	NM_005379	NP_005370			myosin IA						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																		---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57738616	57738617	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57738616_57738617insT	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	57801038	57801039	+	Intron	DEL	AA	-	-	rs141913606		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57801038_57801039delAA	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																		---	---	---	---
MBD6	114785	broad.mit.edu	37	12	57921401	57921401	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57921401delC	uc001soj.1	+	8	2418	c.2194delC	c.(2194-2196)CCCfs	p.P732fs	MBD6_uc001sok.1_Frame_Shift_Del_p.P599fs|MBD6_uc001sol.1_RNA	NM_052897	NP_443129	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	732	Pro-rich.					chromosome|nucleus	chromatin binding|DNA binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
KIF5A	3798	broad.mit.edu	37	12	57962509	57962511	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57962509_57962511delAAA	uc001sor.1	+						KIF5A_uc010srr.1_Intron	NM_004984	NP_004975			kinesin family member 5A						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																		---	---	---	---
KIF5A	3798	broad.mit.edu	37	12	57975862	57975862	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57975862delA	uc001sor.1	+						KIF5A_uc010srr.1_Intron|uc001sos.2_5'Flank	NM_004984	NP_004975			kinesin family member 5A						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	58650060	58650060	+	IGR	DEL	T	-	-	rs66887338		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58650060delT								XRCC6BP1 (299009 upstream) : LRIG3 (615878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	59600773	59600774	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59600773_59600774delTT								LRIG3 (286511 upstream) : SLC16A7 (389074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	60451554	60451554	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60451554delG								SLC16A7 (276147 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	60844194	60844195	+	IGR	INS	-	ACACAT	ACACAT	rs139860170	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60844194_60844195insACACAT								SLC16A7 (668787 upstream) : None (None downstream)																																			---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62125097	62125098	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62125097_62125098insT	uc001sqw.2	-						FAM19A2_uc001sqv.2_Intron|FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62169757	62169757	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62169757delT	uc001sqw.2	-						FAM19A2_uc001sqv.2_Intron|FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62568095	62568096	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62568095_62568096insA	uc001sqw.2	-						FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62615975	62615976	+	Intron	INS	-	AC	AC	rs141466916	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62615975_62615976insAC	uc001sqx.2	-						FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
MON2	23041	broad.mit.edu	37	12	62889227	62889227	+	Intron	DEL	A	-	-	rs80114155		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62889227delA	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srd.1_Intron	NM_015026	NP_055841			MON2 homolog						Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	63752869	63752869	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63752869delA								AVPR1A (206279 upstream) : DPY19L2 (199824 downstream)																																			---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64265418	64265418	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64265418delT	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron	NM_020762	NP_065813			SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)														---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64480988	64480988	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64480988delT	uc010ssp.1	+						SRGAP1_uc001srv.2_Intron	NM_020762	NP_065813			SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)														---	---	---	---
C12orf56	115749	broad.mit.edu	37	12	64679695	64679696	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64679695_64679696delAA	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	64746630	64746630	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64746630delT	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	65369247	65369247	+	RNA	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65369247delT	uc001ssj.1	+	3		c.1111delT								Homo sapiens cDNA FLJ41278 fis, clone BRAMY2037147.																														---	---	---	---
WIF1	11197	broad.mit.edu	37	12	65449388	65449388	+	Intron	DEL	A	-	-	rs140453124		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65449388delA	uc001ssk.2	-							NM_007191	NP_009122			WNT inhibitory factor 1 precursor						multicellular organismal development|Wnt receptor signaling pathway	extracellular region	protein tyrosine kinase activity			ovary(2)|lung(1)|skin(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)				T	HMGA2	pleomorphic salivary gland adenoma								---	---	---	---
Unknown	0	broad.mit.edu	37	12	65666178	65666179	+	IGR	INS	-	TTTCTTTC	TTTCTTTC	rs10666226		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65666178_65666179insTTTCTTTC								LEMD3 (24071 upstream) : MSRB3 (6309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	65875871	65875871	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65875871delT								MSRB3 (15191 upstream) : RPSAP52 (275932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	66103112	66103112	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66103112delA								MSRB3 (242432 upstream) : RPSAP52 (48691 downstream)																																			---	---	---	---
TMBIM4	51643	broad.mit.edu	37	12	66544004	66544004	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66544004delT	uc001stc.2	-						LLPH_uc010ssx.1_Intron|TMBIM4_uc001std.2_Intron|TMBIM4_uc009zqr.2_Intron|TMBIM4_uc001ste.2_Intron|TMBIM4_uc001stf.2_Intron|TMBIM4_uc009zqs.2_Intron	NM_016056	NP_057140			transmembrane BAX inhibitor motif containing 4							integral to membrane	protein binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(28;0.0745)														---	---	---	---
IRAK3	11213	broad.mit.edu	37	12	66638830	66638830	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66638830delT	uc001sth.2	+						IRAK3_uc010ssy.1_Intron	NM_007199	NP_009130			interleukin-1 receptor-associated kinase 3						interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|negative regulation of innate immune response|negative regulation of interleukin-12 production|negative regulation of interleukin-6 production|negative regulation of macrophage cytokine production|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein catabolic process|negative regulation of protein complex disassembly|negative regulation of toll-like receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of macrophage tolerance induction|positive regulation of NF-kappaB transcription factor activity|response to exogenous dsRNA|response to lipopolysaccharide|response to peptidoglycan	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein heterodimerization activity|protein homodimerization activity|protein serine/threonine kinase activity			lung(3)|ovary(2)|breast(2)|central_nervous_system(1)	8				GBM - Glioblastoma multiforme(28;0.0203)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	68486350	68486365	+	IGR	DEL	GAAGAGAAGAAACTGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68486350_68486365delGAAGAGAAGAAACTGA								DYRK2 (429907 upstream) : IFNG (62185 downstream)																																			---	---	---	---
IL26	55801	broad.mit.edu	37	12	68619109	68619109	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68619109delT	uc001stx.1	-							NM_018402	NP_060872			interleukin 26 precursor						cell-cell signaling|negative regulation of epithelial cell proliferation|positive regulation of cytokine secretion|positive regulation of ERK1 and ERK2 cascade|positive regulation of JAK-STAT cascade|positive regulation of protein kinase B signaling cascade|positive regulation of stress-activated MAPK cascade|positive regulation of transcription from RNA polymerase II promoter	cytosol|extracellular space|soluble fraction	cytokine activity				0			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000515)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	68661327	68661327	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68661327delA								IL22 (13942 upstream) : MDM1 (27019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68863623	68863626	+	IGR	DEL	TTTG	-	-	rs10878836	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68863623_68863626delTTTG								MDM1 (137462 upstream) : RAP1B (141026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68955338	68955338	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68955338delA								MDM1 (229177 upstream) : RAP1B (49314 downstream)																																			---	---	---	---
RAP1B	5908	broad.mit.edu	37	12	69020555	69020556	+	Intron	DEL	TT	-	-	rs74812051		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69020555_69020556delTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	69184341	69184341	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69184341delG								SLC35E3 (24490 upstream) : MDM2 (17630 downstream)																																			---	---	---	---
CPM	1368	broad.mit.edu	37	12	69346344	69346345	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69346344_69346345insG	uc001sur.2	-							NM_001874	NP_001865			carboxypeptidase M precursor						anatomical structure morphogenesis|proteolysis	anchored to membrane|cytoplasm|nucleus|plasma membrane	metallocarboxypeptidase activity|zinc ion binding				0	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	70036244	70036244	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70036244delA								LRRC10 (31302 upstream) : BEST3 (896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	70488420	70488420	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70488420delA								RAB3IP (271438 upstream) : CNOT2 (148357 downstream)																																			---	---	---	---
CNOT2	4848	broad.mit.edu	37	12	70739865	70739865	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
PTPRR	5801	broad.mit.edu	37	12	71230087	71230090	+	Intron	DEL	TTTT	-	-	rs113441059		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71230087_71230090delTTTT	uc001swi.1	-							NM_002849	NP_002840			protein tyrosine phosphatase, receptor type, R						in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			skin(2)|ovary(1)	3			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)														---	---	---	---
TSPAN8	7103	broad.mit.edu	37	12	71693809	71693809	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71693809delA	uc001swk.1	-							NM_004616	NP_004607			transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)															---	---	---	---
LGR5	8549	broad.mit.edu	37	12	71931718	71931718	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71931718delT	uc001swl.2	+						LGR5_uc001swm.2_Intron|LGR5_uc001swn.1_Intron	NM_003667	NP_003658			leucine-rich repeat-containing G protein-coupled							integral to plasma membrane	protein-hormone receptor activity			lung(4)|skin(3)|ovary(1)|pancreas(1)	9																		---	---	---	---
RAB21	23011	broad.mit.edu	37	12	72154824	72154826	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72154824_72154826delAAA	uc001swt.2	+							NM_014999	NP_055814			RAB21, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	cleavage furrow|cytoplasmic vesicle membrane|early endosome membrane|endoplasmic reticulum membrane|Golgi membrane	GDP binding|GTP binding|GTPase activity|protein binding				0																		---	---	---	---
RAB21	23011	broad.mit.edu	37	12	72173249	72173249	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72173249delA	uc001swt.2	+							NM_014999	NP_055814			RAB21, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	cleavage furrow|cytoplasmic vesicle membrane|early endosome membrane|endoplasmic reticulum membrane|Golgi membrane	GDP binding|GTP binding|GTPase activity|protein binding				0																		---	---	---	---
TPH2	121278	broad.mit.edu	37	12	72395605	72395605	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72395605delT	uc009zrw.1	+						TPH2_uc001swy.2_Intron	NM_173353	NP_775489			tryptophan hydroxylase 2						aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity			ovary(2)|central_nervous_system(1)|skin(1)	4					L-Tryptophan(DB00150)													---	---	---	---
TPH2	121278	broad.mit.edu	37	12	72415233	72415233	+	Intron	DEL	T	-	-	rs72209893		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72415233delT	uc009zrw.1	+						TPH2_uc001swy.2_Intron	NM_173353	NP_775489			tryptophan hydroxylase 2						aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity			ovary(2)|central_nervous_system(1)|skin(1)	4					L-Tryptophan(DB00150)													---	---	---	---
TRHDE	29953	broad.mit.edu	37	12	73041658	73041659	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73041658_73041659insA	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																		---	---	---	---
CAPS2	84698	broad.mit.edu	37	12	75687722	75687722	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75687722delT	uc001sxk.3	-						CAPS2_uc001sxm.3_Intron|CAPS2_uc009zsa.2_Intron|CAPS2_uc001sxi.3_Intron|CAPS2_uc001sxj.3_Intron|CAPS2_uc001sxl.3_Intron	NM_032606	NP_115995			calcyphosine 2								calcium ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	76016947	76016948	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76016947_76016948delTT								KRR1 (111529 upstream) : PHLDA1 (402280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76353880	76353880	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76353880delA								KRR1 (448462 upstream) : PHLDA1 (65348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76551638	76551639	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76551638_76551639delCA								NAP1L1 (72900 upstream) : BBS10 (186627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76978151	76978152	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76978151_76978152delAA								OSBPL8 (24562 upstream) : ZDHHC17 (179702 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	77020853	77020853	+	IGR	DEL	A	-	-	rs71701218		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77020853delA								OSBPL8 (67264 upstream) : ZDHHC17 (137001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	77345877	77345877	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77345877delT								CSRP2 (73078 upstream) : E2F7 (69150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	77505460	77505461	+	IGR	INS	-	TG	TG	rs148453114	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77505460_77505461insTG								E2F7 (46100 upstream) : NAV3 (719608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	77563824	77563824	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77563824delA								E2F7 (104464 upstream) : NAV3 (661245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	77670954	77670954	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77670954delT								E2F7 (211594 upstream) : NAV3 (554115 downstream)																																			---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78554158	78554159	+	Intron	INS	-	GTGTGTGTGT	GTGTGTGTGT	rs145597374	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78554158_78554159insGTGTGTGTGT	uc001syp.2	+						NAV3_uc001syo.2_Intron|NAV3_uc010sub.1_Intron|NAV3_uc009zsf.2_Intron	NM_014903	NP_055718			neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17															HNSCC(70;0.22)			---	---	---	---
Unknown	0	broad.mit.edu	37	12	78668911	78668911	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78668911delT								NAV3 (62123 upstream) : SYT1 (588862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	78997305	78997305	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78997305delC								NAV3 (390517 upstream) : SYT1 (260468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	79024228	79024228	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79024228delA								NAV3 (417440 upstream) : SYT1 (233545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	79174378	79174379	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79174378_79174379delTG								NAV3 (567590 upstream) : SYT1 (83394 downstream)																																			---	---	---	---
SYT1	6857	broad.mit.edu	37	12	79722698	79722699	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79722698_79722699insA	uc001sys.2	+						SYT1_uc001syt.2_Intron|SYT1_uc001syu.2_Intron|SYT1_uc001syv.2_Intron	NM_001135805	NP_001129277			synaptotagmin I						detection of calcium ion|glutamate secretion|neurotransmitter secretion|protein homooligomerization	cell junction|chromaffin granule membrane|clathrin sculpted acetylcholine transport vesicle membrane|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|clathrin sculpted glutamate transport vesicle membrane|clathrin sculpted monoamine transport vesicle membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	1-phosphatidylinositol binding|low-density lipoprotein particle receptor binding|metal ion binding|syntaxin-1 binding|transporter activity			skin(3)|pancreas(2)|ovary(1)	6																		---	---	---	---
PAWR	5074	broad.mit.edu	37	12	80012014	80012014	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80012014delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	80714026	80714026	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80714026delT								PPP1R12A (384791 upstream) : PTPRQ (124100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	80802571	80802572	+	IGR	INS	-	CTC	CTC	rs149138980	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80802571_80802572insCTC								PPP1R12A (473336 upstream) : PTPRQ (35554 downstream)																																			---	---	---	---
PTPRQ	374462	broad.mit.edu	37	12	81063246	81063246	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81063246delA	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	81105115	81105115	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81105115delT								MYF6 (1864 upstream) : MYF5 (5593 downstream)																																			---	---	---	---
LIN7A	8825	broad.mit.edu	37	12	81275258	81275258	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81275258delA	uc001szj.1	-						LIN7A_uc001szk.1_Intron	NM_004664	NP_004655			lin-7 homolog A						exocytosis|protein complex assembly|protein transport	basolateral plasma membrane|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	L27 domain binding			ovary(1)|skin(1)	2																		---	---	---	---
ACSS3	79611	broad.mit.edu	37	12	81598143	81598143	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81598143delC	uc001szl.1	+						ACSS3_uc001szm.1_Intron|ACSS3_uc001szn.1_Intron	NM_024560	NP_078836			acyl-CoA synthetase short-chain family member 3							mitochondrion	acetate-CoA ligase activity|ATP binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
ACSS3	79611	broad.mit.edu	37	12	81648873	81648873	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81648873delT	uc001szl.1	+	16					ACSS3_uc001szm.1_3'UTR|ACSS3_uc001szn.1_3'UTR	NM_024560	NP_078836			acyl-CoA synthetase short-chain family member 3							mitochondrion	acetate-CoA ligase activity|ATP binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PPFIA2	8499	broad.mit.edu	37	12	81986693	81986693	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81986693delC	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010sui.1_Intron|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	82498141	82498142	+	IGR	DEL	AA	-	-	rs145338497		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82498141_82498142delAA								PPFIA2 (345032 upstream) : CCDC59 (247948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	82530495	82530495	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82530495delT								PPFIA2 (377386 upstream) : CCDC59 (215595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	82728523	82728524	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82728523_82728524insG								PPFIA2 (575414 upstream) : CCDC59 (17566 downstream)																																			---	---	---	---
C12orf26	84190	broad.mit.edu	37	12	82871011	82871011	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82871011delT	uc001szq.2	+							NM_032230	NP_115606			hypothetical protein LOC84190												0																		---	---	---	---
TMTC2	160335	broad.mit.edu	37	12	83236905	83236905	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83236905delT	uc001szt.2	+						TMTC2_uc001szr.1_Intron|TMTC2_uc001szs.1_Intron|TMTC2_uc010suk.1_Intron	NM_152588	NP_689801			transmembrane and tetratricopeptide repeat							endoplasmic reticulum|integral to membrane	binding			ovary(2)	2																		---	---	---	---
TMTC2	160335	broad.mit.edu	37	12	83266993	83266994	+	Intron	DEL	TG	-	-	rs35177760		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83266993_83266994delTG	uc001szt.2	+						TMTC2_uc001szr.1_Intron|TMTC2_uc001szs.1_Intron|TMTC2_uc010suk.1_Intron	NM_152588	NP_689801			transmembrane and tetratricopeptide repeat							endoplasmic reticulum|integral to membrane	binding			ovary(2)	2																		---	---	---	---
TMTC2	160335	broad.mit.edu	37	12	83401803	83401803	+	Intron	DEL	C	-	-	rs1655599	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83401803delC	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	83750527	83750527	+	IGR	DEL	A	-	-	rs34816717		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83750527delA								TMTC2 (222464 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	84555918	84555918	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84555918delA								None (None upstream) : SLC6A15 (697351 downstream)																																			---	---	---	---
ALX1	8092	broad.mit.edu	37	12	85674708	85674708	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85674708delA	uc001tae.3	+							NM_006982	NP_008913			cartilage paired-class homeoprotein 1						brain development|cartilage condensation|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(134;0.134)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	85869628	85869628	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85869628delA								ALX1 (174069 upstream) : RASSF9 (328703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85995551	85995552	+	IGR	DEL	AA	-	-	rs151077344		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85995551_85995552delAA								ALX1 (299992 upstream) : RASSF9 (202779 downstream)																																			---	---	---	---
NTS	4922	broad.mit.edu	37	12	86270630	86270630	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86270630delT	uc001tag.2	+							NM_006183	NP_006174			neurotensin/neuromedin N preproprotein						regulation of blood vessel size|signal transduction	extracellular region|soluble fraction|transport vesicle	neuropeptide hormone activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	88276535	88276535	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88276535delT								None (None upstream) : C12orf50 (97281 downstream)																																			---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88514681	88514681	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88514681delT	uc001tar.2	-						CEP290_uc001tat.2_Intron|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																		---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88524079	88524079	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	88708708	88708709	+	IGR	DEL	TT	-	-	rs10161351	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88708708_88708709delTT								TMTC3 (115045 upstream) : KITLG (177860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89556832	89556832	+	IGR	DEL	T	-	-	rs79893546		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89556832delT								KITLG (582594 upstream) : DUSP6 (185007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89762185	89762185	+	IGR	DEL	T	-	-	rs34566401		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89762185delT								DUSP6 (15889 upstream) : POC1B (51316 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	90692180	90692180	+	IGR	DEL	T	-	-	rs11308067		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90692180delT								LOC338758 (586452 upstream) : C12orf12 (653813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91029215	91029215	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91029215delA								LOC338758 (923487 upstream) : C12orf12 (316778 downstream)																																			---	---	---	---
DCN	1634	broad.mit.edu	37	12	91545279	91545279	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91545279delT	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	92014186	92014189	+	IGR	DEL	AAGG	-	-	rs71853817		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92014186_92014189delAAGG								DCN (437380 upstream) : BTG1 (364677 downstream)																																			---	---	---	---
BTG1	694	broad.mit.edu	37	12	92415465	92415465	+	Intron	DEL	A	-	-	rs78708291		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92415465delA	uc001tbv.1	-						BTG1_uc001tbw.1_Intron|BTG1_uc001tbx.1_Intron|BTG1_uc009zss.1_Intron					Homo sapiens full length insert cDNA clone YW25A12.						cell migration|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of endothelial cell differentiation|positive regulation of myoblast differentiation|regulation of apoptosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|transcription cofactor activity				0		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)						T	MYC	BCLL								---	---	---	---
Unknown	0	broad.mit.edu	37	12	93055224	93055224	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93055224delA								CLLU1 (177768 upstream) : C12orf74 (41616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93434563	93434563	+	IGR	DEL	C	-	-	rs147230147		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93434563delC								EEA1 (111456 upstream) : NUDT4 (337138 downstream)																																			---	---	---	---
UBE2N	7334	broad.mit.edu	37	12	93813167	93813167	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93813167delA	uc001tcp.2	-							NM_003348	NP_003339			ubiquitin-conjugating enzyme E2N						DNA double-strand break processing|double-strand break repair via homologous recombination|histone ubiquitination|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of DNA repair|positive regulation of histone modification|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity|postreplication repair|protein K63-linked ubiquitination|proteolysis|regulation of histone ubiquitination|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus|UBC13-MMS2 complex|UBC13-UEV1A complex|ubiquitin ligase complex	ATP binding|ubiquitin binding|ubiquitin-protein ligase activity				0													Direct_reversal_of_damage|Rad6_pathway					---	---	---	---
Unknown	0	broad.mit.edu	37	12	93958429	93958429	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93958429delA	uc001tcv.1	-						uc001tcu.2_Intron					Homo sapiens cDNA FLJ30045 fis, clone 3NB692001637.																														---	---	---	---
CRADD	8738	broad.mit.edu	37	12	94140559	94140560	+	Intron	DEL	TT	-	-	rs71896069		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94140559_94140560delTT	uc001tda.2	+						CRADD_uc010sur.1_Intron|CRADD_uc010sus.1_Intron	NM_003805	NP_003796			CASP2 and RIPK1 domain containing adaptor with						apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1																		---	---	---	---
CRADD	8738	broad.mit.edu	37	12	94153201	94153201	+	Intron	DEL	A	-	-	rs141079885		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94153201delA	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	94372330	94372334	+	IGR	DEL	AAGAG	-	-	rs10587754		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94372330_94372334delAAGAG								CRADD (83714 upstream) : PLXNC1 (170165 downstream)																																			---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94744395	94744395	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94744395delA	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	94807710	94807711	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94807710_94807711insA	uc001tdd.2	-						CCDC41_uc001tde.2_Intron|CCDC41_uc009zsw.1_Intron|CCDC41_uc001tdf.2_Intron	NM_016122	NP_057206			NY-REN-58 antigen												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	94928518	94928518	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94928518delG								LOC144486 (72176 upstream) : TMCC3 (32382 downstream)																																			---	---	---	---
TMCC3	57458	broad.mit.edu	37	12	94965786	94965787	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94965786_94965787insT	uc001tdj.2	-						TMCC3_uc001tdi.2_Intron	NM_020698	NP_065749			transmembrane and coiled-coil domain family 3							integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	95359575	95359575	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95359575delA								MIR492 (131286 upstream) : NDUFA12 (5537 downstream)																																			---	---	---	---
FGD6	55785	broad.mit.edu	37	12	95500974	95500975	+	Intron	INS	-	T	T	rs148392232	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95500974_95500975insT	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	95579043	95579043	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95579043delA	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																		---	---	---	---
FGD6	55785	broad.mit.edu	37	12	95593954	95593954	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95593954delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	95755652	95755653	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95755652_95755653insT								MIR331 (53363 upstream) : METAP2 (112169 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	95976371	95976371	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95976371delT								USP44 (31108 upstream) : NTN4 (75213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	95977675	95977675	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95977675delC								USP44 (32412 upstream) : NTN4 (73909 downstream)																																			---	---	---	---
LTA4H	4048	broad.mit.edu	37	12	96410770	96410770	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96410770delA	uc001ten.1	-						LTA4H_uc010suy.1_Intron|LTA4H_uc010suz.1_Intron|LTA4H_uc010sva.1_Intron|LTA4H_uc009ztj.2_5'Flank	NM_000895	NP_000886			leukotriene A4 hydrolase						hormone biosynthetic process|inflammatory response|leukotriene biosynthetic process|peptide catabolic process|prostanoid metabolic process|proteolysis	cytosol|nucleus	aminopeptidase activity|epoxide hydrolase activity|leukotriene-A4 hydrolase activity|metallopeptidase activity|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(1)	1																		---	---	---	---
LTA4H	4048	broad.mit.edu	37	12	96418448	96418451	+	Intron	DEL	TTTT	-	-	rs5800241		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96418448_96418451delTTTT	uc001ten.1	-						LTA4H_uc010suy.1_Intron|LTA4H_uc010suz.1_Intron|LTA4H_uc010sva.1_Intron	NM_000895	NP_000886			leukotriene A4 hydrolase						hormone biosynthetic process|inflammatory response|leukotriene biosynthetic process|peptide catabolic process|prostanoid metabolic process|proteolysis	cytosol|nucleus	aminopeptidase activity|epoxide hydrolase activity|leukotriene-A4 hydrolase activity|metallopeptidase activity|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	96535889	96535889	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96535889delT								LTA4H (98591 upstream) : ELK3 (52318 downstream)																																			---	---	---	---
ELK3	2004	broad.mit.edu	37	12	96588323	96588323	+	5'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96588323delA	uc001teo.1	+	1						NM_005230	NP_005221			ELK3 protein						negative regulation of transcription, DNA-dependent|signal transduction	mitochondrion	protein binding|purine-rich negative regulatory element binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	all_cancers(2;0.00173)																	---	---	---	---
ELK3	2004	broad.mit.edu	37	12	96608234	96608234	+	Intron	DEL	A	-	-	rs113949362		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96608234delA	uc001teo.1	+							NM_005230	NP_005221			ELK3 protein						negative regulation of transcription, DNA-dependent|signal transduction	mitochondrion	protein binding|purine-rich negative regulatory element binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	all_cancers(2;0.00173)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	96927779	96927779	+	Intron	DEL	T	-	-	rs5800251		TCGA-BR-4292-01	TCGA-BR-4292-01									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	97446984	97446985	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97446984_97446985insG								NEDD1 (99523 upstream) : RMST (411814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98054663	98054663	+	IGR	DEL	C	-	-	rs10745802	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98054663delC								RMST (95870 upstream) : LOC100128191 (852090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98073980	98073980	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98073980delA								RMST (115187 upstream) : LOC100128191 (832773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98856366	98856366	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98856366delT								RMST (897573 upstream) : LOC100128191 (50387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98866270	98866271	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98866270_98866271delGA								RMST (907477 upstream) : LOC100128191 (40482 downstream)																																			---	---	---	---
TMPO	7112	broad.mit.edu	37	12	98925326	98925326	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98925326delT	uc001tfj.2	+						TMPO_uc001tfi.1_Intron|TMPO_uc001tfk.2_Intron|TMPO_uc001tfl.2_Intron|TMPO_uc001tfh.1_Intron	NM_001032283	NP_001027454			thymopoietin isoform beta							integral to membrane|nuclear inner membrane	DNA binding|lamin binding			ovary(2)	2																		---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	99847745	99847745	+	Intron	DEL	A	-	-	rs79177991		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99847745delA	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
UHRF1BP1L	23074	broad.mit.edu	37	12	100480151	100480151	+	Intron	DEL	G	-	-	rs72356210		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100480151delG	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron|UHRF1BP1L_uc001tgp.2_Intron	NM_015054	NP_055869			UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2																		---	---	---	---
DEPDC4	120863	broad.mit.edu	37	12	100657163	100657163	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100657163delT	uc001thi.2	-						DEPDC4_uc001thh.1_Intron|DEPDC4_uc001thj.1_Intron|DEPDC4_uc009ztv.1_Intron|DEPDC4_uc001thk.1_Intron|DEPDC4_uc001thl.1_Intron	NM_152317	NP_689530			DEP domain containing 4						intracellular signal transduction						0																		---	---	---	---
SCYL2	55681	broad.mit.edu	37	12	100708179	100708179	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100708179delT	uc001thn.2	+						SCYL2_uc009ztw.1_Intron|SCYL2_uc001thm.1_Intron	NM_017988	NP_060458			SCY1-like 2 protein						endosome to lysosome transport|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of clathrin-mediated endocytosis|positive regulation of receptor internalization	clathrin-coated vesicle|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|protein kinase activity|receptor binding			lung(3)|ovary(2)|skin(1)	6																		---	---	---	---
NR1H4	9971	broad.mit.edu	37	12	100906420	100906422	+	Intron	DEL	AAA	-	-	rs35958048		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100906420_100906422delAAA	uc001tht.1	+						NR1H4_uc001thp.1_Intron|NR1H4_uc001thq.1_Intron|NR1H4_uc010svj.1_Intron|NR1H4_uc001thr.1_Intron|NR1H4_uc010svk.1_Intron|NR1H4_uc001ths.1_Intron	NM_005123	NP_005114			nuclear receptor subfamily 1, group H, member 4						bile acid metabolic process|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|thyroid hormone receptor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
ANO4	121601	broad.mit.edu	37	12	101123814	101123815	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101123814_101123815delTC	uc010svl.1	+											Homo sapiens cDNA FLJ34272 fis, clone FEBRA2003128.							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6															HNSCC(74;0.22)			---	---	---	---
SLC5A8	160728	broad.mit.edu	37	12	101598351	101598351	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101598351delA	uc001thz.3	-							NM_145913	NP_666018			solute carrier family 5 (iodide transporter),						apoptosis|sodium ion transport	apical plasma membrane|integral to membrane	monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity				0																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101693442	101693442	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101693442delT	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-4292-01	TCGA-BR-4292-01									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	101760600	101760600	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101760600delT	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																		---	---	---	---
DRAM1	55332	broad.mit.edu	37	12	102301163	102301163	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102301163delT	uc001tix.2	+						DRAM1_uc010svv.1_Intron	NM_018370	NP_060840			DNA-damage regulated autophagy modulator 1						apoptosis|autophagy	integral to membrane|lysosomal membrane				ovary(1)	1																		---	---	---	---
NUP37	79023	broad.mit.edu	37	12	102468960	102468961	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102468960_102468961insT	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	102600280	102600280	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102600280delC								PMCH (8666 upstream) : IGF1 (189365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	102907494	102907494	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102907494delT								IGF1 (33116 upstream) : PAH (324610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	102939815	102939815	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102939815delT								IGF1 (65437 upstream) : PAH (292289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	103520443	103520443	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103520443delA								ASCL1 (166156 upstream) : C12orf42 (110927 downstream)																																			---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104067584	104067584	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104067584delG	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-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
LOC253724	253724	broad.mit.edu	37	12	104292450	104292450	+	Intron	DEL	T	-	-	rs78214723		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104292450delT	uc010swf.1	-							NR_027249				Homo sapiens cDNA FLJ56788 complete cds, moderately similar to Mus musculus 5'-nucleotidase domain containing 3 (Nt5dc3), transcript variant 2, mRNA.												0																		---	---	---	---
TDG	6996	broad.mit.edu	37	12	104376542	104376542	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104376542delA	uc001tkg.2	+						TDG_uc009zuk.2_Intron|TDG_uc010swi.1_Intron|TDG_uc010swj.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					---	---	---	---
NFYB	4801	broad.mit.edu	37	12	104516954	104516955	+	Intron	DEL	AA	-	-	rs78195873		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104516954_104516955delAA	uc001tkl.1	-						NFYB_uc001tkk.1_Intron	NM_006166	NP_006157			nuclear transcription factor Y, beta							CCAAT-binding factor complex	repressing transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	104597414	104597415	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104597414_104597415delGT								NFYB (65374 upstream) : TXNRD1 (9073 downstream)																																			---	---	---	---
TXNRD1	7296	broad.mit.edu	37	12	104611763	104611764	+	Intron	INS	-	AC	AC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104611763_104611764insAC	uc010swk.1	+						TXNRD1_uc001tkm.1_Intron	NM_001093771	NP_001087240			thioredoxin reductase 1 isoform 3						cell redox homeostasis|cellular lipid metabolic process|electron transport chain|nucleobase, nucleoside and nucleotide interconversion|signal transduction|transport	cytosol|nucleolus	electron carrier activity|flavin adenine dinucleotide binding|NADP binding|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity				0																		---	---	---	---
TXNRD1	7296	broad.mit.edu	37	12	104656011	104656018	+	Intron	DEL	AAAAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104656011_104656018delAAAAAAAA	uc010swk.1	+							NM_001093771	NP_001087240			thioredoxin reductase 1 isoform 3						cell redox homeostasis|cellular lipid metabolic process|electron transport chain|nucleobase, nucleoside and nucleotide interconversion|signal transduction|transport	cytosol|nucleolus	electron carrier activity|flavin adenine dinucleotide binding|NADP binding|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity				0																		---	---	---	---
TXNRD1	7296	broad.mit.edu	37	12	104706938	104706938	+	Intron	DEL	A	-	-	rs67922311		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104706938delA	uc010swk.1	+						TXNRD1_uc010swl.1_Intron|TXNRD1_uc010swm.1_Intron|TXNRD1_uc010swn.1_Intron|TXNRD1_uc010swo.1_Intron|TXNRD1_uc010swp.1_Intron|TXNRD1_uc010swq.1_Intron|TXNRD1_uc001tku.2_Intron|TXNRD1_uc009zun.2_Intron|TXNRD1_uc001tko.1_Intron|TXNRD1_uc001tkp.1_Intron	NM_001093771	NP_001087240			thioredoxin reductase 1 isoform 3						cell redox homeostasis|cellular lipid metabolic process|electron transport chain|nucleobase, nucleoside and nucleotide interconversion|signal transduction|transport	cytosol|nucleolus	electron carrier activity|flavin adenine dinucleotide binding|NADP binding|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	104763458	104763458	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104763458delC								TXNRD1 (19400 upstream) : CHST11 (87291 downstream)																																			---	---	---	---
ALDH1L2	160428	broad.mit.edu	37	12	105425254	105425258	+	Intron	DEL	TTTTA	-	-	rs10778362	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105425254_105425258delTTTTA	uc001tlc.2	-						ALDH1L2_uc009zuo.2_Intron|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	105774965	105774967	+	IGR	DEL	CTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105774965_105774967delCTC								C12orf75 (9670 upstream) : NUAK1 (682158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106332002	106332002	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106332002delA								C12orf75 (566707 upstream) : NUAK1 (125123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106425523	106425523	+	IGR	DEL	A	-	-	rs67655303		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106425523delA								C12orf75 (660228 upstream) : NUAK1 (31602 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106650124	106650124	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106650124delA								CKAP4 (8411 upstream) : TCP11L2 (46457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106686584	106686585	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106686584_106686585delAA								CKAP4 (44871 upstream) : TCP11L2 (9996 downstream)																																			---	---	---	---
POLR3B	55703	broad.mit.edu	37	12	106845411	106845412	+	Intron	INS	-	G	G	rs58136863		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106845411_106845412insG	uc001tlp.2	+						POLR3B_uc001tlq.2_Intron	NM_018082	NP_060552			DNA-directed RNA polymerase III B isoform 1						innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	106973871	106973874	+	IGR	DEL	CAGT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106973871_106973874delCAGT								POLR3B (69897 upstream) : RFX4 (3159 downstream)																																			---	---	---	---
RFX4	5992	broad.mit.edu	37	12	107006616	107006618	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107006616_107006618delAAA	uc001tlr.2	+						RFX4_uc010swv.1_Intron|RFX4_uc001tls.2_Intron|RFX4_uc001tlt.2_Intron	NM_213594	NP_998759			regulatory factor X4 isoform c						transcription, DNA-dependent	nucleus	DNA binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
RIC8B	55188	broad.mit.edu	37	12	107268602	107268603	+	Intron	DEL	TT	-	-	rs113492589		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107268602_107268603delTT	uc001tlx.2	+						RIC8B_uc001tly.2_Intron|RIC8B_uc001tlz.2_Intron|RIC8B_uc009zur.2_Intron	NM_018157	NP_060627			resistance to inhibitors of cholinesterase 8						regulation of G-protein coupled receptor protein signaling pathway	cell cortex|cytosol|plasma membrane	G-protein alpha-subunit binding|guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
MTERFD3	80298	broad.mit.edu	37	12	107378791	107378791	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107378791delT	uc001tme.1	-						MTERFD3_uc001tmf.1_Intron|MTERFD3_uc001tmg.1_Intron|MTERFD3_uc001tmh.1_Intron	NM_025198	NP_079474			transcription termination factor-like protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial nucleoid	transcription regulatory region DNA binding				0																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	107844758	107844758	+	Intron	DEL	T	-	-	rs72214307		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107844758delT	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	107941038	107941039	+	Intron	INS	-	AAC	AAC	rs79484076	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107941038_107941039insAAC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	108372694	108372694	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108372694delA								ASCL4 (202274 upstream) : WSCD2 (150817 downstream)																																			---	---	---	---
WSCD2	9671	broad.mit.edu	37	12	108536573	108536574	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108536573_108536574delTC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	108748711	108748712	+	IGR	DEL	TC	-	-	rs67546268		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108748711_108748712delTC								CMKLR1 (15617 upstream) : FICD (160339 downstream)																																			---	---	---	---
SART3	9733	broad.mit.edu	37	12	108935183	108935183	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108935183delA	uc001tmz.1	-						SART3_uc001tmy.1_5'UTR|SART3_uc009zux.1_Intron|SART3_uc010swx.1_Intron|SART3_uc010swy.1_Intron|SART3_uc010swz.1_Intron|SART3_uc001tna.1_Intron	NM_014706	NP_055521			squamous cell carcinoma antigen recognized by T						RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1														Porokeratosis				---	---	---	---
Unknown	0	broad.mit.edu	37	12	109138641	109138644	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109138641_109138644delTTTT								CORO1C (13346 upstream) : SSH1 (37823 downstream)																																			---	---	---	---
SSH1	54434	broad.mit.edu	37	12	109239825	109239825	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109239825delA	uc001tnm.2	-						SSH1_uc001tnn.3_Intron	NM_018984	NP_061857			slingshot 1 isoform 1						actin cytoskeleton organization|cell morphogenesis|cellular response to ATP|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of cellular protein metabolic process|regulation of lamellipodium assembly	cleavage furrow|cytoplasm|cytoskeleton|lamellipodium|midbody|plasma membrane	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(4)	4																		---	---	---	---
USP30	84749	broad.mit.edu	37	12	109499213	109499219	+	Intron	DEL	AAATTTT	-	-	rs75223328		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109499213_109499219delAAATTTT	uc010sxi.1	+						USP30_uc001tnu.3_Intron	NM_032663	NP_116052			ubiquitin specific peptidase 30						ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial outer membrane	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(1)	1																		---	---	---	---
UNG	7374	broad.mit.edu	37	12	109542568	109542568	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109542568delG	uc001tnz.1	+						UNG_uc001toa.1_Intron	NM_080911	NP_550433			uracil-DNA glycosylase isoform UNG2						base-excision repair|interspecies interaction between organisms	mitochondrion|nucleus	protein binding|uracil DNA N-glycosylase activity			lung(1)|central_nervous_system(1)	2													BER_DNA_glycosylases	Immune_Deficiency_with_Hyper-IgM				---	---	---	---
ACACB	32	broad.mit.edu	37	12	109597895	109597897	+	Intron	DEL	AAA	-	-	rs76086314		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109597895_109597897delAAA	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	109638757	109638758	+	Intron	INS	-	G	G	rs141360740	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109638757_109638758insG	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	109646023	109646026	+	Intron	DEL	TTTT	-	-	rs36059668		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109646023_109646026delTTTT	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	109670675	109670675	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109670675delC	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)													---	---	---	---
UBE3B	89910	broad.mit.edu	37	12	109965540	109965541	+	Intron	DEL	AG	-	-	rs112795771		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109965540_109965541delAG	uc001top.2	+						UBE3B_uc001toq.2_Intron|UBE3B_uc001tos.2_Intron|UBE3B_uc001tot.2_5'Flank|UBE3B_uc010sxp.1_5'Flank	NM_130466	NP_569733			ubiquitin protein ligase E3B						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			ovary(2)|lung(2)	4																		---	---	---	---
MVK	4598	broad.mit.edu	37	12	110019240	110019240	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110019240delC	uc001toy.3	+	5	596	c.412delC	c.(412-414)CCCfs	p.P138fs	MVK_uc009zvk.2_Frame_Shift_Del_p.P138fs|MVK_uc010sxr.1_Intron|MVK_uc001toz.3_Intron|MVK_uc001tpc.3_RNA	NM_001114185	NP_001107657	Q03426	KIME_HUMAN	mevalonate kinase	138	ATP (By similarity).				cholesterol biosynthetic process|isoprenoid biosynthetic process	cytosol|peroxisome	ATP binding|identical protein binding|mevalonate kinase activity				0																		---	---	---	---
C12orf34	84915	broad.mit.edu	37	12	110173520	110173520	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110173520delA	uc001tpd.1	+						MGC14436_uc010sxs.1_RNA|MGC14436_uc001tpe.2_RNA|C12orf34_uc001tpf.1_Intron	NM_032829	NP_116218			hypothetical protein LOC84915											ovary(1)	1																		---	---	---	---
TRPV4	59341	broad.mit.edu	37	12	110246843	110246846	+	Intron	DEL	CCAT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110246843_110246846delCCAT	uc001tpj.1	-						TRPV4_uc001tpg.1_Intron|TRPV4_uc001tph.1_Intron|TRPV4_uc001tpi.1_Intron|TRPV4_uc001tpk.1_Intron|TRPV4_uc001tpl.1_Intron	NM_021625	NP_067638			transient receptor potential cation channel,						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																		---	---	---	---
GLTP	51228	broad.mit.edu	37	12	110315728	110315728	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110315728delT	uc001tpm.2	-						GLTP_uc010sxt.1_Intron	NM_016433	NP_057517			glycolipid transfer protein							cytoplasm	glycolipid binding|glycolipid transporter activity				0		Lung NSC(355;2.38e-06)|Breast(359;0.00354)|Myeloproliferative disorder(1001;0.0122)		BRCA - Breast invasive adenocarcinoma(302;0.0025)														---	---	---	---
GLTP	51228	broad.mit.edu	37	12	110321005	110321008	+	5'Flank	DEL	TTTT	-	-	rs72177999		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110321005_110321008delTTTT	uc001tpm.2	-						GLTP_uc010sxt.1_5'Flank	NM_016433	NP_057517			glycolipid transfer protein							cytoplasm	glycolipid binding|glycolipid transporter activity				0		Lung NSC(355;2.38e-06)|Breast(359;0.00354)|Myeloproliferative disorder(1001;0.0122)		BRCA - Breast invasive adenocarcinoma(302;0.0025)														---	---	---	---
GIT2	9815	broad.mit.edu	37	12	110404459	110404460	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110404459_110404460insA	uc001tps.2	-						GIT2_uc001tpq.2_Intron|GIT2_uc001tpv.2_Intron|GIT2_uc001tpu.2_Intron|GIT2_uc001tpt.2_Intron|GIT2_uc010sxu.1_Intron|GIT2_uc001tpw.2_Intron|GIT2_uc010sxv.1_Intron	NM_057169	NP_476510			G protein-coupled receptor kinase interacting						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																		---	---	---	---
GIT2	9815	broad.mit.edu	37	12	110407568	110407569	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110407568_110407569delTT	uc001tps.2	-						GIT2_uc001tpq.2_Intron|GIT2_uc001tpv.2_Intron|GIT2_uc001tpu.2_Intron|GIT2_uc001tpt.2_Intron|GIT2_uc010sxu.1_Intron|GIT2_uc001tpw.2_Intron|GIT2_uc010sxv.1_Intron	NM_057169	NP_476510			G protein-coupled receptor kinase interacting						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																		---	---	---	---
ANKRD13A	88455	broad.mit.edu	37	12	110454330	110454330	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110454330delT	uc001tpx.2	+						ANKRD13A_uc009zvl.1_Intron|ANKRD13A_uc009zvm.1_Intron|ANKRD13A_uc010sxw.1_Intron	NM_033121	NP_149112			ankyrin repeat domain 13												0																		---	---	---	---
C12orf76	400073	broad.mit.edu	37	12	110510754	110510755	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110510754_110510755delAA	uc001tqe.1	-						uc001tqf.1_Intron					Homo sapiens cDNA FLJ11385 fis, clone HEMBA1000520.											large_intestine(1)	1																		---	---	---	---
ATP2A2	488	broad.mit.edu	37	12	110778344	110778344	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110778344delA	uc001tqk.3	+						ATP2A2_uc001tql.3_Intron|ATP2A2_uc010sxy.1_Intron	NM_170665	NP_733765			ATPase, Ca++ transporting, slow twitch 2 isoform						ATP biosynthetic process|cell adhesion|epidermis development|platelet activation|sarcoplasmic reticulum calcium ion transport	integral to plasma membrane|microsome|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	ATP binding|calcium-transporting ATPase activity|protein C-terminus binding|S100 alpha binding			ovary(3)|skin(1)	4																		---	---	---	---
ANAPC7	51434	broad.mit.edu	37	12	110819760	110819765	+	Intron	DEL	AAAAAA	-	-	rs35699984		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110819760_110819765delAAAAAA	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																		---	---	---	---
ANAPC7	51434	broad.mit.edu	37	12	110833403	110833403	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110833403delT	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																		---	---	---	---
ANAPC7	51434	broad.mit.edu	37	12	110834322	110834322	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110834322delT	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																		---	---	---	---
ANAPC7	51434	broad.mit.edu	37	12	110836050	110836050	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110836050delA	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																		---	---	---	---
ARPC3	10094	broad.mit.edu	37	12	110878655	110878655	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110878655delT	uc001tqq.2	-							NM_005719	NP_005710			actin related protein 2/3 complex subunit 3						cellular component movement|regulation of actin filament polymerization	Arp2/3 protein complex|cytoplasm	actin binding|structural constituent of cytoskeleton			ovary(1)	1																		---	---	---	---
C12orf24	29902	broad.mit.edu	37	12	110911024	110911025	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110911024_110911025insT	uc001tqu.3	+						C12orf24_uc010sxz.1_Intron|C12orf24_uc009zvo.2_Intron|C12orf24_uc001tqt.2_Intron|C12orf24_uc001tqv.3_Intron	NM_013300	NP_037432			hypothetical protein LOC29902												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	111240903	111240903	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111240903delT								PPP1CC (60146 upstream) : CCDC63 (43908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	112079054	112079054	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112079054delA								ATXN2 (41574 upstream) : BRAP (897 downstream)																																			---	---	---	---
BRAP	8315	broad.mit.edu	37	12	112096108	112096109	+	Intron	DEL	TT	-	-	rs113348013		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112096108_112096109delTT	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	112167543	112167543	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112167543delT	uc001tsq.2	+						ACAD10_uc001tsp.2_Intron|ACAD10_uc009zvx.2_Intron|ACAD10_uc001tss.1_Intron	NM_025247	NP_079523			acyl-Coenzyme A dehydrogenase family, member 10								acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2																		---	---	---	---
ALDH2	217	broad.mit.edu	37	12	112237276	112237278	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112237276_112237278delTTT	uc001tst.2	+						ALDH2_uc010syi.1_Intron|ALDH2_uc009zvy.2_Intron	NM_000690	NP_000681			mitochondrial aldehyde dehydrogenase 2						carbohydrate metabolic process|ethanol oxidation|neurotransmitter biosynthetic process|xenobiotic metabolic process	mitochondrial matrix	aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase|electron carrier activity			skin(2)|ovary(1)|central_nervous_system(1)	4					Disulfiram(DB00822)|Guanidine(DB00536)|NADH(DB00157)|Nitroglycerin(DB00727)			T	HMGA2	leiomyoma								---	---	---	---
PTPN11	5781	broad.mit.edu	37	12	112866456	112866456	+	Intron	DEL	A	-	-	rs11326544		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112866456delA	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				---	---	---	---
RPH3A	22895	broad.mit.edu	37	12	113189353	113189353	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113189353delT	uc010syl.1	+							NM_001143854	NP_001137326			rabphilin 3A homolog isoform 1						intracellular protein transport	cell junction|synaptic vesicle	Rab GTPase binding|transporter activity|zinc ion binding			ovary(3)|central_nervous_system(2)|skin(2)	7				BRCA - Breast invasive adenocarcinoma(302;0.00453)														---	---	---	---
PLBD2	196463	broad.mit.edu	37	12	113826142	113826144	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113826142_113826144delAAA	uc001tve.2	+						PLBD2_uc001tvf.2_Intron	NM_173542	NP_775813			phospholipase B domain containing 2 isoform 1						lipid catabolic process	lysosomal lumen	hydrolase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	114252418	114252419	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114252418_114252419delTT								LHX5 (342541 upstream) : RBM19 (2124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114654488	114654488	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114654488delA								RBM19 (250312 upstream) : TBX5 (137248 downstream)																																			---	---	---	---
TBX5	6910	broad.mit.edu	37	12	114794045	114794045	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114794045delA	uc001tvo.2	-						TBX5_uc001tvp.2_Intron|TBX5_uc001tvq.2_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)														---	---	---	---
TBX5	6910	broad.mit.edu	37	12	114844656	114844656	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114844656delT	uc001tvo.2	-						TBX5_uc001tvp.2_Intron|TBX5_uc001tvq.2_Intron|TBX5_uc010syv.1_5'Flank|uc001tvs.1_5'Flank	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)														---	---	---	---
TBX3	6926	broad.mit.edu	37	12	115117665	115117665	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115117665delC	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	115137238	115137238	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115137238delT								TBX3 (15269 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115439861	115439862	+	IGR	INS	-	A	A	rs141178092	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115439861_115439862insA								TBX3 (317892 upstream) : MED13L (956521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115800706	115800706	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115800706delT								TBX3 (678737 upstream) : MED13L (595677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115861606	115861607	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115861606_115861607delAC								TBX3 (739637 upstream) : MED13L (534776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	116896745	116896745	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116896745delC								MED13L (181754 upstream) : NCRNA00173 (74482 downstream)																																			---	---	---	---
MAP1LC3B2	643246	broad.mit.edu	37	12	117006276	117006277	+	Intron	DEL	TG	-	-	rs115638726	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117006276_117006277delTG	uc009zwk.1	+							NM_001085481	NP_001078950			microtubule-associated protein 1 light chain 3						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	117080145	117080148	+	IGR	DEL	TTTT	-	-	rs71442986		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117080145_117080148delTTTT								MAP1LC3B2 (65720 upstream) : C12orf49 (73448 downstream)																																			---	---	---	---
C12orf49	79794	broad.mit.edu	37	12	117159673	117159673	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117159673delT	uc001tvz.1	-						C12orf49_uc009zwm.1_Intron	NM_024738	NP_079014			hypothetical protein LOC79794 precursor							extracellular region				ovary(1)	1	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0281)														---	---	---	---
RNFT2	84900	broad.mit.edu	37	12	117193171	117193171	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117193171delT	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	117289549	117289549	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
FBXW8	26259	broad.mit.edu	37	12	117364542	117364542	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117364542delT	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)														---	---	---	---
TESC	54997	broad.mit.edu	37	12	117479145	117479146	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117479145_117479146delTT	uc001twh.2	-						TESC_uc001twi.2_Intron	NM_017899	NP_060369			tescalcin						negative regulation of cell proliferation|positive regulation of megakaryocyte differentiation|positive regulation of transcription, DNA-dependent|regulation of cell adhesion mediated by integrin	cytoplasm|lamellipodium|nucleus|plasma membrane|ruffle	calcium ion binding|magnesium ion binding|phosphatase inhibitor activity|protein binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0297)														---	---	---	---
FBXO21	23014	broad.mit.edu	37	12	117611951	117611951	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117611951delA	uc001twk.2	-						FBXO21_uc001twj.2_Intron|FBXO21_uc009zwq.2_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)														---	---	---	---
FBXO21	23014	broad.mit.edu	37	12	117612801	117612801	+	Intron	DEL	A	-	-	rs138433024		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117612801delA	uc001twk.2	-						FBXO21_uc001twj.2_Intron|FBXO21_uc009zwq.2_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)														---	---	---	---
KSR2	283455	broad.mit.edu	37	12	118120220	118120220	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118120220delT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	118418303	118418303	+	IGR	DEL	A	-	-	rs77438920		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118418303delA								KSR2 (12275 upstream) : RFC5 (36205 downstream)																																			---	---	---	---
RFC5	5985	broad.mit.edu	37	12	118458889	118458889	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118458889delA	uc001twq.2	+						RFC5_uc010syx.1_Intron|RFC5_uc010syy.1_Intron|RFC5_uc010syz.1_Intron|RFC5_uc009zwr.2_Intron	NM_007370	NP_031396			replication factor C 5 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|enzyme binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
TAOK3	51347	broad.mit.edu	37	12	118699666	118699667	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118699666_118699667insT	uc001twx.2	-						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	119270506	119270506	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119270506delT								SUDS3 (414667 upstream) : SRRM4 (148890 downstream)																																			---	---	---	---
CCDC60	160777	broad.mit.edu	37	12	119817123	119817123	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119817123delT	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)														---	---	---	---
CIT	11113	broad.mit.edu	37	12	120229531	120229531	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120229531delT	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)														---	---	---	---
CCDC64	92558	broad.mit.edu	37	12	120510172	120510172	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120510172delA	uc001txl.1	+						CCDC64_uc001txk.2_Intron|CCDC64_uc009zwv.1_Intron|CCDC64_uc010sze.1_Intron|CCDC64_uc010szf.1_Intron	NM_207311	NP_997194			coiled-coil domain containing 64						Golgi to secretory granule transport|neuron projection development	centrosome	dynactin binding|Rab GTPase binding			ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
PXN	5829	broad.mit.edu	37	12	120657166	120657167	+	Intron	INS	-	C	C	rs61741284		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120657166_120657167insC	uc001txt.2	-						PXN_uc001txu.2_5'Flank|PXN_uc001txv.2_Intron|PXN_uc001txx.2_Intron|PXN_uc001txy.2_Intron|PXN_uc001txz.2_RNA|uc001tya.2_RNA	NM_001080855	NP_001074324			paxillin isoform 1						cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)|breast(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
PXN	5829	broad.mit.edu	37	12	120683238	120683238	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120683238delA	uc001txt.2	-						PXN_uc001txx.2_Intron|PXN_uc001txy.2_Intron|PXN_uc001txz.2_Intron	NM_001080855	NP_001074324			paxillin isoform 1						cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)|breast(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
SIRT4	23409	broad.mit.edu	37	12	120750095	120750096	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120750095_120750096insA	uc001tyc.2	+							NM_012240	NP_036372			sirtuin 4						chromatin silencing|negative regulation of insulin secretion|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
COQ5	84274	broad.mit.edu	37	12	120961144	120961144	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120961144delA	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)																	---	---	---	---
CABP1	9478	broad.mit.edu	37	12	121093630	121093635	+	Intron	DEL	GTGCGT	-	-	rs112935060		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121093630_121093635delGTGCGT	uc001tyu.2	+						CABP1_uc001tyv.2_Intron|CABP1_uc001tyw.2_Intron|CABP1_uc001tyx.2_5'Flank	NM_001033677	NP_001028849			calcium binding protein 1 isoform 3							cell cortex|cell junction|Golgi apparatus|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|calcium-dependent protein binding|enzyme inhibitor activity|protein binding			central_nervous_system(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	121193018	121193018	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121193018delT								ACADS (15208 upstream) : SPPL3 (8018 downstream)																																			---	---	---	---
SPPL3	121665	broad.mit.edu	37	12	121202941	121202941	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121202941delA	uc001tzd.2	-						SPPL3_uc009zwz.2_Intron|SPPL3_uc001tzc.2_Intron	NM_139015	NP_620584			signal peptide peptidase 3							integral to membrane	aspartic-type endopeptidase activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
SPPL3	121665	broad.mit.edu	37	12	121235304	121235304	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121235304delT	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	121251474	121251474	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121251474delA	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	121274792	121274792	+	Intron	DEL	T	-	-	rs71453509		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121274792delT	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	121291785	121291786	+	Intron	DEL	AT	-	-	rs11065296	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121291785_121291786delAT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	121379931	121379931	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121379931delT								SPPL3 (37780 upstream) : C12orf27 (27710 downstream)																																			---	---	---	---
HNF1A	6927	broad.mit.edu	37	12	121432115	121432115	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121432115delG	uc001tzg.2	+	4	885	c.862delG	c.(862-864)GGGfs	p.G288fs	HNF1A_uc001tze.1_Frame_Shift_Del_p.G288fs|HNF1A_uc001tzf.2_Frame_Shift_Del_p.G288fs|HNF1A_uc010szn.1_Frame_Shift_Del_p.G288fs	NM_000545	NP_000536	P20823	HNF1A_HUMAN	hepatic nuclear factor-1-alpha	288					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				---	---	---	---
C12orf43	64897	broad.mit.edu	37	12	121444024	121444026	+	Intron	DEL	AAG	-	-	rs144577739		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121444024_121444026delAAG	uc001tzh.1	-						C12orf43_uc009zxa.1_Intron|C12orf43_uc010szo.1_Intron|C12orf43_uc010szp.1_Intron|C12orf43_uc001tzi.1_Intron	NM_022895	NP_075046			hypothetical protein LOC64897												0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
RNF34	80196	broad.mit.edu	37	12	121840361	121840361	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121840361delA	uc001ual.1	+						RNF34_uc010szw.1_Intron|RNF34_uc001uak.1_Intron|RNF34_uc001uam.1_Intron	NM_025126	NP_079402			ring finger protein 34 isoform 2						apoptosis	endomembrane system|membrane|nuclear speck	ligase activity|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)														---	---	---	---
RNF34	80196	broad.mit.edu	37	12	121846782	121846782	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121846782delT	uc001ual.1	+						RNF34_uc010szw.1_Intron|RNF34_uc001uak.1_Intron|RNF34_uc001uam.1_Intron	NM_025126	NP_079402			ring finger protein 34 isoform 2						apoptosis	endomembrane system|membrane|nuclear speck	ligase activity|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)														---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	122018158	122018158	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122018158delG	uc001uat.2	-						KDM2B_uc001uas.2_5'UTR|KDM2B_uc001uau.2_Intron|KDM2B_uc001uav.3_Intron	NM_032590	NP_115979			F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	122053502	122053502	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122053502delT								KDM2B (34582 upstream) : ORAI1 (10953 downstream)																																			---	---	---	---
ORAI1	84876	broad.mit.edu	37	12	122071523	122071523	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122071523delT	uc010szz.1	+							NM_032790	NP_116179			calcium release-activated calcium channel						platelet activation|positive regulation of calcium ion transport	integral to plasma membrane	protein binding|store-operated calcium channel activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)														---	---	---	---
MORN3	283385	broad.mit.edu	37	12	122113167	122113167	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122113167delT	uc001uay.2	-											Homo sapiens morn protein mRNA, complete cds.												0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000409)|Epithelial(86;0.00145)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	122276886	122276886	+	IGR	DEL	T	-	-	rs78762016		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122276886delT								SETD1B (6325 upstream) : HPD (549 downstream)																																			---	---	---	---
WDR66	144406	broad.mit.edu	37	12	122437595	122437595	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122437595delT	uc009zxk.2	+							NM_144668	NP_653269			WD repeat domain 66								calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	122450642	122450643	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122450642_122450643insA								WDR66 (8812 upstream) : BCL7A (9218 downstream)																																			---	---	---	---
BCL7A	605	broad.mit.edu	37	12	122474619	122474620	+	Intron	DEL	TT	-	-	rs68042740		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122474619_122474620delTT	uc001ubp.2	+						BCL7A_uc001ubo.2_Intron	NM_001024808	NP_001019979			B-cell CLL/lymphoma 7A isoform b						negative regulation of transcription, DNA-dependent					ovary(1)|lung(1)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)				T	MYC	BNHL								---	---	---	---
BCL7A	605	broad.mit.edu	37	12	122498868	122498868	+	3'UTR	DEL	A	-	-	rs111336661		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122498868delA	uc001ubp.2	+	6					BCL7A_uc001ubo.2_3'UTR	NM_001024808	NP_001019979			B-cell CLL/lymphoma 7A isoform b						negative regulation of transcription, DNA-dependent					ovary(1)|lung(1)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)				T	MYC	BNHL								---	---	---	---
MLXIP	22877	broad.mit.edu	37	12	122584608	122584608	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122584608delT	uc001ubq.2	+							NM_014938	NP_055753			MLX interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial outer membrane|nucleus	DNA binding			ovary(2)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)														---	---	---	---
VPS33A	65082	broad.mit.edu	37	12	122716609	122716610	+	3'UTR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122716609_122716610delAA	uc001ucd.2	-	13					VPS33A_uc001ucc.2_Intron	NM_022916	NP_075067			vacuolar protein sorting 33A						lysosome localization|melanosome localization|platelet formation|protein transport|regulation of developmental pigmentation|vesicle docking involved in exocytosis	early endosome|late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm	protein binding			skin(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)														---	---	---	---
VPS33A	65082	broad.mit.edu	37	12	122737130	122737131	+	Intron	INS	-	A	A	rs139930631	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122737130_122737131insA	uc001ucd.2	-						VPS33A_uc001ucc.2_Intron	NM_022916	NP_075067			vacuolar protein sorting 33A						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)														---	---	---	---
CLIP1	6249	broad.mit.edu	37	12	122838948	122838948	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122838948delA	uc001ucg.1	-						CLIP1_uc001uch.1_Intron|CLIP1_uc001uci.1_Intron|CLIP1_uc001ucj.1_Intron|CLIP1_uc009zxo.1_Intron|CLIP1_uc010tae.1_Intron	NM_002956	NP_002947			restin isoform a						mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123035788	123035813	+	Intron	DEL	AACCAGTAGTTACTCTAGTAATTATA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123035788_123035813delAACCAGTAGTTACTCTAGTAATTATA	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523			Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123067170	123067170	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123067170delA	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523			Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123073397	123073397	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123073397delT	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523			Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)														---	---	---	---
HIP1R	9026	broad.mit.edu	37	12	123332729	123332729	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123332729delG	uc001udj.1	+						HIP1R_uc001udg.1_Intron|HIP1R_uc001udi.1_Intron|HIP1R_uc001udh.2_Intron	NM_003959	NP_003950			huntingtin interacting protein-1-related						receptor-mediated endocytosis	clathrin coated vesicle membrane|coated pit|perinuclear region of cytoplasm	actin binding|phosphatidylinositol binding			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)														---	---	---	---
PITPNM2	57605	broad.mit.edu	37	12	123618359	123618362	+	Intron	DEL	ACAG	-	-	rs10589925		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123618359_123618362delACAG	uc001uek.1	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	123778163	123778163	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123778163delA								CDK2AP1 (21476 upstream) : SBNO1 (2293 downstream)																																			---	---	---	---
RILPL1	353116	broad.mit.edu	37	12	123999991	123999991	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123999991delT	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)														---	---	---	---
GTF2H3	2967	broad.mit.edu	37	12	124129986	124129986	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124129986delT	uc001ufo.1	+						GTF2H3_uc010tau.1_Intron	NM_001516	NP_001507			general transcription factor IIH, polypeptide 3,						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					---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124317061	124317061	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124317061delT	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	124755001	124755002	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124755001_124755002delAA								ZNF664 (255034 upstream) : FAM101A (18708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	124755972	124755972	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124755972delT								ZNF664 (256005 upstream) : FAM101A (17738 downstream)																																			---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124894231	124894231	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124894231delT	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron	NM_001077261	NP_001070729			nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124923324	124923325	+	Intron	INS	-	AG	AG	rs111304897		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124923324_124923325insAG	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	124923874	124923875	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124923874_124923875delGA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	125090853	125090853	+	IGR	DEL	T	-	-	rs10773097	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125090853delT								NCOR2 (38843 upstream) : SCARB1 (171322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	125210444	125210444	+	IGR	DEL	A	-	-	rs141662532	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125210444delA								NCOR2 (158434 upstream) : SCARB1 (51731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	125212712	125212713	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125212712_125212713delAA								NCOR2 (160702 upstream) : SCARB1 (49462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	125383709	125383709	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125383709delA								SCARB1 (35190 upstream) : UBC (12485 downstream)																																			---	---	---	---
DHX37	57647	broad.mit.edu	37	12	125435672	125435672	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125435672delA	uc001ugy.2	-						DHX37_uc001ugz.1_Intron	NM_032656	NP_116045			DEAH (Asp-Glu-Ala-His) box polypeptide 37								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	125531113	125531113	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125531113delA								BRI3BP (20764 upstream) : AACS (18812 downstream)																																			---	---	---	---
AACS	65985	broad.mit.edu	37	12	125550997	125551001	+	Intron	DEL	TTTTT	-	-	rs35044730		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125550997_125551001delTTTTT	uc001uhc.2	+						AACS_uc009zyg.2_Intron|AACS_uc001uhd.2_Intron	NM_023928	NP_076417			acetoacetyl-CoA synthetase						fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	125754577	125754577	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125754577delA								AACS (126705 upstream) : TMEM132B (56585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	125801210	125801210	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125801210delG								AACS (173338 upstream) : TMEM132B (9952 downstream)																																			---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	126000656	126000657	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126000656_126000657delCA	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	126063910	126063910	+	Intron	DEL	T	-	-	rs78071294		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126063910delT	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	126594244	126594244	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126594244delA								TMEM132B (450655 upstream) : LOC100128554 (332783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126777342	126777342	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126777342delT								TMEM132B (633753 upstream) : LOC100128554 (149685 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127277993	127277994	+	IGR	INS	-	TGTG	TGTG	rs147856536	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127277993_127277994insTGTG								LOC100128554 (320663 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127346382	127346382	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127346382delT								LOC100128554 (389052 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127700024	127700024	+	IGR	DEL	A	-	-	rs78083936		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127700024delA								LOC100128554 (742694 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127914927	127914927	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127914927delA								LOC100128554 (957597 upstream) : TMEM132C (984364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128214866	128214867	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128214866_128214867delAG								None (None upstream) : TMEM132C (684424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128803900	128803901	+	IGR	DEL	GA	-	-	rs71971376		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128803900_128803901delGA								None (None upstream) : TMEM132C (95390 downstream)																																			---	---	---	---
TMEM132C	92293	broad.mit.edu	37	12	129150495	129150496	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129150495_129150496delCA	uc001uhs.3	+							NM_001136103	NP_001129575			transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	129223890	129223890	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129223890delA								TMEM132C (31427 upstream) : SLC15A4 (53849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	129236205	129236205	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129236205delT								TMEM132C (43742 upstream) : SLC15A4 (41534 downstream)																																			---	---	---	---
GLT1D1	144423	broad.mit.edu	37	12	129368746	129368747	+	Intron	DEL	TA	-	-	rs63563663		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129368746_129368747delTA	uc010tbh.1	+						GLT1D1_uc001uhx.1_Intron|GLT1D1_uc001uhy.1_Intron	NM_144669	NP_653270			glycosyltransferase 1 domain containing 1						biosynthetic process	extracellular region	transferase activity, transferring glycosyl groups				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)														---	---	---	---
GLT1D1	144423	broad.mit.edu	37	12	129464298	129464298	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129464298delA	uc010tbh.1	+						GLT1D1_uc001uhx.1_Intron|GLT1D1_uc001uhy.1_Intron	NM_144669	NP_653270			glycosyltransferase 1 domain containing 1						biosynthetic process	extracellular region	transferase activity, transferring glycosyl groups				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	129513099	129513100	+	IGR	INS	-	TCT	TCT	rs148201905	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129513099_129513100insTCT								GLT1D1 (43590 upstream) : TMEM132D (43171 downstream)																																			---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	129608337	129608338	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129608337_129608338delTC	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	129916697	129916704	+	Intron	DEL	TGGATGCT	-	-	rs11279476		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129916697_129916704delTGGATGCT	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	130261005	130261006	+	Intron	INS	-	TA	TA	rs148572373	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130261005_130261006insTA	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	130303153	130303154	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130303153_130303154delTG	uc009zyl.1	-							NM_133448	NP_597705			transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	130773199	130773200	+	IGR	INS	-	TGTGTGTG	TGTGTGTG	rs61940158		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130773199_130773200insTGTGTGTG								FZD10 (122915 upstream) : PIWIL1 (49414 downstream)																																			---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	130935562	130935562	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130935562delC	uc001uil.2	-						RIMBP2_uc001uim.2_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)														---	---	---	---
SFRS8	6433	broad.mit.edu	37	12	132283437	132283438	+	Intron	DEL	AA	-	-	rs76616254		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132283437_132283438delAA	uc001uja.1	+						SFRS8_uc010tbn.1_Intron	NM_004592	NP_004583			splicing factor, arginine/serine-rich 8						mRNA splice site selection|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|RNA binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.44e-07)|Epithelial(86;2.94e-06)|all cancers(50;4.82e-05)														---	---	---	---
ULK1	8408	broad.mit.edu	37	12	132397937	132397938	+	Intron	DEL	AA	-	-	rs80025522		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132397937_132397938delAA	uc001uje.2	+							NM_003565	NP_003556			Unc-51-like kinase 1						autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132538120	132538121	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132538120_132538121insG	uc001ujn.2	+	42	7741_7742	c.7706_7707insG	c.(7705-7707)ACGfs	p.T2569fs	EP400_uc001ujl.2_Frame_Shift_Ins_p.T2568fs|EP400_uc001ujm.2_Frame_Shift_Ins_p.T2488fs	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	2605	Interaction with ZNF42 (By similarity).				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	132540001	132540002	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132540001_132540002delGT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	132641615	132641616	+	IGR	INS	-	CAC	CAC	rs141748931		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132641615_132641616insCAC								NOC4L (4629 upstream) : GALNT9 (39302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	133057988	133057988	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133057988delA								GALNT9 (152083 upstream) : FBRSL1 (9169 downstream)																																			---	---	---	---
POLE	5426	broad.mit.edu	37	12	133214318	133214318	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133214318delA	uc001uks.1	-						POLE_uc001ukq.1_Intron|POLE_uc001ukr.1_Intron|POLE_uc010tbq.1_Intron	NM_006231	NP_006222			DNA-directed DNA polymerase epsilon						base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
ZNF268	10795	broad.mit.edu	37	12	133767906	133767906	+	Intron	DEL	A	-	-	rs75668420		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133767906delA	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	19573341	19573341	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19573341delA								LOC284232 (127232 upstream) : LOC348021 (9058 downstream)																																			---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19645660	19645660	+	Intron	DEL	G	-	-	rs112020856		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19645660delG	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19651281	19651282	+	Intron	INS	-	T	T	rs138485383	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19651281_19651282insT	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
PSPC1	55269	broad.mit.edu	37	13	20279634	20279635	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20279634_20279635delAA	uc001uml.2	-						PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron	NM_001042414	NP_001035879			paraspeckle protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)														---	---	---	---
PSPC1	55269	broad.mit.edu	37	13	20325238	20325238	+	Intron	DEL	C	-	-	rs9508872	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20325238delC	uc001uml.2	-						PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron	NM_001042414	NP_001035879			paraspeckle protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)														---	---	---	---
PSPC1	55269	broad.mit.edu	37	13	20333289	20333290	+	Intron	INS	-	A	A	rs144636506	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20333289_20333290insA	uc001uml.2	-						PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron	NM_001042414	NP_001035879			paraspeckle protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	20871389	20871389	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20871389delT								GJB6 (64855 upstream) : CRYL1 (106420 downstream)																																			---	---	---	---
CRYL1	51084	broad.mit.edu	37	13	21102003	21102003	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21102003delA	uc001une.2	-						CRYL1_uc001unf.2_5'Flank|CRYL1_uc001ung.2_5'Flank	NM_015974	NP_057058			lambda-crystallin						fatty acid metabolic process	cytosol	3-hydroxyacyl-CoA dehydrogenase activity|L-gulonate 3-dehydrogenase activity|NAD+ binding|protein homodimerization activity				0		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)														---	---	---	---
IFT88	8100	broad.mit.edu	37	13	21215419	21215419	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21215419delT	uc001unh.2	+						IFT88_uc001uni.2_Intron|IFT88_uc001unj.2_Intron|IFT88_uc010tcq.1_Intron|IFT88_uc001unk.2_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	21268878	21268879	+	IGR	DEL	AA	-	-	rs76938277		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21268878_21268879delAA								IFT88 (3304 upstream) : IL17D (8603 downstream)																																			---	---	---	---
XPO4	64328	broad.mit.edu	37	13	21392102	21392102	+	Intron	DEL	T	-	-	rs4063933		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21392102delT	uc001unq.3	-							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	21701305	+	IGR	DEL	T	-	-	rs76702376		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21701305delT								LATS2 (65583 upstream) : SAP18 (13348 downstream)																																			---	---	---	---
ZDHHC20	253832	broad.mit.edu	37	13	21951748	21951749	+	Intron	DEL	CT	-	-	rs68104473		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21951748_21951749delCT	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	22060241	22060241	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22060241delA								ZDHHC20 (26818 upstream) : EFHA1 (6599 downstream)																																			---	---	---	---
EFHA1	221154	broad.mit.edu	37	13	22073556	22073558	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22073556_22073558delTTT	uc001uof.2	-						EFHA1_uc010tct.1_Intron	NM_152726	NP_689939			EF-hand domain family, member A1								calcium ion binding				0		all_cancers(29;1.24e-15)|all_epithelial(30;5.4e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000171)|Epithelial(112;0.000398)|OV - Ovarian serous cystadenocarcinoma(117;0.00641)|Lung(94;0.189)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	22303073	22303073	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22303073delT								FGF9 (24433 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22309381	22309383	+	IGR	DEL	TTT	-	-	rs111487380		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22309381_22309383delTTT								FGF9 (30741 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23344637	23344637	+	IGR	DEL	A	-	-	rs67756418		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23344637delA								None (None upstream) : SGCG (410423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23380423	23380423	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23380423delT								None (None upstream) : SGCG (374637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	24052377	24052377	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24052377delT	uc001uos.2	+											Homo sapiens mRNA; cDNA DKFZp313E1940 (from clone DKFZp313E1940).																														---	---	---	---
MIPEP	4285	broad.mit.edu	37	13	24376360	24376360	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24376360delT	uc001uox.3	-							NM_005932	NP_005923			mitochondrial intermediate peptidase precursor						protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)														---	---	---	---
SPATA13	221178	broad.mit.edu	37	13	24686693	24686694	+	Intron	DEL	AC	-	-	rs3075291		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24686693_24686694delAC	uc001upd.1	+						C1QTNF9_uc001upe.2_Intron	NM_153023	NP_694568			spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)														---	---	---	---
SPATA13	221178	broad.mit.edu	37	13	24723479	24723480	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24723479_24723480delTT	uc001upd.1	+						C1QTNF9_uc001upe.2_Intron	NM_153023	NP_694568			spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)														---	---	---	---
SPATA13	221178	broad.mit.edu	37	13	24724691	24724691	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24724691delT	uc001upd.1	+						C1QTNF9_uc001upe.2_Intron	NM_153023	NP_694568			spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)														---	---	---	---
SPATA13	221178	broad.mit.edu	37	13	24772131	24772134	+	Intron	DEL	TGTT	-	-	rs12876136	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24772131_24772134delTGTT	uc001upg.1	+						SPATA13_uc001upd.1_Intron|C1QTNF9_uc001upe.2_Intron|SPATA13_uc001upf.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	25116945	25116945	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25116945delT								PARP4 (29997 upstream) : LOC374491 (24066 downstream)																																			---	---	---	---
CENPJ	55835	broad.mit.edu	37	13	25478344	25478344	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25478344delA	uc001upt.3	-						CENPJ_uc010tdf.1_Intron|CENPJ_uc010aae.2_Intron|CENPJ_uc010aaf.2_Intron|CENPJ_uc001upu.2_5'Flank	NM_018451	NP_060921			centromere protein J						cell division|centriole replication|G2/M transition of mitotic cell cycle|microtubule nucleation|microtubule polymerization	centriole|cytosol|gamma-tubulin small complex|microtubule	protein domain specific binding|tubulin binding			ovary(2)	2		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)														---	---	---	---
TPTE2P1	646405	broad.mit.edu	37	13	25505444	25505445	+	3'UTR	INS	-	T	T	rs117624536		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25505444_25505445insT	uc010tdh.1	-	5					TPTE2P1_uc001upw.2_RNA|TPTE2P1_uc001upx.3_RNA	NR_026730				RecName: Full=C2 tensin-type domain-containing protein ENSP00000371290;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	25635745	25635746	+	IGR	INS	-	C	C	rs56211701		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25635745_25635746insC								TPTE2P1 (93138 upstream) : PABPC3 (34530 downstream)																																			---	---	---	---
MTMR6	9107	broad.mit.edu	37	13	25856750	25856751	+	Intron	DEL	TT	-	-	rs72144705		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25856750_25856751delTT	uc001uqf.3	-						MTMR6_uc001uqe.1_Intron	NM_004685	NP_004676			myotubularin related protein 6							cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)|skin(2)	4		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26093513	26093513	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26093513delT	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron|ATP8A2_uc001uql.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	26163931	26163931	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26163931delA	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	26246692	26246693	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26246692_26246693insT	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	26466945	26466946	+	Intron	DEL	TT	-	-	rs35638068		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26466945_26466946delTT	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	26628462	26628464	+	IGR	DEL	TTT	-	-	rs72032057		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26628462_26628464delTTT								SHISA2 (3264 upstream) : RNF6 (77789 downstream)																																			---	---	---	---
USP12	219333	broad.mit.edu	37	13	27669302	27669302	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27669302delT	uc001uqy.2	-							NM_182488	NP_872294			ubiquitin thiolesterase 12						protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(1)	1		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	27925971	27925971	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27925971delT								RASL11A (78144 upstream) : GTF3A (72710 downstream)																																			---	---	---	---
POLR1D	51082	broad.mit.edu	37	13	28239644	28239644	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28239644delT	uc001urp.2	+						POLR1D_uc010aam.2_Intron|POLR1D_uc001urq.2_Intron	NM_152705	NP_689918			polymerase (RNA) I polypeptide D isoform 2						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein dimerization activity				0		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0758)|OV - Ovarian serous cystadenocarcinoma(117;0.1)|Epithelial(112;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	28507810	28507810	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28507810delT								PDX1 (7359 upstream) : ATP5EP2 (11533 downstream)																																			---	---	---	---
PAN3	255967	broad.mit.edu	37	13	28719461	28719461	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28719461delT	uc010tdo.1	+							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)														---	---	---	---
PAN3	255967	broad.mit.edu	37	13	28737189	28737189	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28737189delT	uc010tdo.1	+							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)														---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28886057	28886057	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28886057delA	uc001usb.3	-						FLT1_uc010aap.2_Intron|FLT1_uc010aaq.2_Intron|FLT1_uc001usa.3_Intron	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28969913	28969913	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28969913delT	uc001usb.3	-						FLT1_uc010aar.1_Intron|FLT1_uc001usc.3_Intron|FLT1_uc010aas.1_Intron|FLT1_uc010aat.1_Intron	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	29327233	29327233	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29327233delA								SLC46A3 (34083 upstream) : MTUS2 (271515 downstream)																																			---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	29832520	29832521	+	Intron	INS	-	A	A	rs113379163		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29832520_29832521insA	uc001usl.3	+							NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
LOC100188949	100188949	broad.mit.edu	37	13	30917048	30917048	+	Intron	DEL	A	-	-	rs34189555		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30917048delA	uc001usu.2	-							NR_024464				full-length cDNA clone CS0DG007YC17 of B cells (Ramos cell line) of Homo sapiens (human).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	30994429	30994430	+	IGR	DEL	AC	-	-	rs145806081		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30994429_30994430delAC								LOC100188949 (46393 upstream) : HMGB1 (38451 downstream)																																			---	---	---	---
USPL1	10208	broad.mit.edu	37	13	31195197	31195197	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31195197delT	uc001utc.2	+						USPL1_uc001utb.2_Intron|USPL1_uc001utd.2_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	31198768	31198768	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31198768delA	uc001utc.2	+						USPL1_uc001utb.2_Intron|USPL1_uc001utd.2_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	31267156	31267156	+	IGR	DEL	T	-	-	rs71436403		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31267156delT								USPL1 (33470 upstream) : ALOX5AP (20459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31392052	31392053	+	IGR	DEL	TT	-	-	rs71674131		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31392052_31392053delTT								ALOX5AP (53496 upstream) : C13orf33 (88259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31652513	31652520	+	IGR	DEL	AAGAAAGA	-	-	rs7986217		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31652513_31652520delAAGAAAGA								C13orf26 (103362 upstream) : HSPH1 (58245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31993078	31993081	+	IGR	DEL	AGAA	-	-	rs72173481		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31993078_31993081delAGAA								B3GALTL (86669 upstream) : RXFP2 (320598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	32170840	32170840	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32170840delT								B3GALTL (264431 upstream) : RXFP2 (142839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	32592981	32592981	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32592981delT								EEF1DP3 (59261 upstream) : FRY (12456 downstream)																																			---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33250148	33250148	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33250148delT	uc010abf.2	+						PDS5B_uc001uuo.2_Intron|PDS5B_uc010abg.2_Intron|PDS5B_uc010teb.1_Intron	NM_015032	NP_055847			PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	34680797	34680797	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34680797delT								RFC3 (140103 upstream) : NBEA (835659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	34800591	34800591	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34800591delT								RFC3 (259897 upstream) : NBEA (715865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	34923084	34923085	+	IGR	INS	-	T	T	rs143232519	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34923084_34923085insT								RFC3 (382390 upstream) : NBEA (593371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	35451659	35451659	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35451659delA								RFC3 (910965 upstream) : NBEA (64797 downstream)																																			---	---	---	---
NBEA	26960	broad.mit.edu	37	13	35605639	35605639	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35605639delT	uc001uvb.2	+							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	36260632	36260632	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36260632delT								NBEA (13760 upstream) : DCLK1 (82491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	36708640	36708640	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36708640delG								DCLK1 (3176 upstream) : SOHLH2 (33707 downstream)																																			---	---	---	---
SOHLH2	54937	broad.mit.edu	37	13	36759298	36759298	+	Intron	DEL	T	-	-	rs34353129		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36759298delT	uc001uvj.2	-						SOHLH2_uc010tei.1_Intron	NM_017826	NP_060296			spermatogenesis and oogenesis specific basic						cell differentiation|multicellular organismal development|oogenesis|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding				0		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)														---	---	---	---
SPG20	23111	broad.mit.edu	37	13	36902971	36902971	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36902971delA	uc001uvn.2	-						SPG20_uc010ten.1_Intron|SPG20_uc001uvm.2_Intron|SPG20_uc001uvo.2_Intron|SPG20_uc001uvq.2_Intron|SPG20_uc001uvp.2_Intron	NM_001142296	NP_001135768			spartin						cell death	cytoplasm	ubiquitin protein ligase binding				0		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	38105621	38105622	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38105621_38105622insA								CSNK1A1L (425820 upstream) : POSTN (31098 downstream)																																			---	---	---	---
POSTN	10631	broad.mit.edu	37	13	38171302	38171302	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38171302delA	uc001uwo.3	-						POSTN_uc001uwp.3_Intron|POSTN_uc001uwr.2_Intron|POSTN_uc001uwq.2_Intron|POSTN_uc010teu.1_Intron|POSTN_uc010tev.1_Intron|POSTN_uc010tew.1_Intron|POSTN_uc010tex.1_Intron	NM_006475	NP_006466			periostin, osteoblast specific factor isoform 1						cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)														---	---	---	---
TRPC4	7223	broad.mit.edu	37	13	38342808	38342809	+	Intron	DEL	CG	-	-	rs113635164		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38342808_38342809delCG	uc001uws.2	-						TRPC4_uc010abv.2_Intron|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	38559315	38559316	+	IGR	INS	-	GGATGGATGGAAGGAAGGAAGGAA	GGATGGATGGAAGGAAGGAAGGAA	rs145602911	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38559315_38559316insGGATGGATGGAAGGAAGGAAGGAA								TRPC4 (115376 upstream) : UFM1 (364626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	38961106	38961106	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38961106delG								UFM1 (23964 upstream) : FREM2 (300067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	39507209	39507209	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39507209delA								FREM2 (45944 upstream) : STOML3 (32854 downstream)																																			---	---	---	---
C13orf23	80209	broad.mit.edu	37	13	39600600	39600600	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39600600delA	uc001uwy.2	-						C13orf23_uc001uwz.2_Intron	NM_025138	NP_079414			hypothetical protein LOC80209 isoform 1											ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	39725148	39725148	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39725148delA								NHLRC3 (100906 upstream) : LHFP (191882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	40626355	40626356	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40626355_40626356delGA								COG6 (260553 upstream) : LOC646982 (294917 downstream)																																			---	---	---	---
LOC646982	646982	broad.mit.edu	37	13	40949480	40949480	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40949480delA	uc010tfa.1	-						LOC646982_uc001uxj.3_Intron	NR_024507				Homo sapiens cDNA, FLJ17553.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	41609973	41609975	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41609973_41609975delAAA								ELF1 (16465 upstream) : WBP4 (25722 downstream)																																			---	---	---	---
WBP4	11193	broad.mit.edu	37	13	41638204	41638205	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41638204_41638205delTT	uc001uxt.2	+						WBP4_uc010tfd.1_Intron	NM_007187	NP_009118			WW domain-containing binding protein 4						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	41849635	41849636	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41849635_41849636delTT								MTRF1 (11893 upstream) : NAA16 (35705 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	41880520	41880520	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41880520delA								MTRF1 (42778 upstream) : NAA16 (4821 downstream)																																			---	---	---	---
NAA16	79612	broad.mit.edu	37	13	41889915	41889915	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41889915delT	uc001uyf.2	+						NAA16_uc010tfg.1_Intron|NAA16_uc001uye.3_Intron|NAA16_uc001uyd.3_Intron	NM_024561	NP_078837			NMDA receptor regulated 1-like protein isoform						N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent	cytoplasm|transcription factor complex	binding			central_nervous_system(1)	1																		---	---	---	---
NAA16	79612	broad.mit.edu	37	13	41941505	41941505	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41941505delT	uc001uyf.2	+						NAA16_uc010tfg.1_Intron	NM_024561	NP_078837			NMDA receptor regulated 1-like protein isoform						N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent	cytoplasm|transcription factor complex	binding			central_nervous_system(1)	1																		---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42393184	42393184	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42393184delA	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)														---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42393532	42393533	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42393532_42393533insA	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	42733617	42733619	+	Intron	DEL	AGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42733617_42733619delAGA	uc001uyl.1	+						DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_Intron|DGKH_uc010tfi.1_Intron|DGKH_uc010tfj.1_Intron|DGKH_uc001uyn.1_Intron|DGKH_uc001uyo.1_Intron|DGKH_uc001uyp.2_Intron	NM_178009	NP_821077			diacylglycerol kinase, eta isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	43986299	43986300	+	Intron	INS	-	A	A	rs111397000		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43986299_43986300insA	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	44464520	44464520	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	44855163	44855164	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44855163_44855164delCA								LOC121838 (250565 upstream) : SERP2 (92814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	45379179	45379179	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45379179delA								TSC22D1 (228478 upstream) : NUFIP1 (134205 downstream)																																			---	---	---	---
KIAA1704	55425	broad.mit.edu	37	13	45607568	45607569	+	3'UTR	INS	-	AGAAG	AGAAG	rs145166775	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45607568_45607569insAGAAG	uc001uzs.2	+	9					KIAA1704_uc001uzt.2_3'UTR|uc001uzu.2_RNA					SubName: Full=KIAA1704, isoform CRA_a; SubName: Full=cDNA FLJ76951;											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	45673381	45673381	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45673381delA								KIAA1704 (65639 upstream) : GTF2F2 (21250 downstream)																																			---	---	---	---
LOC100190939	100190939	broad.mit.edu	37	13	45935845	45935845	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45935845delT	uc010tfr.1	+						LOC100190939_uc001vac.2_Intron	NR_024458				Homo sapiens pp13759 mRNA, complete cds.												0																		---	---	---	---
LOC100190939	100190939	broad.mit.edu	37	13	45935993	45935993	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45935993delT	uc010tfr.1	+						LOC100190939_uc001vac.2_Intron	NR_024458				Homo sapiens pp13759 mRNA, complete cds.												0																		---	---	---	---
CPB2	1361	broad.mit.edu	37	13	46627545	46627545	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46627545delT	uc001vaw.2	-	11					uc001vau.1_Intron|uc001vav.1_Intron|CPB2_uc001vax.2_3'UTR|ZC3H13_uc001vas.1_5'Flank|ZC3H13_uc001vat.1_5'Flank	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	46865210	46865210	+	IGR	DEL	A	-	-	rs35667786		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46865210delA								LCP1 (108751 upstream) : C13orf18 (50929 downstream)																																			---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47217051	47217051	+	Intron	DEL	A	-	-	rs33914665		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47217051delA	uc001vbj.2	+						LRCH1_uc010acp.2_Intron|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931			leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47279680	47279681	+	Intron	INS	-	T	T	rs146461842	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47279680_47279681insT	uc001vbj.2	+						LRCH1_uc010acp.2_3'UTR|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931			leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47301640	47301640	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47301640delT	uc001vbj.2	+						LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931			leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	48431624	48431624	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48431624delT								HTR2A (960574 upstream) : SUCLA2 (85168 downstream)																																			---	---	---	---
MED4	29079	broad.mit.edu	37	13	48661989	48661989	+	Intron	DEL	A	-	-	rs77350157		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48661989delA	uc001vby.1	-						MED4_uc010tge.1_Intron|MED4_uc010tgf.1_Intron	NM_014166	NP_054885			mediator complex subunit 4						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	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		all_cancers(8;2.93e-25)|all_epithelial(8;4.38e-13)|all_lung(13;7.37e-06)|all_hematologic(8;8.61e-05)|Breast(56;0.000141)|Lung NSC(96;0.000518)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.00559)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;5.18e-07)														---	---	---	---
RB1	5925	broad.mit.edu	37	13	48965757	48965757	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48965757delT	uc001vcb.2	+						LPAR6_uc001vcc.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.?(4)		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)			---	---	---	---
RB1	5925	broad.mit.edu	37	13	49037805	49037805	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49037805delT	uc001vcb.2	+							NM_000321	NP_000312			retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(6)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49761194	49761195	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49761194_49761195insT	uc001vcm.2	+						FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron|FNDC3A_uc001vcp.1_Intron|FNDC3A_uc001vcq.2_Intron	NM_001079673	NP_001073141			fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49761480	49761480	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49761480delT	uc001vcm.2	+						FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron|FNDC3A_uc001vcp.1_Intron|FNDC3A_uc001vcq.2_Intron	NM_001079673	NP_001073141			fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
CAB39L	81617	broad.mit.edu	37	13	50014978	50014979	+	Intron	DEL	AC	-	-	rs147142005		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50014978_50014979delAC	uc001vcx.2	-						CAB39L_uc010adf.2_Intron	NM_001079670	NP_001073138			calcium binding protein 39-like						cell cycle arrest|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol	protein binding				0		Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226)														---	---	---	---
PHF11	51131	broad.mit.edu	37	13	50098427	50098427	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50098427delA	uc001vdb.2	+						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)														---	---	---	---
RCBTB1	55213	broad.mit.edu	37	13	50137793	50137793	+	Intron	DEL	A	-	-	rs111876242		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50137793delA	uc001vde.1	-							NM_018191	NP_060661			regulator of chromosome condensation (RCC1) and						cell cycle|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(1)	1		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|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;4.7e-09)														---	---	---	---
RCBTB1	55213	broad.mit.edu	37	13	50143556	50143556	+	Intron	DEL	A	-	-	rs11311610		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50143556delA	uc001vde.1	-							NM_018191	NP_060661			regulator of chromosome condensation (RCC1) and						cell cycle|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(1)	1		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|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;4.7e-09)														---	---	---	---
KPNA3	3839	broad.mit.edu	37	13	50324770	50324770	+	Intron	DEL	A	-	-	rs113160769		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50324770delA	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)														---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	50833278	50833279	+	Intron	DEL	TT	-	-	rs71190371		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50833278_50833279delTT	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	51133533	51133533	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51133533delA	uc001vet.1	+											Homo sapiens mRNA for B-cell neoplasia associated transcript, (BCMS gene), splice variant D, non coding transcript.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	51246351	51246351	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51246351delC								DLEU1 (143681 upstream) : DLEU7 (40408 downstream)																																			---	---	---	---
GUCY1B2	2974	broad.mit.edu	37	13	51590473	51590473	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51590473delA	uc001vfd.3	-						GUCY1B2_uc010tgo.1_Intron|GUCY1B2_uc001vfc.3_Intron					SubName: Full=Guanylate cyclase 1, soluble, beta 2;												0																		---	---	---	---
GUCY1B2	2974	broad.mit.edu	37	13	51638359	51638360	+	Intron	INS	-	A	A	rs138396945	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51638359_51638360insA	uc001vfd.3	-						GUCY1B2_uc010tgo.1_Intron|GUCY1B2_uc001vfc.3_Intron					SubName: Full=Guanylate cyclase 1, soluble, beta 2;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	51677836	51677837	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51677836_51677837insA								GUCY1B2 (22838 upstream) : FAM124A (118670 downstream)																																			---	---	---	---
INTS6	26512	broad.mit.edu	37	13	51997464	51997465	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51997464_51997465delGT	uc001vfk.2	-						INTS6_uc001vfj.2_Intron|INTS6_uc001vfl.2_Intron	NM_012141	NP_036273			integrator complex subunit 6 isoform a						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	52041893	52041896	+	IGR	DEL	GATC	-	-	rs72003525	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52041893_52041896delGATC								INTS6 (14618 upstream) : WDFY2 (116588 downstream)																																			---	---	---	---
WDFY2	115825	broad.mit.edu	37	13	52163482	52163482	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52163482delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	53552654	53552654	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53552654delT								PCDH8 (129880 upstream) : OLFM4 (50318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	53666478	53666478	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53666478delA								OLFM4 (40292 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	53772907	53772907	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53772907delA								OLFM4 (146721 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54210554	54210555	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54210554_54210555delTG								OLFM4 (584368 upstream) : MIR1297 (675552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56320795	56320796	+	IGR	INS	-	AC	AC	rs150771591	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56320795_56320796insAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56649090	56649090	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56649090delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56735742	56735742	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56735742delT								None (None upstream) : PRR20C (979310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56879719	56879719	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56879719delT								None (None upstream) : PRR20C (835333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	59326367	59326367	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59326367delT								None (None upstream) : DIAPH3 (913358 downstream)																																			---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60306584	60306585	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60306584_60306585delTT	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	60666497	60666498	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60666497_60666498insA	uc001vht.2	-						DIAPH3_uc001vhw.1_Intron|DIAPH3_uc010aed.1_Intron|DIAPH3_uc010aee.1_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	60703797	60703797	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60703797delA	uc001vht.2	-						DIAPH3_uc001vhw.1_Intron|DIAPH3_uc010aed.1_Intron|DIAPH3_uc010aee.1_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-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61058809	61058810	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61058809_61058810delTT	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	61423293	61423293	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61423293delA								TDRD3 (275281 upstream) : PCDH20 (560528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	62573287	62573287	+	IGR	DEL	T	-	-	rs76378563		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62573287delT								PCDH20 (571208 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63387197	63387197	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63387197delT								None (None upstream) : OR7E156P (924371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63636192	63636192	+	IGR	DEL	A	-	-	rs138659113		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63636192delA								None (None upstream) : OR7E156P (675376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63754733	63754734	+	IGR	INS	-	GA	GA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63754733_63754734insGA								None (None upstream) : OR7E156P (556834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	64137205	64137206	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64137205_64137206delTC								None (None upstream) : OR7E156P (174362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65116905	65116905	+	IGR	DEL	A	-	-	rs17088301	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65116905delA								OR7E156P (800204 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65432888	65432888	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65432888delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65863475	65863476	+	IGR	DEL	TG	-	-	rs71802072		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65863475_65863476delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66217171	66217172	+	IGR	INS	-	TG	TG	rs141111532	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66217171_66217172insTG								None (None upstream) : PCDH9 (659795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66399577	66399577	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66399577delA								None (None upstream) : PCDH9 (477390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66440957	66440957	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66440957delC								None (None upstream) : PCDH9 (436010 downstream)																																			---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67418143	67418144	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67418143_67418144insT	uc001vik.2	-						PCDH9_uc010aei.2_Intron|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)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67727300	67727300	+	Intron	DEL	T	-	-	rs35270745		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67727300delT	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)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67743255	67743255	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67743255delA	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	68327596	68327596	+	IGR	DEL	T	-	-	rs74596495		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68327596delT								PCDH9 (523128 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68397502	68397503	+	IGR	DEL	TT	-	-	rs111241914		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68397502_68397503delTT								PCDH9 (593034 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68539910	68539911	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68539910_68539911delGT								PCDH9 (735442 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68635852	68635852	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68635852delA								PCDH9 (831384 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68967146	68967146	+	IGR	DEL	A	-	-	rs145319506		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68967146delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69467061	69467061	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69467061delA								None (None upstream) : KLHL1 (807665 downstream)																																			---	---	---	---
KLHL1	57626	broad.mit.edu	37	13	70425032	70425033	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70425032_70425033insT	uc001vip.2	-						KLHL1_uc010thm.1_Intron	NM_020866	NP_065917			kelch-like 1 protein						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	70966626	70966626	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70966626delT								ATXN8OS (252741 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71013821	71013822	+	IGR	INS	-	TCCT	TCCT	rs71771238		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71013821_71013822insTCCT								ATXN8OS (299936 upstream) : DACH1 (998276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71336484	71336486	+	IGR	DEL	GAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71336484_71336486delGAA								ATXN8OS (622599 upstream) : DACH1 (675612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71340246	71340246	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71340246delT								ATXN8OS (626361 upstream) : DACH1 (671852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71833029	71833029	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71833029delT								None (None upstream) : DACH1 (179069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71876266	71876267	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71876266_71876267insA								None (None upstream) : DACH1 (135831 downstream)																																			---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72131053	72131053	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72131053delT	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	72734535	72734536	+	IGR	DEL	TT	-	-	rs67318371		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72734535_72734536delTT								DACH1 (293205 upstream) : C13orf37 (547959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73813092	73813092	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73813092delT								KLF5 (161417 upstream) : KLF12 (447058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	74050439	74050440	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74050439_74050440insA								KLF5 (398764 upstream) : KLF12 (209710 downstream)																																			---	---	---	---
KLF12	11278	broad.mit.edu	37	13	74326865	74326865	+	Intron	DEL	A	-	-	rs58056051		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74326865delA	uc001vjf.2	-						KLF12_uc010aeq.2_Intron	NM_007249	NP_009180			Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)														---	---	---	---
KLF12	11278	broad.mit.edu	37	13	74704783	74704787	+	Intron	DEL	AAAAA	-	-	rs66572960		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74704783_74704787delAAAAA	uc001vjf.2	-						KLF12_uc010aeq.2_Intron|KLF12_uc001vjg.3_Intron	NM_007249	NP_009180			Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	75739787	75739787	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75739787delA								None (None upstream) : LOC647288 (72103 downstream)																																			---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	76054180	76054180	+	Intron	DEL	C	-	-	rs67495268		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76054180delC	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)														---	---	---	---
UCHL3	7347	broad.mit.edu	37	13	76127781	76127781	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76127781delT	uc001vjq.2	+							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)														---	---	---	---
UCHL3	7347	broad.mit.edu	37	13	76144383	76144384	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76144383_76144384insT	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	76232197	76232197	+	Intron	DEL	T	-	-	rs78179993		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76232197delT	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	76950543	76950543	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76950543delT								LMO7 (516539 upstream) : KCTD12 (503761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77385524	77385527	+	IGR	DEL	TCTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77385524_77385527delTCTC								LMO7 (951520 upstream) : KCTD12 (68777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77526470	77526471	+	IGR	DEL	TT	-	-	rs78658340		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77526470_77526471delTT								BTF3L1 (23247 upstream) : CLN5 (39588 downstream)																																			---	---	---	---
FBXL3	26224	broad.mit.edu	37	13	77592668	77592668	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77592668delA	uc001vkd.2	-							NM_012158	NP_036290			F-box and leucine-rich repeat protein 3						regulation of circadian rhythm|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity				0		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.218)		GBM - Glioblastoma multiforme(99;0.0521)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77722257	77722257	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77722257delT	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	77728552	77728552	+	Intron	DEL	A	-	-	rs144699563	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77728552delA	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	77780725	77780725	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77780725delA	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	77813254	77813255	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77813254_77813255insA	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	77849050	77849050	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77849050delT	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	78006446	78006446	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78006446delA								MYCBP2 (105269 upstream) : SCEL (103363 downstream)																																			---	---	---	---
SCEL	8796	broad.mit.edu	37	13	78184275	78184275	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	78348877	78348878	+	IGR	DEL	TT	-	-	rs111265102		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78348877_78348878delTT								SLAIN1 (10500 upstream) : EDNRB (120738 downstream)																																			---	---	---	---
EDNRB	1910	broad.mit.edu	37	13	78475267	78475267	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78475267delA	uc001vko.2	-	4	1135	c.877delT	c.(877-879)TATfs	p.Y293fs	EDNRB_uc001vkq.1_Frame_Shift_Del_p.Y293fs|uc001vkn.1_Intron|EDNRB_uc010aez.1_Frame_Shift_Del_p.Y293fs|EDNRB_uc001vkp.1_Frame_Shift_Del_p.Y376fs	NM_001122659	NP_001116131	P24530	EDNRB_HUMAN	endothelin receptor type B isoform 1 precursor	293	Helical; Name=5; (Potential).				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)													---	---	---	---
RNF219	79596	broad.mit.edu	37	13	79217451	79217451	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79217451delA	uc001vkw.1	-						RNF219_uc010afb.1_Intron|RNF219_uc010afc.2_Intron	NM_024546	NP_078822			ring finger protein 219								zinc ion binding			large_intestine(2)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	79335843	79335843	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79335843delA								RNF219 (101143 upstream) : RBM26 (558257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79423336	79423348	+	IGR	DEL	TTTTTTTTTTTTT	-	-	rs71203096		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79423336_79423348delTTTTTTTTTTTTT								RNF219 (188636 upstream) : RBM26 (470752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79531173	79531174	+	IGR	INS	-	A	A	rs140886912	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79531173_79531174insA								RNF219 (296473 upstream) : RBM26 (362926 downstream)																																			---	---	---	---
NDFIP2	54602	broad.mit.edu	37	13	80116648	80116648	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80116648delT	uc001vlf.2	+						NDFIP2_uc010tib.1_Intron|NDFIP2_uc001vlg.2_Intron	NM_019080	NP_061953			Nedd4 family interacting protein 2 isoform 1						negative regulation of gene expression|negative regulation of protein transport|negative regulation of transporter activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of protein ubiquitination	endoplasmic reticulum|Golgi membrane|integral to membrane|mitochondrion|multivesicular body membrane|perinuclear region of cytoplasm	signal transducer activity|WW domain binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0196)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	81130774	81130775	+	IGR	DEL	AG	-	-	rs35925866		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81130774_81130775delAG								SPRY2 (215688 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81396018	81396018	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81396018delT								SPRY2 (480932 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81697776	81697777	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81697776_81697777delTT								SPRY2 (782690 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82469505	82469505	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82469505delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83669745	83669746	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83669745_83669746delCT								None (None upstream) : SLITRK1 (781598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	84574063	84574063	+	IGR	DEL	T	-	-	rs111338936		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84574063delT								SLITRK1 (117535 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	84963588	84963590	+	IGR	DEL	TTT	-	-	rs113561063		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84963588_84963590delTTT								SLITRK1 (507060 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	84998799	84998799	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84998799delA								SLITRK1 (542271 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85459793	85459794	+	IGR	DEL	TT	-	-	rs11458833		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85459793_85459794delTT								None (None upstream) : SLITRK6 (907128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86116296	86116297	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86116296_86116297insA								None (None upstream) : SLITRK6 (250625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86147655	86147656	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86147655_86147656delAA								None (None upstream) : SLITRK6 (219266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88786824	88786824	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88786824delA								SLITRK5 (454956 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89000326	89000327	+	IGR	INS	-	GAAG	GAAG	rs141385241	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89000326_89000327insGAAG								SLITRK5 (668458 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89164167	89164167	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89164167delA								SLITRK5 (832299 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89255387	89255387	+	IGR	DEL	A	-	-	rs67170713		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89255387delA								SLITRK5 (923519 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89365967	89365967	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89365967delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90105703	90105704	+	IGR	INS	-	GAGA	GAGA	rs145854517	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90105703_90105704insGAGA								None (None upstream) : MIR622 (777732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90330990	90330991	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90330990_90330991delAA								None (None upstream) : MIR622 (552445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90439182	90439182	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90439182delA								None (None upstream) : MIR622 (444254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90684675	90684675	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90684675delT								None (None upstream) : MIR622 (198761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91673833	91673833	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91673833delC								LOC144776 (94982 upstream) : MIR17HG (326241 downstream)																																			---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92091451	92091451	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92091451delG	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	92398594	92398594	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92398594delA	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	92635598	92635599	+	Intron	INS	-	A	A	rs67441943		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92635598_92635599insA	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	92725555	92725555	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92725555delG	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	93787153	93787153	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93787153delT								GPC5 (267668 upstream) : GPC6 (91925 downstream)																																			---	---	---	---
GPC6	10082	broad.mit.edu	37	13	93927589	93927590	+	Intron	DEL	TG	-	-	rs9584099	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93927589_93927590delTG	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	94643173	94643173	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94643173delA	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	94686441	94686442	+	Intron	INS	-	AGAA	AGAA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94686441_94686442insAGAA	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	94754040	94754040	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94754040delA	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	94890732	94890733	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94890732_94890733insG	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)																---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95769769	95769770	+	Intron	INS	-	T	T	rs150267615	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95769769_95769770insT	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95865381	95865381	+	Intron	DEL	A	-	-	rs67292848		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95865381delA	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron|ABCC4_uc001vmf.2_Intron|ABCC4_uc010afl.1_Intron|ABCC4_uc010afm.1_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95955956	95955957	+	5'Flank	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95955956_95955957delAA	uc001vmd.3	-						ABCC4_uc010afk.2_5'Flank|ABCC4_uc001vme.2_5'Flank|ABCC4_uc010tih.1_5'Flank|ABCC4_uc001vmf.2_5'Flank|ABCC4_uc010afl.1_5'Flank|ABCC4_uc010afm.1_5'Flank	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
CLDN10	9071	broad.mit.edu	37	13	96179821	96179822	+	Intron	DEL	AA	-	-	rs35494686		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96179821_96179822delAA	uc001vmg.2	+						CLDN10_uc010tii.1_Intron	NM_182848	NP_878268			claudin 10 isoform a						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)															---	---	---	---
CLDN10	9071	broad.mit.edu	37	13	96207305	96207306	+	Intron	INS	-	G	G	rs9561902	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96207305_96207306insG	uc001vmh.2	+						CLDN10_uc001vmg.2_Intron|CLDN10_uc010tii.1_Intron	NM_006984	NP_008915			claudin 10 isoform b						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)															---	---	---	---
DNAJC3	5611	broad.mit.edu	37	13	96373895	96373896	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96373895_96373896insG	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	97010306	97010306	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97010306delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	98553819	98553819	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98553819delA								RAP2A (433568 upstream) : IPO5 (52110 downstream)																																			---	---	---	---
IPO5	3843	broad.mit.edu	37	13	98666535	98666536	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98666535_98666536delAA	uc001vne.2	+							NM_002271	NP_002262			importin 5						interspecies interaction between organisms|NLS-bearing substrate import into nucleus|ribosomal protein import into nucleus	cytoplasm|nuclear pore|nucleolus	GTPase inhibitor activity|protein transporter activity|Ran GTPase binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	98762553	98762553	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98762553delT								IPO5 (86004 upstream) : FARP1 (32263 downstream)																																			---	---	---	---
FARP1	10160	broad.mit.edu	37	13	98962335	98962337	+	Intron	DEL	TTT	-	-	rs145514451		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98962335_98962337delTTT	uc001vnj.2	+						FARP1_uc001vnh.2_Intron	NM_005766	NP_005757			FERM, RhoGEF, and pleckstrin domain protein 1						regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	99316800	99316800	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99316800delA								STK24 (87404 upstream) : SLC15A1 (19257 downstream)																																			---	---	---	---
DOCK9	23348	broad.mit.edu	37	13	99502312	99502312	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	99809765	99809766	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99809765_99809766insTG								DOCK9 (71105 upstream) : UBAC2 (42913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	99809800	99809803	+	IGR	DEL	TGTT	-	-	rs9582286		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99809800_99809803delTGTT								DOCK9 (71140 upstream) : UBAC2 (42876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	100072055	100072057	+	IGR	DEL	TCC	-	-	rs72238814		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100072055_100072057delTCC								UBAC2 (33304 upstream) : TM9SF2 (81671 downstream)																																			---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100406845	100406846	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100406845_100406846delTT	uc001vok.2	+						CLYBL_uc010tix.1_Intron|CLYBL_uc010tiy.1_Intron	NM_206808	NP_996531			citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100530388	100530388	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100530388delA	uc001vok.2	+						CLYBL_uc010tiy.1_3'UTR	NM_206808	NP_996531			citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
PCCA	5095	broad.mit.edu	37	13	100825991	100825993	+	Intron	DEL	GTA	-	-	rs151318449		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100825991_100825993delGTA	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	100866688	100866688	+	Intron	DEL	T	-	-	rs76174855		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100866688delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	101412296	101412297	+	IGR	INS	-	TC	TC	rs150830593	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101412296_101412297insTC								TMTC4 (85193 upstream) : NALCN (293833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	101492650	101492650	+	IGR	DEL	A	-	-	rs35369205		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101492650delA								TMTC4 (165547 upstream) : NALCN (213480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	101610267	101610267	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101610267delA								TMTC4 (283164 upstream) : NALCN (95863 downstream)																																			---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101710717	101710717	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101710717delG	uc001vox.1	-							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)																	---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101879005	101879006	+	Intron	INS	-	CCATTCAGAC	CCATTCAGAC	rs146141498	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101879005_101879006insCCATTCAGAC	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)																	---	---	---	---
FGF14	2259	broad.mit.edu	37	13	102702096	102702096	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102702096delC	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	102975235	102975235	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102975235delA	uc001vpf.2	-						uc001vph.1_Intron|uc001vpg.1_Intron	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	103726908	103726909	+	IGR	DEL	TT	-	-	rs79218534		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103726908_103726909delTT								SLC10A2 (7712 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	103926843	103926843	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103926843delT								SLC10A2 (207647 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104293549	104293549	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104293549delT								SLC10A2 (574353 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104786238	104786238	+	IGR	DEL	A	-	-	rs67956059		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104786238delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104790382	104790383	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104790382_104790383delGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106371058	106371059	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106371058_106371059insA	uc001vqf.1	+											Homo sapiens cDNA FLJ25324 fis, clone TST00330.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	106643373	106643374	+	IGR	INS	-	TTGCA	TTGCA	rs59572153		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106643373_106643374insTTGCA								DAOA (499991 upstream) : EFNB2 (498724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107117154	107117154	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107117154delA								DAOA (973772 upstream) : EFNB2 (24944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107304264	107304264	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107304264delT								ARGLU1 (83750 upstream) : FAM155A (516616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107539162	107539162	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107539162delT								ARGLU1 (318648 upstream) : FAM155A (281718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107574297	107574297	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107574297delG								ARGLU1 (353783 upstream) : FAM155A (246583 downstream)																																			---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	107908732	107908732	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107908732delA	uc001vql.2	-							NM_001080396	NP_001073865			family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1																		---	---	---	---
TNFSF13B	10673	broad.mit.edu	37	13	108955486	108955486	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108955486delT	uc001vqr.2	+						TNFSF13B_uc010agj.2_Intron|TNFSF13B_uc001vqs.1_Intron	NM_006573	NP_006564			tumor necrosis factor superfamily, member 13b						cell proliferation|immune response|signal transduction	extracellular space|integral to membrane|plasma membrane|soluble fraction	cytokine activity|tumor necrosis factor receptor binding				0	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	110460419	110460419	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110460419delC								IRS2 (21505 upstream) : COL4A1 (340892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110755858	110755858	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110755858delT								IRS2 (316944 upstream) : COL4A1 (45453 downstream)																																			---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110879734	110879735	+	Intron	INS	-	AC	AC	rs34362010		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110879734_110879735insAC	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836			alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)															---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110908230	110908231	+	Intron	INS	-	A	A	rs147787666		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110908230_110908231insA	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836			alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)															---	---	---	---
COL4A2	1284	broad.mit.edu	37	13	111002114	111002116	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111002114_111002116delTTT	uc001vqx.2	+							NM_001846	NP_001837			alpha 2 type IV collagen preproprotein						angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	111649416	111649416	+	IGR	DEL	A	-	-	rs150104318		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111649416delA								ANKRD10 (82000 upstream) : ARHGEF7 (118208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	111685616	111685617	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111685616_111685617delAG								ANKRD10 (118200 upstream) : ARHGEF7 (82007 downstream)																																			---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111953300	111953301	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111953300_111953301delTT	uc010tjo.1	+						ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron	NM_003899	NP_003890			PAK-interacting exchange factor beta isoform a						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	112220755	112220755	+	IGR	DEL	C	-	-	rs71714032		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112220755delC								C13orf16 (224162 upstream) : SOX1 (501158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112506545	112506545	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112506545delA								C13orf16 (509952 upstream) : SOX1 (215368 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112682654	112682674	+	IGR	DEL	CCAGCCAGGAGAGAGGACAGT	-	-	rs61955688	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112682654_112682674delCCAGCCAGGAGAGAGGACAGT								C13orf16 (686061 upstream) : SOX1 (39239 downstream)																																			---	---	---	---
SOX1	6656	broad.mit.edu	37	13	112721860	112721860	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112721860delC	uc001vsb.1	+							NM_005986	NP_005977			SRY (sex determining region Y)-box 1						chromatin organization	nucleus	core promoter sequence-specific DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	all_lung(23;0.000652)|Lung NSC(43;0.017)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	all_cancers(25;0.000331)|Lung NSC(25;0.0496)|all_lung(25;0.0831)|all_epithelial(44;0.0868)|Breast(118;0.231)		OV - Ovarian serous cystadenocarcinoma(48;0.132)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	113099612	113099645	+	IGR	DEL	GGAGACTGAGGTGAACAGAGCAGGATGGGGGTGC	-	-	rs60816959		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113099612_113099645delGGAGACTGAGGTGAACAGAGCAGGATGGGGGTGC								C13orf28 (10611 upstream) : TUBGCP3 (39683 downstream)																																			---	---	---	---
TUBGCP3	10426	broad.mit.edu	37	13	113219277	113219277	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113219277delA	uc001vse.1	-						TUBGCP3_uc010tjq.1_Intron|TUBGCP3_uc001vsf.2_Intron|TUBGCP3_uc001vsg.1_Intron	NM_006322	NP_006313			tubulin, gamma complex associated protein 3						G2/M transition of mitotic cell cycle|microtubule nucleation|single fertilization	centriole|cytosol|polar microtubule	gamma-tubulin binding|structural constituent of cytoskeleton			central_nervous_system(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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	113258039	113258040	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113258039_113258040insA								TUBGCP3 (15558 upstream) : C13orf35 (43318 downstream)																																			---	---	---	---
MCF2L	23263	broad.mit.edu	37	13	113707889	113707889	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113707889delG	uc001vsu.2	+						MCF2L_uc001vsq.2_Intron|MCF2L_uc010tjr.1_Intron|MCF2L_uc001vsr.2_Intron|MCF2L_uc001vss.3_Intron|MCF2L_uc010tjs.1_Intron|MCF2L_uc001vst.1_Intron	NM_001112732	NP_001106203			MCF.2 cell line derived transforming						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)																---	---	---	---
Unknown	0	broad.mit.edu	37	13	114025814	114025814	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114025814delC								GRTP1 (7351 upstream) : ADPRHL1 (50446 downstream)																																			---	---	---	---
DCUN1D2	55208	broad.mit.edu	37	13	114136181	114136182	+	Intron	DEL	AA	-	-	rs67350890		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114136181_114136182delAA	uc001vtr.1	-						DCUN1D2_uc001vts.1_Intron|DCUN1D2_uc010agw.1_Intron	NM_001014283	NP_001014305			DCN1, defective in cullin neddylation 1, domain												0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.029)|GBM - Glioblastoma multiforme(44;0.234)															---	---	---	---
CDC16	8881	broad.mit.edu	37	13	115022545	115022545	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115022545delT	uc001vuk.1	+						CDC16_uc001vul.1_Intron|CDC16_uc001vum.1_Intron|CDC16_uc001vun.1_Intron|CDC16_uc001vuo.1_Intron	NM_003903	NP_003894			anaphase-promoting complex, subunit 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cell proliferation|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|centrosome|cytosol|nucleoplasm|spindle microtubule	binding				0	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)															---	---	---	---
UPF3A	65110	broad.mit.edu	37	13	115057211	115057211	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
UPF3A	65110	broad.mit.edu	37	13	115058859	115058859	+	Intron	DEL	A	-	-	rs111799077		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115058859delA	uc001vup.2	+						UPF3A_uc001vuq.2_Intron|UPF3A_uc001vus.2_Intron|UPF3A_uc001vur.2_Intron|UPF3A_uc001vut.2_Intron|UPF3A_uc001vuu.2_Intron	NM_023011	NP_075387			UPF3 regulator of nonsense transcripts homolog A						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	14	19017325	19017325	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19017325delA								None (None upstream) : OR11H12 (360269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19077550	19077553	+	IGR	DEL	GTGA	-	-	rs28669066	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19077550_19077553delGTGA								None (None upstream) : OR11H12 (300041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19437610	19437610	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19437610delT								OR11H12 (59038 upstream) : POTEG (115755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19463099	19463103	+	IGR	DEL	TTTTT	-	-	rs150422992		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19463099_19463103delTTTTT								OR11H12 (84527 upstream) : POTEG (90262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19890158	19890160	+	Intron	DEL	GCC	-	-	rs112695101		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19890158_19890160delGCC	uc001vvq.1	-						uc001vvr.1_Intron|uc010ahe.1_Intron					Homo sapiens cDNA FLJ12852 fis, clone NT2RP2003445.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	20238336	20238336	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20238336delT								OR4Q3 (21810 upstream) : OR4M1 (10146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	20303601	20303601	+	IGR	DEL	G	-	-	rs78822023	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20303601delG								OR4N2 (7071 upstream) : OR4K2 (40826 downstream)																																			---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20845375	20845376	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20845375_20845376delAA	uc001vxe.2	-						TEP1_uc010ahk.2_Intron|TEP1_uc010tlf.1_Intron|TEP1_uc010tlg.1_Intron|TEP1_uc010tlh.1_Intron	NM_007110	NP_009041			telomerase-associated protein 1						telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)														---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20865920	20865921	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20865920_20865921insT	uc001vxe.2	-						TEP1_uc010tlf.1_Intron|TEP1_uc010tlg.1_Intron	NM_007110	NP_009041			telomerase-associated protein 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	21014704	21014704	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21014704delA								RNASE10 (35390 upstream) : RNASE9 (9549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	21095067	21095068	+	IGR	INS	-	TGTT	TGTT	rs147830498	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21095067_21095068insTGTT								RNASE12 (36085 upstream) : OR6S1 (13787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	21289387	21289388	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21289387_21289388delAA								RNASE1 (18351 upstream) : RNASE3 (70174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	21302182	21302183	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21302182_21302183delAA								RNASE1 (31146 upstream) : RNASE3 (57379 downstream)																																			---	---	---	---
METT11D1	64745	broad.mit.edu	37	14	21460882	21460882	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21460882delT	uc001vyn.2	+						METT11D1_uc010tlk.1_3'UTR|METT11D1_uc001vym.2_Intron|METT11D1_uc001vyo.2_Intron|METT11D1_uc001vyp.2_Intron|METT11D1_uc001vyq.2_Intron	NM_022734	NP_073571			methyltransferase 11 domain containing 1 isoform						translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)														---	---	---	---
RPGRIP1	57096	broad.mit.edu	37	14	21788458	21788458	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21788458delT	uc001wag.2	+						RPGRIP1_uc001wah.2_Intron|RPGRIP1_uc001wai.2_Intron|RPGRIP1_uc001waj.1_5'Flank|RPGRIP1_uc001wak.2_5'Flank|RPGRIP1_uc010aim.2_5'Flank|RPGRIP1_uc001wal.2_5'Flank	NM_020366	NP_065099			retinitis pigmentosa GTPase regulator						response to stimulus|visual perception	cilium				ovary(4)|breast(2)|pancreas(1)	7	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)														---	---	---	---
SUPT16H	11198	broad.mit.edu	37	14	21841474	21841474	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21841474delA	uc001wao.2	-						SUPT16H_uc001wap.2_Intron	NM_007192	NP_009123			chromatin-specific transcription elongation						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)														---	---	---	---
TOX4	9878	broad.mit.edu	37	14	21964624	21964624	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21964624delA	uc001waz.2	+						TOX4_uc001wba.2_Intron|TOX4_uc010tlu.1_Intron|TOX4_uc010tlv.1_Intron	NM_014828	NP_055643			epidermal Langerhans cell protein LCP1							chromatin|nucleus|PTW/PP1 phosphatase complex	DNA binding|protein binding			ovary(1)	1	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22251182	22251183	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22251182_22251183insT	uc010tmf.1	+											SubName: Full=Putative uncharacterized protein ENSP00000374943;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22433684	22433684	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22433684delT	uc001wbw.2	+						uc010tmg.1_Intron|uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22748573	22748573	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22748573delA	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|uc010tmr.1_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22892202	22892203	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22892202_22892203delAA	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|uc001wds.1_Intron|uc001wdv.3_Intron|uc001wdt.1_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	23204197	23204197	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23204197delA								ABHD4 (122940 upstream) : OXA1L (31534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	23214255	23214255	+	IGR	DEL	T	-	-	rs76309520		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23214255delT								ABHD4 (132998 upstream) : OXA1L (21476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	23241305	23241305	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23241305delA								OXA1L (307 upstream) : SLC7A7 (1129 downstream)																																			---	---	---	---
SLC7A7	9056	broad.mit.edu	37	14	23250230	23250230	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23250230delA	uc001wgr.3	-						SLC7A7_uc001wgs.3_Intron|SLC7A7_uc001wgt.3_Intron|SLC7A7_uc001wgu.3_Intron|SLC7A7_uc001wgv.3_Intron	NM_003982	NP_003973			solute carrier family 7 member 7						blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity			ovary(1)|breast(1)	2	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)														---	---	---	---
MRPL52	122704	broad.mit.edu	37	14	23297182	23297182	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23297182delT	uc001wgw.3	+						MRPL52_uc001wgx.3_5'Flank|MRPL52_uc001wgy.3_5'Flank|MRPL52_uc001wgz.3_5'Flank|MRPL52_uc001wha.3_5'Flank|MRPL52_uc001whb.3_5'Flank	NM_178336	NP_848026			mitochondrial ribosomal protein L52 isoform a						translation	mitochondrial large ribosomal subunit	structural constituent of ribosome				0	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)														---	---	---	---
MMP14	4323	broad.mit.edu	37	14	23309722	23309725	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23309722_23309725delTTTT	uc001whc.2	+							NM_004995	NP_004986			matrix metalloproteinase 14 preproprotein							extracellular matrix|integral to plasma membrane|melanosome	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	23436811	23436811	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23436811delT								HAUS4 (10476 upstream) : JUB (3601 downstream)																																			---	---	---	---
CDH24	64403	broad.mit.edu	37	14	23516384	23516384	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23516384delT	uc001wil.2	-	14					CDH24_uc001wik.3_RNA|CDH24_uc010akf.2_3'UTR	NM_022478	NP_071923			cadherin-like 24 isoform 1						adherens junction organization|cell junction assembly|cell-cell adhesion|homophilic cell adhesion	cell-cell junction|cell-cell junction|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|delta-catenin binding			central_nervous_system(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)														---	---	---	---
ACIN1	22985	broad.mit.edu	37	14	23554219	23554219	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23554219delA	uc001wit.3	-						ACIN1_uc010akg.2_Intron|ACIN1_uc010tnj.1_Intron	NM_014977	NP_055792			apoptotic chromatin condensation inducer 1						apoptotic chromosome condensation|erythrocyte differentiation|positive regulation of monocyte differentiation	cytosol	ATPase activity|enzyme binding|nucleic acid binding|nucleotide binding			ovary(2)|large_intestine(1)|skin(1)	4	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)														---	---	---	---
ACIN1	22985	broad.mit.edu	37	14	23562791	23562791	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23562791delA	uc001wit.3	-						ACIN1_uc010akg.2_Intron|ACIN1_uc010tnj.1_Intron|C14orf119_uc001wiu.2_5'Flank	NM_014977	NP_055792			apoptotic chromatin condensation inducer 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	23717512	23717513	+	IGR	DEL	TT	-	-	rs74604409		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23717512_23717513delTT								SLC7A8 (64663 upstream) : HOMEZ (25331 downstream)																																			---	---	---	---
HOMEZ	57594	broad.mit.edu	37	14	23745310	23745310	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23745310delA	uc001wja.2	-	2	1275	c.1127delT	c.(1126-1128)TTAfs	p.L376fs	HOMEZ_uc001wjb.2_Frame_Shift_Del_p.L378fs	NM_020834	NP_065885	Q8IX15	HOMEZ_HUMAN	homeodomain leucine zipper protein	376	Homeobox 2.					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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	24340424	24340424	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24340424delA								DHRS2 (225578 upstream) : C14orf165 (51035 downstream)																																			---	---	---	---
LRRC16B	90668	broad.mit.edu	37	14	24526941	24526941	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24526941delG	uc001wlj.2	+							NM_138360	NP_612369			leucine rich repeat containing 16B											ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(265;0.019)												OREG0022615	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RABGGTA	5875	broad.mit.edu	37	14	24739364	24739364	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24739364delG	uc001wof.2	-						RABGGTA_uc001woe.2_5'Flank|RABGGTA_uc001wog.2_Intron|RABGGTA_uc001woh.2_Intron|RABGGTA_uc001woi.2_Intron	NM_004581	NP_004572			Rab geranylgeranyltransferase alpha						visual perception		Rab geranylgeranyltransferase activity|zinc ion binding				0				GBM - Glioblastoma multiforme(265;0.0184)														---	---	---	---
STXBP6	29091	broad.mit.edu	37	14	25303208	25303208	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25303208delT	uc001wpu.2	-						STXBP6_uc001wpv.2_Intron|STXBP6_uc001wpw.2_Intron|STXBP6_uc001wpx.1_Intron	NM_014178	NP_054897			amisyn						vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	25647137	25647138	+	IGR	INS	-	C	C	rs149512178	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25647137_25647138insC								STXBP6 (127966 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	25706475	25706476	+	IGR	DEL	AC	-	-	rs138831101		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25706475_25706476delAC								STXBP6 (187304 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26860267	26860267	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26860267delA								None (None upstream) : NOVA1 (54823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28623718	28623719	+	IGR	INS	-	GA	GA	rs142893558	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28623718_28623719insGA								None (None upstream) : FOXG1 (612568 downstream)																																			---	---	---	---
C14orf23	387978	broad.mit.edu	37	14	29261305	29261305	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29261305delA	uc001wqf.2	+	3	446	c.342delA	c.(340-342)CTAfs	p.L114fs		NR_026731				RecName: Full=Uncharacterized protein C14orf23;											central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	29468499	29468499	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29468499delA								C14orf23 (204500 upstream) : PRKD1 (577190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	29487667	29487668	+	IGR	DEL	TA	-	-	rs11844846	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29487667_29487668delTA								C14orf23 (223668 upstream) : PRKD1 (558021 downstream)																																			---	---	---	---
G2E3	55632	broad.mit.edu	37	14	31070941	31070942	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31070941_31070942insA	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																		---	---	---	---
G2E3	55632	broad.mit.edu	37	14	31071214	31071214	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31071214delA	uc001wqk.2	+	10	1041	c.887delA	c.(886-888)CAAfs	p.Q296fs	G2E3_uc010tpe.1_Frame_Shift_Del_p.Q211fs|G2E3_uc010tpf.1_Frame_Shift_Del_p.Q250fs	NM_017769	NP_060239	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin ligase	296					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																		---	---	---	---
G2E3	55632	broad.mit.edu	37	14	31074772	31074772	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31074772delA	uc001wqk.2	+	11	1226	c.1072delA	c.(1072-1074)AAAfs	p.K358fs	G2E3_uc010tpe.1_Intron|G2E3_uc010tpf.1_Frame_Shift_Del_p.K312fs	NM_017769	NP_060239	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin ligase	358					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																		---	---	---	---
G2E3	55632	broad.mit.edu	37	14	31080860	31080860	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31080860delT	uc001wqk.2	+						G2E3_uc010tpf.1_Intron|G2E3_uc001wql.1_5'UTR	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																		---	---	---	---
STRN3	29966	broad.mit.edu	37	14	31470747	31470747	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31470747delA	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)														---	---	---	---
AP4S1	11154	broad.mit.edu	37	14	31553965	31553965	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31553965delT	uc001wqy.3	+						AP4S1_uc001wqw.3_Intron|AP4S1_uc001wqx.3_Intron|AP4S1_uc010amh.2_Intron|AP4S1_uc001wqz.3_Intron	NM_001128126	NP_001121598			adaptor-related protein complex 4, sigma 1							coated pit|Golgi apparatus	protein transporter activity				0	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.221)	GBM - Glioblastoma multiforme(265;0.00553)														---	---	---	---
HEATR5A	25938	broad.mit.edu	37	14	31772316	31772316	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31772316delA	uc001wrf.3	-						HEATR5A_uc010ami.2_Intron	NM_015473	NP_056288			HEAT repeat containing 5A								binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)														---	---	---	---
NUBPL	80224	broad.mit.edu	37	14	32295067	32295067	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32295067delT	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)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	32976748	32976749	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32976748_32976749delTT	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	32979360	32979361	+	Intron	INS	-	T	T	rs147453764	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32979360_32979361insT	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	33020848	33020849	+	Intron	INS	-	TTTG	TTTG	rs142970529	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33020848_33020849insTTTG	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	33153950	33153950	+	Intron	DEL	T	-	-	rs71822752		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33153950delT	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	33179814	33179814	+	Intron	DEL	C	-	-	rs10146478	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33179814delC	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)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	33415552	33415553	+	Intron	INS	-	CA	CA	rs5807694		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33415552_33415553insCA	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	34669510	34669513	+	IGR	DEL	GATG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34669510_34669513delGATG								EGLN3 (249223 upstream) : C14orf147 (232632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	34875575	34875576	+	IGR	INS	-	T	T	rs147674730	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34875575_34875576insT								EGLN3 (455288 upstream) : C14orf147 (26569 downstream)																																			---	---	---	---
SNX6	58533	broad.mit.edu	37	14	35098346	35098346	+	Intron	DEL	C	-	-	rs28454795	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35098346delC	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	35296292	35296293	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35296292_35296293delTC	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	35473293	35473295	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35473293_35473295delAAA	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)														---	---	---	---
FAM177A1	283635	broad.mit.edu	37	14	35550218	35550218	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35550218delT	uc001wsp.2	+						FAM177A1_uc001wsq.2_Intron	NM_001079519	NP_001072987			hypothetical protein LOC283635 isoform 2												0																		---	---	---	---
KIAA0391	9692	broad.mit.edu	37	14	35617625	35617625	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35617625delT	uc001wsy.1	+						KIAA0391_uc010tps.1_Intron|KIAA0391_uc001wsz.1_Intron|KIAA0391_uc001wta.2_Intron|KIAA0391_uc001wtb.1_Intron|KIAA0391_uc001wtc.1_Intron	NM_014672	NP_055487			mitochondrial RNase P protein 3 precursor						tRNA processing	mitochondrion					0	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)														---	---	---	---
PSMA6	5687	broad.mit.edu	37	14	35777176	35777176	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35777176delA	uc001wtd.2	+						KIAA0391_uc001wta.2_Intron|PSMA6_uc010tpt.1_Intron|PSMA6_uc010tpu.1_Intron	NM_002791	NP_002782			proteasome alpha 6 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|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)														---	---	---	---
PSMA6	5687	broad.mit.edu	37	14	35786430	35786430	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35786430delT	uc001wtd.2	+						KIAA0391_uc001wta.2_Intron|PSMA6_uc010tpt.1_Intron|PSMA6_uc010tpu.1_Intron	NM_002791	NP_002782			proteasome alpha 6 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|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)														---	---	---	---
NFKBIA	4792	broad.mit.edu	37	14	35871169	35871169	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35871169delT	uc001wtf.3	-	6					NFKBIA_uc001wte.3_3'UTR|NFKBIA_uc001wtg.3_3'UTR|NFKBIA_uc010amo.2_RNA	NM_020529	NP_065390			nuclear factor of kappa light polypeptide gene						anti-apoptosis|apoptosis|cellular response to cold|cytoplasmic sequestering of NF-kappaB|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of DNA binding|negative regulation of lipid storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|I-kappaB/NF-kappaB complex|nucleus|plasma membrane	identical protein binding|NF-kappaB binding|nuclear localization sequence binding|ubiquitin protein ligase binding			breast(2)	2	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	35973011	35973011	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35973011delT								NFKBIA (99051 upstream) : INSM2 (30237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	35986421	35986421	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35986421delA								NFKBIA (112461 upstream) : INSM2 (16827 downstream)																																			---	---	---	---
RALGAPA1	253959	broad.mit.edu	37	14	36039716	36039716	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36039716delT	uc001wti.2	-						RALGAPA1_uc010amp.2_Intron|RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron	NM_014990	NP_055805			Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4																		---	---	---	---
RALGAPA1	253959	broad.mit.edu	37	14	36094781	36094781	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36094781delA	uc001wti.2	-						RALGAPA1_uc010amp.2_Intron|RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron	NM_014990	NP_055805			Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4																		---	---	---	---
MBIP	51562	broad.mit.edu	37	14	36777407	36777407	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36777407delA	uc001wtm.2	-						MBIP_uc001wto.2_Intron|MBIP_uc010tpy.1_Intron|MBIP_uc001wtn.2_Intron	NM_016586	NP_057670			MAP3K12 binding inhibitory protein 1 isoform 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	36846944	36846945	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36846944_36846945insA								MBIP (57062 upstream) : SFTA3 (95551 downstream)																																			---	---	---	---
SFTA3	253970	broad.mit.edu	37	14	36960302	36960302	+	Intron	DEL	T	-	-	rs77224944	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36960302delT	uc001wtr.2	-						SFTA3_uc001wtq.2_Intron|SFTA3_uc001wts.2_Intron	NM_001101341	NP_001094811			surfactant associated 3												0																		---	---	---	---
SLC25A21	89874	broad.mit.edu	37	14	37297307	37297326	+	Intron	DEL	ATGTGAGGTCTTCTGGGACC	-	-	rs6145300		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37297307_37297326delATGTGAGGTCTTCTGGGACC	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)														---	---	---	---
SLC25A21	89874	broad.mit.edu	37	14	37437038	37437039	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37437038_37437039delTG	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	37754802	37754803	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37754802_37754803delTT	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	38327931	38327931	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38327931delT	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38591278	38591279	+	IGR	INS	-	TG	TG	rs146585047	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38591278_38591279insTG								FOXA1 (526789 upstream) : SSTR1 (85925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	39079483	39079483	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39079483delA								CLEC14A (353909 upstream) : SEC23A (421640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	39082628	39082629	+	IGR	DEL	TT	-	-	rs79955671		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39082628_39082629delTT								CLEC14A (357054 upstream) : SEC23A (418494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	39133093	39133093	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39133093delA								CLEC14A (407519 upstream) : SEC23A (368030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41769377	41769378	+	IGR	DEL	TT	-	-	rs71440730	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41769377_41769378delTT								None (None upstream) : LRFN5 (307386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41967153	41967153	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41967153delT								None (None upstream) : LRFN5 (109611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	42652561	42652561	+	IGR	DEL	A	-	-	rs11314412		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42652561delA								LRFN5 (278811 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43809432	43809433	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43809432_43809433delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43978703	43978703	+	IGR	DEL	G	-	-	rs78308216		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43978703delG								None (None upstream) : FSCB (994652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44165894	44165896	+	IGR	DEL	AAA	-	-	rs77971740		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44165894_44165896delAAA								None (None upstream) : FSCB (807459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44708915	44708915	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44708915delT								None (None upstream) : FSCB (264440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44813662	44813662	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44813662delA								None (None upstream) : FSCB (159693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	45338583	45338586	+	IGR	DEL	GTGT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45338583_45338586delGTGT								FSCB (362084 upstream) : C14orf28 (27921 downstream)																																			---	---	---	---
KLHL28	54813	broad.mit.edu	37	14	45406330	45406331	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45406330_45406331insT	uc001wvq.2	-						KLHL28_uc001wvr.2_Intron	NM_017658	NP_060128			BTB (POZ) domain containing 5											ovary(1)	1																		---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45475110	45475110	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45475110delT	uc001wvv.2	+						FAM179B_uc001wvw.2_Intron|FAM179B_uc010anc.2_Intron|FAM179B_uc001wvu.2_Intron	NM_015091	NP_055906			hypothetical protein LOC23116								binding			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
C14orf106	55320	broad.mit.edu	37	14	45686484	45686484	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45686484delA	uc001wwf.2	-							NM_018353	NP_060823			chromosome 14 open reading frame 106						cell division|CenH3-containing nucleosome assembly at centromere|mitosis	chromosome, centromeric region|nucleoplasm	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	45784955	45784955	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45784955delT								C14orf106 (62350 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	45997196	45997196	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45997196delA								C14orf106 (274591 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46125590	46125590	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46125590delT								C14orf106 (402985 upstream) : RPL10L (994632 downstream)																																			---	---	---	---
MDGA2	161357	broad.mit.edu	37	14	47338140	47338140	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47338140delT	uc001wwj.3	-						MDGA2_uc001wwh.3_Intron|MDGA2_uc001wwi.3_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	47942101	47942101	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47942101delT	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	48286874	48286874	+	IGR	DEL	T	-	-	rs139256511	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48286874delT								MDGA2 (142886 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	48388149	48388149	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48388149delA								MDGA2 (244161 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	48438118	48438118	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48438118delT								MDGA2 (294130 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	48674094	48674094	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48674094delT								MDGA2 (530106 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	48686971	48686972	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48686971_48686972delTC								MDGA2 (542983 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	49785521	49785522	+	IGR	INS	-	GAAGGAAGGAAGGAAG	GAAGGAAGGAAGGAAG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49785521_49785522insGAAGGAAGGAAGGAAG								None (None upstream) : SDCCAG1 (247505 downstream)																																			---	---	---	---
SDCCAG1	9147	broad.mit.edu	37	14	50247296	50247296	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50247296delA	uc010anj.1	-						KLHDC2_uc001wwx.2_Intron|KLHDC2_uc001wwy.2_Intron|KLHDC2_uc010anp.2_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-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50470550_50470551delTT	uc001wxi.1	-						uc010tqj.1_5'Flank	NM_001012706	NP_001012724			hypothetical protein LOC283551												0																		---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50935639	50935639	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50935639delA	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)																	---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50952368	50952368	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50952368delA	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)																	---	---	---	---
ABHD12B	145447	broad.mit.edu	37	14	51339941	51339941	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51339941delT	uc001wys.2	+						ABHD12B_uc001wyq.2_Intron|ABHD12B_uc001wyr.2_Intron|ABHD12B_uc010any.2_Intron	NM_181533	NP_853511			abhydrolase domain containing 12B isoform b								hydrolase activity			breast(1)	1	all_epithelial(31;0.00481)|Breast(41;0.148)																	---	---	---	---
PYGL	5836	broad.mit.edu	37	14	51374921	51374922	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51374921_51374922insA	uc001wyu.2	-						PYGL_uc010tqq.1_Intron|PYGL_uc001wyv.2_Intron|PYGL_uc001wyt.2_Intron	NM_002863	NP_002854			liver glycogen phosphorylase isoform 1						glucose homeostasis|glucose metabolic process|glycogen catabolic process	cytosol|soluble fraction	AMP binding|ATP binding|bile acid binding|drug binding|glucose binding|glycogen phosphorylase activity|protein homodimerization activity|purine base binding|pyridoxal phosphate binding			skin(1)	1	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)|Pyridoxal Phosphate(DB00114)|Riboflavin(DB00140)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	51590418	51590427	+	IGR	DEL	GTGTGTGTGT	-	-	rs72380452		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51590418_51590427delGTGTGTGTGT								TRIM9 (27996 upstream) : TMX1 (116459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	51591297	51591298	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51591297_51591298insA								TRIM9 (28875 upstream) : TMX1 (115588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	51744162	51744162	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51744162delA								TMX1 (19792 upstream) : FRMD6 (211693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	52251719	52251719	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52251719delA								FRMD6 (54277 upstream) : GNG2 (62233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	52642169	52642169	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52642169delA								NID2 (106223 upstream) : PTGDR (92262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	52690295	52690296	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52690295_52690296delTC								NID2 (154349 upstream) : PTGDR (44135 downstream)																																			---	---	---	---
TXNDC16	57544	broad.mit.edu	37	14	52985809	52985809	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52985809delA	uc001wzs.2	-						TXNDC16_uc010tqu.1_Intron|TXNDC16_uc010aoe.2_Intron	NM_020784	NP_065835			thioredoxin domain containing 16 isoform 1						cell redox homeostasis	extracellular region					0	Breast(41;0.0716)																	---	---	---	---
GPR137C	283554	broad.mit.edu	37	14	53052553	53052553	+	Intron	DEL	A	-	-	rs79691788		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53052553delA	uc001wzu.3	+						GPR137C_uc001wzt.3_Intron	NM_001099652	NP_001093122			G protein-coupled receptor 137C							integral to membrane					0	Breast(41;0.0716)																	---	---	---	---
GPR137C	283554	broad.mit.edu	37	14	53101641	53101641	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																	---	---	---	---
ERO1L	30001	broad.mit.edu	37	14	53153284	53153291	+	Intron	DEL	TGGTAGAT	-	-	rs72002747		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53153284_53153291delTGGTAGAT	uc001wzv.2	-						ERO1L_uc001wzw.2_Intron|ERO1L_uc010aof.2_Intron	NM_014584	NP_055399			ERO1-like precursor						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)																	---	---	---	---
STYX	6815	broad.mit.edu	37	14	53235544	53235545	+	Intron	DEL	TA	-	-	rs2274274	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53235544_53235545delTA	uc010tqy.1	+						STYX_uc001xaa.2_Intron	NM_001130701	NP_001124173			serine/threonine/tyrosine interacting protein						protein dephosphorylation|spermatogenesis	cytoplasm	protein tyrosine/serine/threonine phosphatase activity				0	Breast(41;0.176)																	---	---	---	---
FERMT2	10979	broad.mit.edu	37	14	53341920	53341920	+	Intron	DEL	A	-	-	rs141261474		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53341920delA	uc001xad.2	-						FERMT2_uc001xac.2_Intron|FERMT2_uc001xae.2_Intron|FERMT2_uc001xaf.2_Intron	NM_006832	NP_006823			fermitin family homolog 2 isoform 1						actin cytoskeleton organization|cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytosol|focal adhesion|stress fiber	binding				0	Breast(41;0.0342)																	---	---	---	---
FERMT2	10979	broad.mit.edu	37	14	53396377	53396378	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53396377_53396378delCT	uc001xad.2	-						FERMT2_uc001xac.2_Intron|FERMT2_uc001xae.2_Intron|FERMT2_uc001xaf.2_Intron	NM_006832	NP_006823			fermitin family homolog 2 isoform 1						actin cytoskeleton organization|cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytosol|focal adhesion|stress fiber	binding				0	Breast(41;0.0342)																	---	---	---	---
DDHD1	80821	broad.mit.edu	37	14	53513440	53513441	+	3'UTR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53513440_53513441delAA	uc001xai.2	-	13					DDHD1_uc001xaj.2_3'UTR|DDHD1_uc001xah.2_3'UTR|DDHD1_uc001xag.2_3'UTR	NM_001160148	NP_001153620			DDHD domain containing 1 isoform c						lipid catabolic process	cytoplasm	hydrolase activity|metal ion binding			ovary(2)	2	Breast(41;0.037)																	---	---	---	---
DDHD1	80821	broad.mit.edu	37	14	53527795	53527795	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53527795delA	uc001xai.2	-						DDHD1_uc001xaj.2_Intron|DDHD1_uc001xah.2_Intron|DDHD1_uc001xag.2_Intron|DDHD1_uc001xak.1_Intron	NM_001160148	NP_001153620			DDHD domain containing 1 isoform c						lipid catabolic process	cytoplasm	hydrolase activity|metal ion binding			ovary(2)	2	Breast(41;0.037)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	53670359	53670359	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53670359delA								DDHD1 (50313 upstream) : BMP4 (746098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54098513	54098513	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54098513delA								DDHD1 (478467 upstream) : BMP4 (317944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54346761	54346761	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54346761delA								DDHD1 (726715 upstream) : BMP4 (69696 downstream)																																			---	---	---	---
CNIH	10175	broad.mit.edu	37	14	54894605	54894605	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54894605delA	uc001xat.1	-						CNIH_uc001xav.1_Intron	NM_005776	NP_005767			cornichon-like						immune response|intracellular signal transduction|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane					0				GBM - Glioblastoma multiforme(112;0.00341)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	54916140	54916141	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54916140_54916141insG								CNIH (7992 upstream) : GMFB (25068 downstream)																																			---	---	---	---
GCH1	2643	broad.mit.edu	37	14	55316058	55316058	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55316058delA	uc001xbh.1	-						GCH1_uc001xbi.1_Intron|GCH1_uc001xbj.1_Intron|GCH1_uc001xbk.1_Intron|GCH1_uc010aol.1_Intron|GCH1_uc001xbl.1_Intron	NM_001024024	NP_001019195			GTP cyclohydrolase 1 isoform 1						dopamine biosynthetic process|GTP catabolic process|neuromuscular process controlling posture|nitric oxide biosynthetic process|positive regulation of nitric-oxide synthase activity|protein homooligomerization|response to interferon-gamma|response to lipopolysaccharide|response to pain|response to tumor necrosis factor|tetrahydrobiopterin biosynthetic process|tetrahydrofolate biosynthetic process	cytoplasmic vesicle|cytosol|nuclear membrane|protein complex	GTP binding|GTP cyclohydrolase I activity|protein homodimerization activity|zinc ion binding			skin(1)	1																		---	---	---	---
GCH1	2643	broad.mit.edu	37	14	55352630	55352630	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55352630delA	uc001xbh.1	-						GCH1_uc001xbi.1_Intron|GCH1_uc001xbj.1_Intron|GCH1_uc001xbk.1_Intron|GCH1_uc010aol.1_Intron|GCH1_uc001xbl.1_Intron	NM_001024024	NP_001019195			GTP cyclohydrolase 1 isoform 1						dopamine biosynthetic process|GTP catabolic process|neuromuscular process controlling posture|nitric oxide biosynthetic process|positive regulation of nitric-oxide synthase activity|protein homooligomerization|response to interferon-gamma|response to lipopolysaccharide|response to pain|response to tumor necrosis factor|tetrahydrobiopterin biosynthetic process|tetrahydrofolate biosynthetic process	cytoplasmic vesicle|cytosol|nuclear membrane|protein complex	GTP binding|GTP cyclohydrolase I activity|protein homodimerization activity|zinc ion binding			skin(1)	1																		---	---	---	---
WDHD1	11169	broad.mit.edu	37	14	55429903	55429907	+	Intron	DEL	GGGGG	-	-	rs61977047		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55429903_55429907delGGGGG	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	55474134	55474135	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55474134_55474135insC	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																		---	---	---	---
WDHD1	11169	broad.mit.edu	37	14	55480040	55480040	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55480040delA	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	55684771	55684771	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55684771delA								DLGAP5 (26375 upstream) : FBXO34 (53250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	55728026	55728026	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55728026delA								DLGAP5 (69630 upstream) : FBXO34 (9995 downstream)																																			---	---	---	---
FBXO34	55030	broad.mit.edu	37	14	55880258	55880258	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55880258delT	uc001xbv.2	+						KIAA0831_uc001xbx.1_5'Flank	NM_152231				F-box only protein 34											ovary(2)|lung(2)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	57281474	57281475	+	Intron	INS	-	GT	GT	rs148090260		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57281474_57281475insGT	uc001xcr.1	+											Homo sapiens cDNA clone IMAGE:5492202, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	57550098	57550099	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57550098_57550099insA								OTX2 (272914 upstream) : EXOC5 (119097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	57561742	57561742	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57561742delT								OTX2 (284558 upstream) : EXOC5 (107454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	57816997	57816998	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57816997_57816998delTT								MUDENG (60201 upstream) : NAA30 (40273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	58408428	58408428	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58408428delA								SLC35F4 (344813 upstream) : C14orf37 (62381 downstream)																																			---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58604644	58604644	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58604644delT	uc001xdc.2	-						C14orf37_uc010tro.1_Intron|C14orf37_uc001xdd.2_Intron|C14orf37_uc001xde.2_Intron	NM_001001872	NP_001001872			hypothetical protein LOC145407 precursor							integral to membrane	binding				0																		---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58604646	58604646	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58604646delA	uc001xdc.2	-						C14orf37_uc010tro.1_Intron|C14orf37_uc001xdd.2_Intron|C14orf37_uc001xde.2_Intron	NM_001001872	NP_001001872			hypothetical protein LOC145407 precursor							integral to membrane	binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	59026869	59026872	+	IGR	DEL	AAAA	-	-	rs72207484		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59026869_59026872delAAAA								KIAA0586 (11321 upstream) : DACT1 (73914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	60785474	60785475	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60785474_60785475insA								PPM1A (19671 upstream) : C14orf39 (117200 downstream)																																			---	---	---	---
C14orf39	317761	broad.mit.edu	37	14	60933595	60933595	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60933595delA	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)														---	---	---	---
C14orf39	317761	broad.mit.edu	37	14	60950600	60950600	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
SIX1	6495	broad.mit.edu	37	14	61113356	61113356	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61113356delA	uc001xfb.3	-							NM_005982	NP_005973			SIX homeobox 1						branching involved in ureteric bud morphogenesis|embryonic cranial skeleton morphogenesis|epithelial cell differentiation|inner ear morphogenesis|mesonephric tubule formation|metanephric mesenchyme development|myoblast migration|negative regulation of neuron apoptosis|organ induction|pattern specification process|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of ureteric bud formation|protein localization to nucleus|regulation of branch elongation involved in ureteric bud branching|regulation of neuron differentiation|skeletal muscle tissue development|thymus development|thyroid gland development	nucleolus|transcription factor complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0201)														---	---	---	---
MNAT1	4331	broad.mit.edu	37	14	61311916	61311916	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61311916delT	uc001xfd.2	+						MNAT1_uc001xfe.2_Intron	NM_002431	NP_002422			menage a trois 1 (CAK assembly factor)						cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein complex assembly|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cytoplasm|holo TFIIH complex	protein N-terminus binding|zinc ion binding			ovary(1)|lung(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.0174)									Direct_reversal_of_damage|NER					---	---	---	---
SLC38A6	145389	broad.mit.edu	37	14	61512604	61512605	+	Intron	DEL	AA	-	-	rs75772430		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61512604_61512605delAA	uc001xfg.1	+						SLC38A6_uc001xfh.1_Intron|SLC38A6_uc001xfi.2_Intron|SLC38A6_uc001xfj.1_Intron|SLC38A6_uc001xfk.2_Intron|SLC38A6_uc010trz.1_Intron	NM_153811	NP_722518			solute carrier family 38, member 6						amino acid transport|sodium ion transport	integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(108;0.0981)														---	---	---	---
SLC38A6	145389	broad.mit.edu	37	14	61529216	61529217	+	Intron	DEL	TT	-	-	rs140162517		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61529216_61529217delTT	uc001xfh.1	+						SLC38A6_uc001xfi.2_Intron|SLC38A6_uc001xfk.2_Intron|SLC38A6_uc010trz.1_Intron	NM_153811	NP_722518			solute carrier family 38, member 6						amino acid transport|sodium ion transport	integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(108;0.0981)														---	---	---	---
PRKCH	5583	broad.mit.edu	37	14	61728386	61728387	+	Intron	INS	-	T	T	rs138788544	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61728386_61728387insT	uc010tsa.1	+							NM_006255	NP_006246			protein kinase C, eta						intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	62145453	62145454	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62145453_62145454insA								PRKCH (127758 upstream) : HIF1A (16665 downstream)																																			---	---	---	---
HIF1A	3091	broad.mit.edu	37	14	62212360	62212360	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62212360delA	uc001xfq.2	+						HIF1A_uc001xfr.2_Intron|HIF1A_uc001xfs.2_Intron	NM_001530	NP_001521			hypoxia-inducible factor 1, alpha subunit						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	62372479	62372479	+	IGR	DEL	C	-	-	rs10610485		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62372479delC								SNAPC1 (109334 upstream) : SYT16 (81324 downstream)																																			---	---	---	---
SYT16	83851	broad.mit.edu	37	14	62522775	62522775	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62522775delT	uc001xfu.1	+						SYT16_uc010tsd.1_Intron	NM_031914	NP_114120			synaptotagmin XIV-like											central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)														---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63242168	63242168	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63242168delA	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	63455098	63455098	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63455098delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	63834525	63834525	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63834525delA								GPHB5 (49962 upstream) : PPP2R5E (6830 downstream)																																			---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63969871	63969871	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63969871delT	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)														---	---	---	---
WDR89	112840	broad.mit.edu	37	14	64072727	64072727	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64072727delT	uc001xgh.2	-						WDR89_uc001xgi.2_Intron	NM_001008726	NP_001008726			WD repeat domain 89												0				OV - Ovarian serous cystadenocarcinoma(108;0.00543)|all cancers(60;0.0181)|BRCA - Breast invasive adenocarcinoma(234;0.101)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	64114119	64114119	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64114119delA								WDR89 (5528 upstream) : SGPP1 (36818 downstream)																																			---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64587949	64587949	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64587949delA	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron|SYNE2_uc010apy.2_Intron|SYNE2_uc010apz.1_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)														---	---	---	---
C14orf50	145376	broad.mit.edu	37	14	65039221	65039221	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65039221delT	uc001xhl.1	+							NM_172365	NP_758953			hypothetical protein LOC145376											skin(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00382)|all cancers(60;0.00427)|BRCA - Breast invasive adenocarcinoma(234;0.0488)														---	---	---	---
PLEKHG3	26030	broad.mit.edu	37	14	65204502	65204502	+	Intron	DEL	C	-	-	rs77641956		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65204502delC	uc001xho.1	+						PLEKHG3_uc001xhn.1_Intron|PLEKHG3_uc001xhp.2_Intron|PLEKHG3_uc010aqh.1_Intron|PLEKHG3_uc001xhq.1_5'Flank	NM_015549	NP_056364			pleckstrin homology domain containing, family G,						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)														---	---	---	---
FNTB	2342	broad.mit.edu	37	14	65398251	65398251	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65398251delA	uc010tsl.1	+						CHURC1_uc010tsj.1_Intron|CHURC1_uc010tsk.1_Intron|FNTB_uc010tsm.1_Intron|CHURC1_uc001xhv.1_Intron|CHURC1_uc001xhw.1_Intron	NM_002028	NP_002019			farnesyltransferase, CAAX box, beta						protein farnesylation	microtubule associated complex	protein binding|protein farnesyltransferase activity			ovary(1)	1				all cancers(60;0.00115)|OV - Ovarian serous cystadenocarcinoma(108;0.00412)|BRCA - Breast invasive adenocarcinoma(234;0.011)														---	---	---	---
MAX	4149	broad.mit.edu	37	14	65571717	65571718	+	5'Flank	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65571717_65571718insG	uc001xif.1	-						MAX_uc001xic.1_5'Flank|MAX_uc001xie.1_5'Flank|MAX_uc010aql.1_5'Flank|MAX_uc001xig.1_5'Flank|MAX_uc001xih.1_5'Flank|MAX_uc001xii.1_5'Flank|MAX_uc001xij.1_5'Flank|MAX_uc001xik.2_5'Flank	NM_002382	NP_002373			MAX protein isoform a						transcription from RNA polymerase II promoter	cytoplasm|MLL1 complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			lung(1)	1				all cancers(60;0.000776)|OV - Ovarian serous cystadenocarcinoma(108;0.00359)|BRCA - Breast invasive adenocarcinoma(234;0.00999)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	65622373	65622374	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65622373_65622374delAA								MAX (53146 upstream) : LOC645431 (254939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	65816812	65816812	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65816812delA								MAX (247585 upstream) : LOC645431 (60501 downstream)																																			---	---	---	---
FUT8	2530	broad.mit.edu	37	14	66042344	66042344	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66042344delT	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	66149225	66149225	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66149225delA	uc001xin.2	+						FUT8_uc001xio.2_Intron|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Intron|FUT8_uc001xiq.2_Intron|FUT8_uc001xis.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	66752427	66752428	+	IGR	INS	-	CACA	CACA	rs35579291		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66752427_66752428insCACA								FUT8 (542466 upstream) : C14orf53 (200681 downstream)																																			---	---	---	---
MPP5	64398	broad.mit.edu	37	14	67762040	67762040	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67762040delA	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	68070719	68070720	+	IGR	INS	-	T	T	rs111607022		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68070719_68070720insT								PIGH (3702 upstream) : ARG2 (15859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	68079851	68079851	+	IGR	DEL	T	-	-	rs35284636		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68079851delT								PIGH (12834 upstream) : ARG2 (6728 downstream)																																			---	---	---	---
VTI1B	10490	broad.mit.edu	37	14	68128897	68128899	+	Intron	DEL	AAA	-	-	rs72397926		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68128897_68128899delAAA	uc001xjt.2	-						VTI1B_uc010aqp.2_Intron|VTI1B_uc001xju.2_Intron	NM_006370	NP_006361			vesicle transport through interaction with						cell proliferation|cellular membrane fusion|intracellular protein transport|vesicle docking involved in exocytosis	endomembrane system|integral to membrane					0				all cancers(60;0.000344)|OV - Ovarian serous cystadenocarcinoma(108;0.00212)|BRCA - Breast invasive adenocarcinoma(234;0.00941)														---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68654963	68654963	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68654963delT	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	68923014	68923015	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68923014_68923015insT	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	69041609	69041609	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69041609delG	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					---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	69057051	69057051	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69057051delA	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					---	---	---	---
ZFP36L1	677	broad.mit.edu	37	14	69260002	69260002	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69260002delA	uc001xkh.1	-						ZFP36L1_uc001xki.1_5'Flank	NM_004926	NP_004917			butyrate response factor 1						regulation of mRNA stability	cytosol|nucleus	DNA binding|mRNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	69321595	69321595	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69321595delT								C14orf181 (58405 upstream) : ACTN1 (19246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	69469597	69469597	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69469597delA								ACTN1 (23514 upstream) : DCAF5 (48041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	69486078	69486079	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69486078_69486079insA								ACTN1 (39995 upstream) : DCAF5 (31559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	69494353	69494353	+	IGR	DEL	A	-	-	rs35143122		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69494353delA								ACTN1 (48270 upstream) : DCAF5 (23285 downstream)																																			---	---	---	---
SLC39A9	55334	broad.mit.edu	37	14	69902398	69902398	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69902398delT	uc001xle.2	+						SLC39A9_uc010aqx.2_Intron|SLC39A9_uc001xlf.3_Intron|SLC39A9_uc001xlg.3_Intron	NM_018375	NP_060845			solute carrier family 39 (zinc transporter),						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	70057475	70057475	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70057475delA								C14orf162 (19557 upstream) : KIAA0247 (20835 downstream)																																			---	---	---	---
SMOC1	64093	broad.mit.edu	37	14	70486869	70486869	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70486869delT	uc001xls.1	+						SMOC1_uc001xlt.1_Intron	NM_022137	NP_071420			secreted modular calcium-binding protein 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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	70784181	70784182	+	IGR	INS	-	GT	GT	rs151284709	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70784181_70784182insGT								ADAM21P1 (69663 upstream) : COX16 (7617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	71021259	71021260	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71021259_71021260delAC								ADAM20 (19527 upstream) : MED6 (29698 downstream)																																			---	---	---	---
MAP3K9	4293	broad.mit.edu	37	14	71214836	71214838	+	Intron	DEL	AAT	-	-	rs67586961	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71214836_71214838delAAT	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	71386630	71386630	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71386630delA	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)														---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	72095663	72095663	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72095663delT	uc001xms.2	+						SIPA1L1_uc001xmt.2_Intron|SIPA1L1_uc001xmu.2_Intron|SIPA1L1_uc001xmv.2_Intron|SIPA1L1_uc010ttm.1_Intron	NM_015556	NP_056371			signal-induced proliferation-associated 1 like						actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)														---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	72129027	72129027	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72129027delA	uc001xms.2	+						SIPA1L1_uc001xmt.2_Intron|SIPA1L1_uc001xmu.2_Intron|SIPA1L1_uc001xmv.2_Intron|SIPA1L1_uc010ttm.1_Intron	NM_015556	NP_056371			signal-induced proliferation-associated 1 like						actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	72371613	72371614	+	IGR	INS	-	T	T	rs61159722	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72371613_72371614insT								SIPA1L1 (165495 upstream) : RGS6 (27542 downstream)																																			---	---	---	---
RGS6	9628	broad.mit.edu	37	14	72493935	72493936	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72493935_72493936delAG	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron	NM_004296	NP_004287			regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)														---	---	---	---
DPF3	8110	broad.mit.edu	37	14	73300277	73300277	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73300277delA	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)														---	---	---	---
DPF3	8110	broad.mit.edu	37	14	73360711	73360711	+	Intron	DEL	T	-	-	rs76743039		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73360711delT	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)														---	---	---	---
ZFYVE1	53349	broad.mit.edu	37	14	73441450	73441451	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73441450_73441451insC	uc001xnm.2	-						ZFYVE1_uc001xnl.2_Intron|ZFYVE1_uc010arj.2_Intron	NM_021260	NP_067083			zinc finger, FYVE domain containing 1 isoform 1							endoplasmic reticulum|Golgi stack|perinuclear region of cytoplasm	1-phosphatidylinositol binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|zinc ion binding			skin(1)	1		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)														---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73563894	73563895	+	Intron	INS	-	TTTTC	TTTTC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73563894_73563895insTTTTC	uc001xno.2	+						RBM25_uc001xnn.3_Intron|RBM25_uc010ttu.1_Intron|RBM25_uc001xnp.2_Intron	NM_021239	NP_067062			RNA binding motif protein 25						apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)														---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73578581	73578581	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73578581delA	uc001xno.2	+						RBM25_uc010ttu.1_Intron|RBM25_uc001xnp.2_Intron	NM_021239	NP_067062			RNA binding motif protein 25						apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	73691306	73691306	+	IGR	DEL	T	-	-	rs35493156		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73691306delT								PSEN1 (908 upstream) : PAPLN (12899 downstream)																																			---	---	---	---
PAPLN	89932	broad.mit.edu	37	14	73703600	73703603	+	5'Flank	DEL	AGAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73703600_73703603delAGAA	uc010ttx.1	+						PAPLN_uc001xnw.3_5'Flank|PAPLN_uc010arl.2_5'Flank|PAPLN_uc010ttw.1_5'Flank|PAPLN_uc010tty.1_5'Flank	NM_173462	NP_775733			papilin							proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase inhibitor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)														---	---	---	---
PAPLN	89932	broad.mit.edu	37	14	73718481	73718481	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73718481delG	uc010ttx.1	+	8	943	c.780delG	c.(778-780)GAGfs	p.E260fs	PAPLN_uc001xnw.3_Frame_Shift_Del_p.E233fs|PAPLN_uc010arl.2_RNA|PAPLN_uc010ttw.1_RNA|PAPLN_uc010tty.1_Frame_Shift_Del_p.E260fs	NM_173462	NP_775733	O95428	PPN_HUMAN	papilin	260						proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase inhibitor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	74096352	74096353	+	IGR	INS	-	T	T	rs72316955		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74096352_74096353insT								ACOT6 (9762 upstream) : DNAL1 (15225 downstream)																																			---	---	---	---
C14orf43	91748	broad.mit.edu	37	14	74205773	74205773	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
LIN52	91750	broad.mit.edu	37	14	74564627	74564627	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74564627delT	uc001xpp.2	+						LIN52_uc010asb.2_Intron	NM_001024674	NP_001019845			lin-52 homolog											breast(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00471)														---	---	---	---
LIN52	91750	broad.mit.edu	37	14	74610692	74610692	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74610692delT	uc001xpp.2	+						LIN52_uc010asb.2_Intron	NM_001024674	NP_001019845			lin-52 homolog											breast(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00471)														---	---	---	---
LIN52	91750	broad.mit.edu	37	14	74642415	74642416	+	Intron	DEL	AC	-	-	rs35602442		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74642415_74642416delAC	uc001xpp.2	+						LIN52_uc010asb.2_Intron	NM_001024674	NP_001019845			lin-52 homolog											breast(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00471)														---	---	---	---
KIAA0317	9870	broad.mit.edu	37	14	75137987	75137989	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75137987_75137989delTTT	uc001xqb.2	-						KIAA0317_uc010tut.1_Intron|KIAA0317_uc001xqc.2_Intron	NM_001039479	NP_001034568			hypothetical protein LOC9870						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|intracellular	ubiquitin-protein ligase activity			ovary(2)|kidney(1)|central_nervous_system(1)|pancreas(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00404)														---	---	---	---
YLPM1	56252	broad.mit.edu	37	14	75265533	75265533	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75265533delA	uc001xqj.3	+	5	3657	c.3533delA	c.(3532-3534)GAAfs	p.E1178fs	YLPM1_uc001xql.3_RNA	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	983	Arg-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	75978395	75978395	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75978395delA								JDP2 (38993 upstream) : BATF (10389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	76025541	76025542	+	IGR	INS	-	TCC	TCC	rs146332207	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76025541_76025542insTCC								BATF (12214 upstream) : FLVCR2 (19398 downstream)																																			---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76352963	76352963	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76352963delT	uc001xrx.2	+						TTLL5_uc010ask.1_Intron|TTLL5_uc001xrz.2_Intron|TTLL5_uc001xsa.2_Intron	NM_015072	NP_055887			tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76413090	76413092	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76413090_76413092delAAA	uc001xrx.2	+						TTLL5_uc001xsa.2_Intron	NM_015072	NP_055887			tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
C14orf118	55668	broad.mit.edu	37	14	76620616	76620617	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76620616_76620617insA	uc001xsh.2	+						C14orf118_uc001xsi.2_Intron|C14orf118_uc001xsj.1_Intron|C14orf118_uc001xsk.1_5'UTR|C14orf118_uc001xsl.2_5'Flank	NM_017926	NP_060396			hypothetical protein LOC55668 isoform 1											ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.0172)														---	---	---	---
ESRRB	2103	broad.mit.edu	37	14	76907067	76907068	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76907067_76907068delTC	uc001xsq.1	+						ESRRB_uc001xsr.2_Intron|ESRRB_uc001xso.2_Intron	NM_004452	NP_004443			estrogen-related receptor beta							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.0213)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	77073246	77073246	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77073246delT								ESRRB (105068 upstream) : VASH1 (154989 downstream)																																			---	---	---	---
ANGEL1	23357	broad.mit.edu	37	14	77272011	77272011	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77272011delA	uc001xsv.2	-						ANGEL1_uc010tvf.1_Intron	NM_015305	NP_056120			angel homolog 1											ovary(2)|central_nervous_system(1)|skin(1)	4			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	77372409	77372412	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77372409_77372412delTTTT								C14orf166B (35764 upstream) : C14orf4 (118476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77373415	77373416	+	IGR	DEL	TG	-	-	rs72092454		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77373415_77373416delTG								C14orf166B (36770 upstream) : C14orf4 (117472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77450484	77450484	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77450484delT								C14orf166B (113839 upstream) : C14orf4 (40404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77509323	77509323	+	IGR	DEL	T	-	-	rs72404515		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77509323delT								C14orf4 (14289 upstream) : KIAA1737 (55255 downstream)																																			---	---	---	---
SPTLC2	9517	broad.mit.edu	37	14	78045138	78045138	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78045138delA	uc001xub.2	-							NM_004863	NP_004854			serine palmitoyltransferase, long chain base							integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			upper_aerodigestive_tract(1)|ovary(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
SPTLC2	9517	broad.mit.edu	37	14	78071524	78071528	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78071524_78071528delTTTTT	uc001xub.2	-							NM_004863	NP_004854			serine palmitoyltransferase, long chain base							integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			upper_aerodigestive_tract(1)|ovary(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
ADCK1	57143	broad.mit.edu	37	14	78385256	78385257	+	Intron	INS	-	T	T	rs75948717	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78385256_78385257insT	uc001xui.2	+						ADCK1_uc010tvo.1_Intron|ADCK1_uc001xuj.2_Intron|ADCK1_uc001xuk.1_Intron	NM_020421	NP_065154			aarF domain containing kinase 1 isoform a							extracellular region	ATP binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	78565912	78565912	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78565912delT								ADCK1 (165616 upstream) : NRXN3 (71016 downstream)																																			---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79434392	79434399	+	Intron	DEL	CCCCCCCC	-	-	rs148023649		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79434392_79434399delCCCCCCCC	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	79679969	79679969	+	Intron	DEL	G	-	-	rs75083405		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79679969delG	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	79694131	79694138	+	Intron	DEL	TCCTCCCT	-	-	rs61995409		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79694131_79694138delTCCTCCCT	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	79812609	79812609	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79812609delA	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	80210760	80210761	+	Intron	INS	-	C	C	rs148006524	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80210760_80210761insC	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	80297215	80297215	+	Intron	DEL	G	-	-	rs11308238		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80297215delG	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	80572228	80572229	+	IGR	DEL	AT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80572228_80572229delAT								NRXN3 (241470 upstream) : DIO2 (91641 downstream)																																			---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81035150	81035150	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81035150delA	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	81115987	81115987	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81115987delA	uc001xux.2	-						C14orf145_uc010asz.1_Intron	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	81661686	81661686	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81661686delA	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)														---	---	---	---
GTF2A1	2957	broad.mit.edu	37	14	81680191	81680192	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81680191_81680192delTT	uc001xvf.1	-						GTF2A1_uc010atb.1_Intron|GTF2A1_uc001xvg.1_Intron|GTF2A1_uc001xvh.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	81909192	81909192	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81909192delC								STON2 (15444 upstream) : SEL1L (30048 downstream)																																			---	---	---	---
SEL1L	6400	broad.mit.edu	37	14	81970417	81970417	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81970417delT	uc010tvv.1	-						SEL1L_uc001xvo.3_Intron	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	82159349	82159351	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82159349_82159351delTTT								SEL1L (159144 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82535701	82535702	+	IGR	INS	-	TCCC	TCCC	rs28394171		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82535701_82535702insTCCC								SEL1L (535496 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83981145	83981145	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83981145delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84139255	84139256	+	IGR	INS	-	AT	AT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84139255_84139256insAT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84625360	84625361	+	IGR	INS	-	AAAC	AAAC	rs148874769	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84625360_84625361insAAAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85620062	85620062	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85620062delT								None (None upstream) : FLRT2 (376426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86693503	86693503	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86693503delT								FLRT2 (599234 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86931999	86931999	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86931999delA								FLRT2 (837730 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86979999	86980002	+	IGR	DEL	AAGG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86979999_86980002delAAGG								FLRT2 (885730 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87464443	87464443	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87464443delA								None (None upstream) : GALC (839721 downstream)																																			---	---	---	---
ZC3H14	79882	broad.mit.edu	37	14	89030207	89030207	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89030207delT	uc001xww.2	+						ZC3H14_uc010twd.1_Intron|ZC3H14_uc010twe.1_Intron|ZC3H14_uc001xwx.2_Intron|ZC3H14_uc010twf.1_Intron|ZC3H14_uc001xwy.2_Intron	NM_024824	NP_079100			zinc finger CCCH-type containing 14 isoform 1							cytoplasm|cytoplasm|nuclear speck	protein binding|RNA binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
EML5	161436	broad.mit.edu	37	14	89092785	89092785	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89092785delG	uc001xxg.2	-						EML5_uc001xxf.2_Intron|EML5_uc001xxh.1_Intron	NM_183387	NP_899243			echinoderm microtubule associated protein like							cytoplasm|microtubule				ovary(3)	3																		---	---	---	---
TTC8	123016	broad.mit.edu	37	14	89311984	89311984	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89311984delA	uc010ath.2	+						TTC8_uc010atg.1_Intron|TTC8_uc001xxl.2_Intron|TTC8_uc010ati.2_Intron|TTC8_uc001xxm.2_Intron|TTC8_uc010atj.2_Intron|TTC8_uc001xxi.2_Intron|TTC8_uc001xxj.2_Intron|TTC8_uc001xxk.2_Intron	NM_198309	NP_938051			tetratricopeptide repeat domain 8 isoform B						cilium assembly|establishment of anatomical structure orientation|sensory processing	BBSome|centrosome|cilium membrane|microtubule basal body	protein binding				0														Bardet-Biedl_syndrome				---	---	---	---
FOXN3	1112	broad.mit.edu	37	14	89925517	89925517	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89925517delA	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	89925528	89925529	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89925528_89925529delAA	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	90137195	90137196	+	IGR	INS	-	A	A	rs34508788		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90137195_90137196insA								FOXN3 (51701 upstream) : C14orf143 (126275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	90203628	90203629	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90203628_90203629insT								FOXN3 (118134 upstream) : C14orf143 (59842 downstream)																																			---	---	---	---
C14orf143	90141	broad.mit.edu	37	14	90405831	90405831	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90405831delC	uc001xxt.2	-						C14orf143_uc001xxs.2_Intron|C14orf143_uc001xxv.1_Intron|C14orf143_uc001xxw.1_Intron|C14orf143_uc001xxx.1_Intron	NM_145231	NP_660274			hypothetical protein LOC90141								calcium ion binding				0		all_cancers(154;0.136)		Epithelial(152;0.194)												OREG0022862	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	90976073	90976073	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90976073delT								CALM1 (101463 upstream) : TTC7B (30860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	91002255	91002256	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91002255_91002256delAG								CALM1 (127645 upstream) : TTC7B (4677 downstream)																																			---	---	---	---
TTC7B	145567	broad.mit.edu	37	14	91086924	91086924	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91086924delG	uc001xyp.2	-						TTC7B_uc001xyo.2_Intron|TTC7B_uc010ats.2_Intron	NM_001010854	NP_001010854			tetratricopeptide repeat domain 7B								binding			ovary(2)	2		Melanoma(154;0.222)																---	---	---	---
TTC7B	145567	broad.mit.edu	37	14	91169933	91169933	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91169933delA	uc001xyp.2	-							NM_001010854	NP_001010854			tetratricopeptide repeat domain 7B								binding			ovary(2)	2		Melanoma(154;0.222)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	91331398	91331398	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91331398delT								TTC7B (48637 upstream) : RPS6KA5 (5769 downstream)																																			---	---	---	---
C14orf159	80017	broad.mit.edu	37	14	91672728	91672728	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91672728delT	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)														---	---	---	---
CCDC88C	440193	broad.mit.edu	37	14	91792546	91792546	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91792546delT	uc010aty.2	-							NM_001080414	NP_001073883			DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)																---	---	---	---
CCDC88C	440193	broad.mit.edu	37	14	91826597	91826606	+	Intron	DEL	CACACACACA	-	-	rs72159664		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91826597_91826606delCACACACACA	uc010aty.2	-						CCDC88C_uc010twk.1_Intron	NM_001080414	NP_001073883			DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)																---	---	---	---
CCDC88C	440193	broad.mit.edu	37	14	91872131	91872131	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91872131delA	uc010aty.2	-						CCDC88C_uc010twk.1_Intron|CCDC88C_uc001xzl.3_Intron	NM_001080414	NP_001073883			DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)																---	---	---	---
TC2N	123036	broad.mit.edu	37	14	92258906	92258907	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92258906_92258907delAA	uc001xzu.3	-						TC2N_uc001xzt.3_Intron|TC2N_uc010auc.2_Intron|TC2N_uc001xzv.3_Intron	NM_001128595	NP_001122067			tandem C2 domains, nuclear							nucleus				upper_aerodigestive_tract(1)	1				COAD - Colon adenocarcinoma(157;0.218)														---	---	---	---
TC2N	123036	broad.mit.edu	37	14	92280498	92280499	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92280498_92280499delGA	uc001xzu.3	-						TC2N_uc001xzt.3_Intron|TC2N_uc010auc.2_Intron|TC2N_uc001xzv.3_Intron	NM_001128595	NP_001122067			tandem C2 domains, nuclear							nucleus				upper_aerodigestive_tract(1)	1				COAD - Colon adenocarcinoma(157;0.218)														---	---	---	---
TC2N	123036	broad.mit.edu	37	14	92287796	92287796	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92287796delA	uc001xzu.3	-						TC2N_uc001xzt.3_Intron|TC2N_uc010auc.2_Intron|TC2N_uc001xzv.3_Intron	NM_001128595	NP_001122067			tandem C2 domains, nuclear							nucleus				upper_aerodigestive_tract(1)	1				COAD - Colon adenocarcinoma(157;0.218)														---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92479623	92479623	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92479623delA	uc001xzy.2	-						TRIP11_uc010auf.1_Intron	NM_004239	NP_004230			thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)				T	PDGFRB	AML								---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92604781	92604781	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92604781delT	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	92623949	92623949	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92623949delT	uc001yah.1	+							NM_017437	NP_059133			cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	92705865	92705866	+	IGR	INS	-	T	T	rs150679543	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92705865_92705866insT								CPSF2 (75322 upstream) : SLC24A4 (83059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	92705868	92705869	+	IGR	INS	-	T	T	rs67564335	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92705868_92705869insT								CPSF2 (75325 upstream) : SLC24A4 (83056 downstream)																																			---	---	---	---
UBR7	55148	broad.mit.edu	37	14	93689089	93689091	+	Intron	DEL	AAA	-	-	rs74540552		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93689089_93689091delAAA	uc001ybm.3	+						UBR7_uc001ybn.3_Intron|UBR7_uc010auq.2_Intron	NM_175748	NP_786924			ubiquitin protein ligase E3 component n-recognin								ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
BTBD7	55727	broad.mit.edu	37	14	93718657	93718660	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93718657_93718660delAAAA	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	94092008	94092009	+	Intron	INS	-	T	T	rs139753225	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94092008_94092009insT	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-4292-01	TCGA-BR-4292-01									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	94399552	94399553	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94399552_94399553insA								FAM181A (3608 upstream) : ASB2 (960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	94999984	94999985	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94999984_94999985insA								SERPINA12 (15803 upstream) : SERPINA4 (27794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	95363423	95363424	+	IGR	INS	-	ATGC	ATGC	rs145889084		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95363423_95363424insATGC								GSC (126924 upstream) : DICER1 (189141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	95367216	95367216	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95367216delG								GSC (130717 upstream) : DICER1 (185349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	96045832	96045832	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96045832delA								GLRX5 (34777 upstream) : TCL6 (71003 downstream)																																			---	---	---	---
C14orf132	56967	broad.mit.edu	37	14	96503496	96503496	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96503496delA	uc001yff.3	+							NR_023938				Homo sapiens clone 25027 mRNA sequence.												0																		---	---	---	---
BDKRB2	624	broad.mit.edu	37	14	96700470	96700470	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96700470delA	uc010avm.1	+						BDKRB2_uc010avl.1_Intron|BDKRB2_uc010twu.1_Intron|BDKRB2_uc001yfg.2_Intron	NM_000623	NP_000614			bradykinin receptor B2						arachidonic acid secretion|elevation of cytosolic calcium ion concentration|transmembrane receptor protein tyrosine kinase signaling pathway	endosome|integral to plasma membrane	bradykinin receptor activity|phosphatidylinositol phospholipase C activity|protease binding|protein heterodimerization activity|type 1 angiotensin receptor binding			ovary(3)|breast(1)|kidney(1)	5		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)														---	---	---	---
ATG2B	55102	broad.mit.edu	37	14	96794878	96794878	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96794878delA	uc001yfi.2	-							NM_018036	NP_060506			ATG2 autophagy related 2 homolog B											ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)														---	---	---	---
AK7	122481	broad.mit.edu	37	14	96953557	96953559	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96953557_96953559delAAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	97521232	97521232	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97521232delT								VRK1 (173282 upstream) : C14orf64 (870715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	97671088	97671088	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97671088delT								VRK1 (323138 upstream) : C14orf64 (720859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99237850	99237850	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99237850delT								C14orf177 (53753 upstream) : BCL11B (397777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99398543	99398544	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99398543_99398544insG								C14orf177 (214446 upstream) : BCL11B (237083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99429704	99429706	+	IGR	DEL	GAG	-	-	rs2933338	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99429704_99429706delGAG								C14orf177 (245607 upstream) : BCL11B (205921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99751563	99751563	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99751563delT								BCL11B (13741 upstream) : SETD3 (112521 downstream)																																			---	---	---	---
SETD3	84193	broad.mit.edu	37	14	99876318	99876318	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99876318delG	uc001ygc.2	-						SETD3_uc001ygd.2_3'UTR	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)																---	---	---	---
CCDC85C	317762	broad.mit.edu	37	14	100006491	100006492	+	Intron	DEL	AG	-	-	rs150810128	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100006491_100006492delAG	uc010avr.2	-							NM_001144995	NP_001138467			coiled-coil domain containing 85C												0																		---	---	---	---
CCDC85C	317762	broad.mit.edu	37	14	100044584	100044585	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100044584_100044585delTG	uc010avr.2	-							NM_001144995	NP_001138467			coiled-coil domain containing 85C												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	100701703	100701704	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100701703_100701704delTT								DEGS2 (75691 upstream) : YY1 (3398 downstream)																																			---	---	---	---
WARS	7453	broad.mit.edu	37	14	100833386	100833386	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100833386delA	uc001yhf.1	-						WARS_uc001yhg.1_Intron|WARS_uc001yhh.1_Intron|WARS_uc001yhi.1_Intron|WARS_uc001yhj.1_Intron|WARS_uc001yhk.1_Intron|WARS_uc001yhl.1_Intron|WARS_uc010twz.1_Intron	NM_173701	NP_776049			tryptophanyl-tRNA synthetase isoform a						angiogenesis|negative regulation of cell proliferation|regulation of angiogenesis|tryptophanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|protein binding|tryptophan-tRNA ligase activity			breast(1)	1		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)													---	---	---	---
DLK1	8788	broad.mit.edu	37	14	101194869	101194869	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101194869delA	uc001yhs.3	+						DLK1_uc001yhu.3_Intron	NM_003836	NP_003827			delta-like 1 homolog precursor						multicellular organismal development	extracellular space|integral to membrane|soluble fraction				ovary(2)|breast(1)|skin(1)	4		Melanoma(154;0.155)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	101669954	101669954	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101669954delT								MIR656 (136816 upstream) : DIO3OS (348606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	101949208	101949209	+	IGR	DEL	AA	-	-	rs79648604		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101949208_101949209delAA								MIR656 (416070 upstream) : DIO3OS (69351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	102046527	102046528	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102046527_102046528insA								DIO3 (16738 upstream) : C14orf72 (150246 downstream)																																			---	---	---	---
WDR20	91833	broad.mit.edu	37	14	102661700	102661700	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102661700delA	uc001ykz.2	+						WDR20_uc001yky.1_Intron|WDR20_uc001yla.2_Intron|WDR20_uc001ylb.2_Intron|WDR20_uc010txu.1_Intron|WDR20_uc001ylc.2_Intron|WDR20_uc001yld.2_Intron|WDR20_uc001yle.2_Intron|WDR20_uc001ylf.2_Intron	NM_144574	NP_653175			WD repeat domain 20 isoform 2												0																		---	---	---	---
RAGE	5891	broad.mit.edu	37	14	102704947	102704947	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102704947delC	uc001ylm.2	-						RAGE_uc010txv.1_Intron|RAGE_uc001yln.2_Intron|RAGE_uc001ylh.2_Intron|RAGE_uc001yll.2_Intron|RAGE_uc001ylj.2_Intron|RAGE_uc001ylk.2_Intron	NM_014226	NP_055041			MAPK/MAK/MRK overlapping kinase						signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
RAGE	5891	broad.mit.edu	37	14	102722601	102722601	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102722601delT	uc001ylm.2	-						RAGE_uc010txv.1_Intron|RAGE_uc001yln.2_Intron	NM_014226	NP_055041			MAPK/MAK/MRK overlapping kinase						signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
TECPR2	9895	broad.mit.edu	37	14	102944718	102944718	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102944718delA	uc001ylw.1	+						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																		---	---	---	---
RCOR1	23186	broad.mit.edu	37	14	103070132	103070133	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103070132_103070133insT	uc001ymb.2	+							NM_015156	NP_055971			REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1																		---	---	---	---
RCOR1	23186	broad.mit.edu	37	14	103157623	103157626	+	Intron	DEL	AATA	-	-	rs35833952		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103157623_103157626delAATA	uc001ymb.2	+							NM_015156	NP_055971			REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	103615591	103615599	+	IGR	DEL	AAAAAAAAA	-	-	rs141928659		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103615591_103615599delAAAAAAAAA								TNFAIP2 (11815 upstream) : EIF5 (184894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	103770205	103770206	+	IGR	INS	-	AG	AG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103770205_103770206insAG								TNFAIP2 (166429 upstream) : EIF5 (30287 downstream)																																			---	---	---	---
PPP1R13B	23368	broad.mit.edu	37	14	104255028	104255030	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104255028_104255030delAAA	uc001yof.1	-						PPP1R13B_uc001yog.1_Intron	NM_015316	NP_056131			apoptosis-stimulating protein of p53, 1						apoptosis|induction of apoptosis|negative regulation of cell cycle	cytoplasm|nucleus|plasma membrane	protein binding			ovary(1)	1		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)																---	---	---	---
PPP1R13B	23368	broad.mit.edu	37	14	104258536	104258539	+	Intron	DEL	TGTA	-	-	rs143780105		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104258536_104258539delTGTA	uc001yof.1	-						PPP1R13B_uc001yog.1_Intron	NM_015316	NP_056131			apoptosis-stimulating protein of p53, 1						apoptosis|induction of apoptosis|negative regulation of cell cycle	cytoplasm|nucleus|plasma membrane	protein binding			ovary(1)	1		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)																---	---	---	---
CDCA4	55038	broad.mit.edu	37	14	105483560	105483561	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105483560_105483561delTT	uc001yqa.2	-						CDCA4_uc001yqb.2_Intron	NM_145701	NP_663747			cell division cycle associated 4							nucleus				ovary(1)	1		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.142)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	105604429	105604429	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105604429delC								GPR132 (72675 upstream) : JAG2 (3648 downstream)																																			---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105686239	105686239	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105686239delG	uc001yqp.2	-						BRF1_uc010tyo.1_Intron|BRF1_uc010typ.1_Intron|BRF1_uc001yqk.2_Intron|BRF1_uc001yql.2_Intron|BRF1_uc001yqo.2_Intron|BRF1_uc010axg.1_Intron|BRF1_uc001yqn.2_Intron|BRF1_uc010axh.1_Intron|BRF1_uc010axi.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)														---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105736091	105736091	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105736091delC	uc001yqp.2	-						BRF1_uc010tyo.1_Intron|BRF1_uc010typ.1_Intron|BRF1_uc010axg.1_Intron|BRF1_uc001yqr.2_Intron	NM_001519	NP_001510			transcription initiation factor IIIB isoform 1						positive regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	105870112	105870112	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105870112delA	uc010axk.1	+											Homo sapiens cDNA clone IMAGE:40132624.																														---	---	---	---
MTA1	9112	broad.mit.edu	37	14	105890837	105890837	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105890837delT	uc001yqx.2	+						MTA1_uc001yqy.2_Intron	NM_004689	NP_004680			metastasis associated protein						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)														---	---	---	---
CRIP2	1397	broad.mit.edu	37	14	105945901	105945901	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105945901delC	uc001yrd.1	+						CRIP2_uc010tyr.1_Intron|CRIP2_uc001yre.1_Intron|CRIP2_uc001yrf.1_Intron|CRIP2_uc001yrg.2_Intron|CRIP2_uc001yrh.1_Intron	NM_001312	NP_001303			cysteine-rich protein 2								zinc ion binding				0		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.235)														---	---	---	---
KIAA0125	9834	broad.mit.edu	37	14	106364837	106364837	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106364837delG	uc001ysq.2	+						ADAM6_uc010tyt.1_Intron|KIAA0125_uc001ysr.2_Intron					SubName: Full=HCG2029388, isoform CRA_d; SubName: Full=FAM30A protein;												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107118059	107118060	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107118059_107118060delAC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107235429	107235429	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	20402789	20402789	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20402789delT								None (None upstream) : GOLGA6L6 (334305 downstream)																																			---	---	---	---
OR4N4	283694	broad.mit.edu	37	15	22356134	22356135	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22356134_22356135insA	uc001yuc.1	+						LOC727924_uc001yua.2_Intron|LOC727924_uc001yub.1_Intron	NM_001005241	NP_001005241			olfactory receptor, family 4, subfamily N,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	22440159	22440159	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22440159delT	uc001yug.2	-	1										full-length cDNA clone CS0DI014YE21 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	22546946	22546946	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22546946delC								MIR1268 (33666 upstream) : GOLGA8DP (155339 downstream)																																			---	---	---	---
TUBGCP5	114791	broad.mit.edu	37	15	22840983	22840983	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22840983delT	uc001yur.3	+						TUBGCP5_uc001yuq.2_Intron	NM_052903	NP_443135			tubulin, gamma complex associated protein 5						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)														---	---	---	---
CYFIP1	23191	broad.mit.edu	37	15	22939037	22939037	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22939037delT	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)														---	---	---	---
HERC2P2	400322	broad.mit.edu	37	15	23360359	23360361	+	Intron	DEL	TCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23360359_23360361delTCT	uc001yvr.2	-						HERC2P2_uc010ayf.1_Intron					RecName: Full=Putative HERC2-like protein 3;												0																		---	---	---	---
HERC2P2	400322	broad.mit.edu	37	15	23373765	23373765	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23373765delT	uc001yvr.2	-						HERC2P2_uc010ayf.1_Intron					RecName: Full=Putative HERC2-like protein 3;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	23588807	23588807	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23588807delT								GOLGA8E (140384 upstream) : MKRN3 (221647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	23659246	23659248	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23659246_23659248delTTT								GOLGA8E (210823 upstream) : MKRN3 (151206 downstream)																																			---	---	---	---
MKRN3	7681	broad.mit.edu	37	15	23832911	23832912	+	Intron	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23832911_23832912insTG	uc001ywi.2	+											SubName: Full=MKRN3 protein;							ribonucleoprotein complex	ligase activity|nucleic acid binding|zinc ion binding			lung(6)|large_intestine(2)|ovary(2)	10		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	24424377	24424378	+	IGR	INS	-	A	A	rs112293970		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24424377_24424378insA								PWRN2 (9282 upstream) : PWRN1 (354461 downstream)																																			---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25222783	25222784	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25222783_25222784insA	uc001ywp.1	+						SNRPN_uc001ywq.1_Intron|SNRPN_uc001ywr.1_Intron|SNRPN_uc001yws.1_Intron|SNRPN_uc001ywt.1_Intron|SNRPN_uc001ywv.1_Intron|SNRPN_uc001yww.1_Intron|SNRPN_uc001ywx.1_Intron|SNRPN_uc001ywz.1_Intron|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_Intron	NM_022807	NP_073718			small nuclear ribonucleoprotein polypeptide N						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)										Prader-Willi_syndrome				---	---	---	---
SNORD115-13	100033450	broad.mit.edu	37	15	25437762	25437763	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25437762_25437763insG	uc001yzf.1	+						SNORD115-13_uc001yzh.2_5'Flank|SNORD115-14_uc001yzj.1_5'Flank					Homo sapiens clone Rt-11 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	25905629	25905629	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25905629delA								UBE3A (221501 upstream) : ATP10A (18233 downstream)																																			---	---	---	---
ATP10A	57194	broad.mit.edu	37	15	25938698	25938698	+	Intron	DEL	A	-	-	rs34992027		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25938698delA	uc010ayu.2	-							NM_024490	NP_077816			ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)														---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27384506	27384507	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27384506_27384507delGA	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092			gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28122530	28122530	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28122530delT	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				---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28204530	28204531	+	Intron	INS	-	A	A	rs139385658	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28204530_28204531insA	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	28388215	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28388214_28388215delAA	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	28441813	28441814	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28441813_28441814insT	uc001zbj.2	-						HERC2_uc001zbk.1_Intron	NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28517828	28517828	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28517828delA	uc001zbj.2	-						HERC2_uc001zbl.1_Intron	NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29592356	29592359	+	Intron	DEL	ATGG	-	-	rs113604351		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29592356_29592359delATGG	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29666111	29666111	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29666111delA	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
TJP1	7082	broad.mit.edu	37	15	30022801	30022801	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30022801delA	uc001zcr.2	-						TJP1_uc010azl.2_Intron|TJP1_uc001zcq.2_Intron|TJP1_uc001zcs.2_Intron	NM_003257	NP_003248			tight junction protein 1 isoform a						cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	30175784	30175784	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30175784delT								TJP1 (61078 upstream) : FAM7A3 (220151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	30277931	30277931	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30277931delT								TJP1 (163225 upstream) : FAM7A3 (118004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	31600451	31600452	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31600451_31600452insC								TRPM1 (206527 upstream) : KLF13 (18631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	31766948	31766948	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31766948delT								KLF13 (96847 upstream) : OTUD7A (8382 downstream)																																			---	---	---	---
CHRNA7	1139	broad.mit.edu	37	15	32426364	32426365	+	Intron	DEL	TT	-	-	rs34701272		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32426364_32426365delTT	uc001zft.2	+						CHRNA7_uc010bae.1_Intron|CHRNA7_uc010baf.2_Intron|CHRNA7_uc010bah.1_Intron|CHRNA7_uc010bai.1_Intron|CHRNA7_uc010baj.1_Intron|CHRNA7_uc010bak.2_Intron	NM_000746	NP_000737			cholinergic receptor, nicotinic, alpha 7						activation of MAPK activity|calcium ion transport|cellular calcium ion homeostasis|memory|negative regulation of tumor necrosis factor production|positive regulation of angiogenesis|positive regulation of cell proliferation|response to hypoxia|response to nicotine	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|beta-amyloid binding|chloride channel regulator activity|nicotinic acetylcholine-activated cation-selective channel activity|protein homodimerization activity|toxin binding			ovary(1)	1		all_lung(180;6.35e-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)	Nicotine(DB00184)|Varenicline(DB01273)													---	---	---	---
CHRNA7	1139	broad.mit.edu	37	15	32444644	32444644	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32444644delA	uc001zft.2	+						CHRNA7_uc010bae.1_Intron|CHRNA7_uc010baf.2_Intron|CHRNA7_uc010bah.1_Intron|CHRNA7_uc010bai.1_Intron|CHRNA7_uc010baj.1_Intron|CHRNA7_uc010bak.2_Intron	NM_000746	NP_000737			cholinergic receptor, nicotinic, alpha 7						activation of MAPK activity|calcium ion transport|cellular calcium ion homeostasis|memory|negative regulation of tumor necrosis factor production|positive regulation of angiogenesis|positive regulation of cell proliferation|response to hypoxia|response to nicotine	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|beta-amyloid binding|chloride channel regulator activity|nicotinic acetylcholine-activated cation-selective channel activity|protein homodimerization activity|toxin binding			ovary(1)	1		all_lung(180;6.35e-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)	Nicotine(DB00184)|Varenicline(DB01273)													---	---	---	---
ARHGAP11A	9824	broad.mit.edu	37	15	32927960	32927960	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33171868	33171868	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33171868delT	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)														---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33187562	33187562	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33187562delA	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)														---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33336483	33336484	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33336483_33336484insG	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)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33927074	33927074	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33927074delT	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)														---	---	---	---
C15orf24	56851	broad.mit.edu	37	15	34380341	34380341	+	Intron	DEL	A	-	-	rs145275758		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34380341delA	uc001zhm.2	-						C15orf24_uc001zhn.2_Intron	NM_020154	NP_064539			chromosome 15 open reading frame 24 precursor							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	34543443	34543443	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)													---	---	---	---
SLC12A6	9990	broad.mit.edu	37	15	34544637	34544637	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34544637delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	34835558	34835558	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34835558delT								GOLGA8B (7336 upstream) : GJD2 (209121 downstream)																																			---	---	---	---
AQR	9716	broad.mit.edu	37	15	35166856	35166856	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35166856delT	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)														---	---	---	---
ATPBD4	89978	broad.mit.edu	37	15	35803907	35803907	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35803907delA	uc001zja.2	-						ATPBD4_uc001ziz.2_Intron	NM_080650	NP_542381			ATP binding domain 4 isoform 1												0		all_epithelial(112;2.11e-09)|Lung NSC(122;2.38e-08)|all_lung(180;3.65e-07)		all cancers(64;9.9e-19)|GBM - Glioblastoma multiforme(113;2.01e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	36075915	36075915	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36075915delC	uc001zjc.2	+											Homo sapiens, Similar to LOC161538, clone IMAGE:5199550, mRNA.																														---	---	---	---
MEIS2	4212	broad.mit.edu	37	15	37226580	37226580	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37226580delT	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)														---	---	---	---
MEIS2	4212	broad.mit.edu	37	15	37329090	37329090	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37329090delT	uc001zjr.2	-	8	1862	c.825delA	c.(823-825)AAAfs	p.K275fs	MEIS2_uc001zjl.2_Frame_Shift_Del_p.K262fs|MEIS2_uc010ucj.1_Frame_Shift_Del_p.K262fs|MEIS2_uc001zjm.2_Frame_Shift_Del_p.K187fs|MEIS2_uc001zjn.2_Frame_Shift_Del_p.K129fs|MEIS2_uc001zjo.2_Frame_Shift_Del_p.K275fs|MEIS2_uc001zjp.2_Frame_Shift_Del_p.K275fs|MEIS2_uc001zjs.2_Frame_Shift_Del_p.K275fs|MEIS2_uc001zju.2_Frame_Shift_Del_p.K262fs|MEIS2_uc001zjt.2_Frame_Shift_Del_p.K275fs	NM_170675	NP_733775	O14770	MEIS2_HUMAN	Meis homeobox 2 isoform c	275					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	37660564	37660564	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37660564delT								MEIS2 (267064 upstream) : TMCO5A (566263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38000075	38000075	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38000075delA								MEIS2 (606575 upstream) : TMCO5A (226752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38449141	38449141	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38449141delA	uc001zjy.2	-											Homo sapiens, clone IMAGE:3923347, mRNA.																														---	---	---	---
FAM98B	283742	broad.mit.edu	37	15	38743998	38743998	+	5'Flank	DEL	T	-	-	rs11435441		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38743998delT	uc001zkb.1	+						FAM98B_uc001zkc.2_5'Flank	NM_001042429	NP_001035894			family with sequence similarity 98, member B							tRNA-splicing ligase complex	protein binding			ovary(1)	1		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)														---	---	---	---
RASGRP1	10125	broad.mit.edu	37	15	38792549	38792549	+	Intron	DEL	G	-	-	rs12904148	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38792549delG	uc001zke.3	-						RASGRP1_uc010bbe.2_Intron|RASGRP1_uc010bbf.2_Intron|RASGRP1_uc010bbg.2_Intron|RASGRP1_uc001zkd.3_Intron	NM_005739	NP_005730			RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)														---	---	---	---
RASGRP1	10125	broad.mit.edu	37	15	38842026	38842026	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38842026delA	uc001zke.3	-						RASGRP1_uc001zkd.3_Intron	NM_005739	NP_005730			RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	38973656	38973657	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38973656_38973657insT								RASGRP1 (116649 upstream) : C15orf53 (15142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39119987	39119987	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39119987delA								C15orf53 (127748 upstream) : C15orf54 (422898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39567410	39567411	+	IGR	INS	-	A	A	rs151059645	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39567410_39567411insA								C15orf54 (20362 upstream) : THBS1 (305869 downstream)																																			---	---	---	---
THBS1	7057	broad.mit.edu	37	15	39887099	39887099	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39887099delT	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)													---	---	---	---
GPR176	11245	broad.mit.edu	37	15	40202765	40202765	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40202765delA	uc001zkj.1	-						GPR176_uc001zkk.1_Intron	NM_007223	NP_009154			G protein-coupled receptor 176						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)														---	---	---	---
EIF2AK4	440275	broad.mit.edu	37	15	40282595	40282595	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40282595delT	uc001zkm.1	+						EIF2AK4_uc010bbj.1_Intron|EIF2AK4_uc001zkn.1_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)														---	---	---	---
EIF2AK4	440275	broad.mit.edu	37	15	40314943	40314943	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40314943delT	uc001zkm.1	+						EIF2AK4_uc010bbj.1_Intron|EIF2AK4_uc001zkn.1_Intron|EIF2AK4_uc001zko.1_Intron|EIF2AK4_uc010bbk.1_Intron	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	40477243	40477243	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40477243delT	uc001zkx.3	+						BUB1B_uc010ucl.1_Intron	NM_001211	NP_001202			budding uninhibited by benzimidazoles 1 beta						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)				Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				---	---	---	---
BUB1B	701	broad.mit.edu	37	15	40491636	40491636	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40491636delT	uc001zkx.3	+						BUB1B_uc010ucl.1_Intron	NM_001211	NP_001202			budding uninhibited by benzimidazoles 1 beta						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)				Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				---	---	---	---
CASC5	57082	broad.mit.edu	37	15	40949220	40949220	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40949220delT	uc010bbs.1	+						CASC5_uc010bbt.1_Intron	NM_170589	NP_733468			cancer susceptibility candidate 5 isoform 1						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)														---	---	---	---
RAD51	5888	broad.mit.edu	37	15	41020654	41020655	+	Intron	DEL	AA	-	-	rs34910367		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41020654_41020655delAA	uc001zmi.3	+						RAD51_uc010bbw.2_Intron|RAD51_uc010bbx.2_Intron|RAD51_uc001zmk.3_Intron|RAD51_uc001zml.3_Intron	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					---	---	---	---
SPINT1	6692	broad.mit.edu	37	15	41137333	41137333	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41137333delT	uc001zna.2	+						SPINT1_uc001znb.2_Intron|SPINT1_uc001znc.2_Intron|SPINT1_uc010ucs.1_Intron	NM_181642	NP_857593			serine peptidase inhibitor, Kunitz type 1							extracellular region|membrane fraction	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		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;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)														---	---	---	---
INO80	54617	broad.mit.edu	37	15	41364284	41364284	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41364284delA	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023			INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
NUSAP1	51203	broad.mit.edu	37	15	41641965	41641966	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41641965_41641966delTT	uc001zns.3	+						NUSAP1_uc001znq.3_Intron|NUSAP1_uc001znr.3_Intron|NUSAP1_uc010bce.2_Intron|NUSAP1_uc001znt.3_Intron|NUSAP1_uc001znv.3_Intron|NUSAP1_uc001znu.3_Intron|NUSAP1_uc010ucw.1_Intron|NUSAP1_uc001znw.3_Intron	NM_016359	NP_057443			nucleolar and spindle associated protein 1						cytokinesis after mitosis|establishment of mitotic spindle localization|mitotic chromosome condensation|positive regulation of mitosis	chromosome|cytoplasm|nucleolus	DNA binding				0		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)														---	---	---	---
RTF1	23168	broad.mit.edu	37	15	41726823	41726825	+	Intron	DEL	TTT	-	-	rs142035079		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41726823_41726825delTTT	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)														---	---	---	---
MGA	23269	broad.mit.edu	37	15	41943881	41943897	+	Intron	DEL	TTCCCCTCTCTTACCCC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41943881_41943897delTTCCCCTCTCTTACCCC	uc001zog.1	+							NM_001080541	NP_001074010			MAX-interacting protein isoform 2							MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
MGA	23269	broad.mit.edu	37	15	41961004	41961004	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41961004delT	uc001zog.1	+						MGA_uc010ucy.1_Intron|MGA_uc010ucz.1_Intron	NM_001080541	NP_001074010			MAX-interacting protein isoform 2							MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
MAPKBP1	23005	broad.mit.edu	37	15	42076206	42076207	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42076206_42076207insA	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)														---	---	---	---
JMJD7-PLA2G4B	8681	broad.mit.edu	37	15	42135578	42135578	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42135578delG	uc010bco.2	+						JMJD7-PLA2G4B_uc001zoo.3_Intron|JMJD7-PLA2G4B_uc010bcn.2_Intron|JMJD7-PLA2G4B_uc001zoq.3_Intron|JMJD7-PLA2G4B_uc001zor.1_5'UTR	NM_001114633	NP_001108105			phospholipase A2, group IVB						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																		---	---	---	---
SPTBN5	51332	broad.mit.edu	37	15	42183748	42183748	+	Intron	DEL	G	-	-	rs3837680		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42183748delG	uc001zos.2	-						uc010bcp.1_5'Flank	NM_016642	NP_057726			spectrin, beta, non-erythrocytic 5						actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	42394288	42394288	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42394288delA								PLA2G4D (7536 upstream) : PLA2G4F (39111 downstream)																																			---	---	---	---
TTBK2	146057	broad.mit.edu	37	15	43106056	43106056	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43106056delA	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771			tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43252975	43252975	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43252975delT	uc001zqq.2	-							NM_174916	NP_777576			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
EPB42	2038	broad.mit.edu	37	15	43504267	43504267	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43504267delA	uc001zra.3	-						EPB42_uc001zqz.3_5'Flank|EPB42_uc010bde.2_Intron|EPB42_uc001zrb.3_Intron|EPB42_uc010udm.1_Intron	NM_001114134	NP_001107606			erythrocyte membrane protein band 4.2 isoform 2						erythrocyte maturation|peptide cross-linking|regulation of cell shape	cytoplasm|cytoskeleton|plasma membrane	ATP binding|protein binding|protein-glutamine gamma-glutamyltransferase activity|structural constituent of cytoskeleton			ovary(2)	2		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;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)														---	---	---	---
LCMT2	9836	broad.mit.edu	37	15	43622774	43622774	+	5'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43622774delA	uc001zrg.2	-	1					LCMT2_uc010udn.1_5'UTR|ADAL_uc001zrh.2_5'Flank|ADAL_uc010udo.1_5'Flank	NM_014793	NP_055608			leucine carboxyl methyltransferase 2						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)													---	---	---	---
ELL3	80237	broad.mit.edu	37	15	44067474	44067474	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44067474delA	uc001zsw.1	-						ELL3_uc001zsv.1_Intron|ELL3_uc001zsx.1_Intron|uc001zsy.2_5'Flank	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)														---	---	---	---
FRMD5	84978	broad.mit.edu	37	15	44385545	44385545	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44385545delA	uc001ztl.2	-						FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281			FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)														---	---	---	---
CTDSPL2	51496	broad.mit.edu	37	15	44811330	44811330	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44811330delT	uc001ztr.2	+						CTDSPL2_uc001zts.2_Intron|CTDSPL2_uc001ztt.2_Intron|CTDSPL2_uc010bdv.2_Intron	NM_016396	NP_057480			CTD (carboxy-terminal domain, RNA polymerase II,								phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)														---	---	---	---
SPG11	80208	broad.mit.edu	37	15	44949207	44949209	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44949207_44949209delAAA	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	45000430	45000430	+	IGR	DEL	T	-	-	rs78032870		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45000430delT								PATL2 (31344 upstream) : B2M (3255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	45120167	45120167	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45120167delT								TRIM69 (60142 upstream) : C15orf43 (128736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	45220930	45220930	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45220930delT								TRIM69 (160905 upstream) : C15orf43 (27973 downstream)																																			---	---	---	---
C15orf43	145645	broad.mit.edu	37	15	45253675	45253676	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45253675_45253676delAA	uc001zuk.2	+							NM_152448	NP_689661			hypothetical protein LOC145645												0		all_cancers(109;3.68e-08)|all_epithelial(112;1.05e-06)|Lung NSC(122;1.42e-05)|all_lung(180;0.000112)|Melanoma(134;0.0192)		all cancers(107;7.64e-17)|GBM - Glioblastoma multiforme(94;2.03e-06)														---	---	---	---
DUOX2	50506	broad.mit.edu	37	15	45395902	45395902	+	Intron	DEL	T	-	-	rs75922593		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45395902delT	uc010bea.2	-						DUOX2_uc001zun.2_Intron	NM_014080	NP_054799			dual oxidase 2 precursor						cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)														---	---	---	---
DUOXA1	90527	broad.mit.edu	37	15	45412115	45412115	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45412115delG	uc001zuq.1	-						DUOXA1_uc010uem.1_Intron|DUOXA1_uc001zup.2_Intron|DUOXA1_uc010bec.2_Intron|DUOXA1_uc001zur.1_Intron|DUOXA1_uc010bed.1_Intron	NM_144565	NP_653166			Numb-interacting protein						protein transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	45677548	45677548	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45677548delA	uc001zvd.2	-											Homo sapiens cDNA clone IMAGE:5298801.																														---	---	---	---
SLC30A4	7782	broad.mit.edu	37	15	45811601	45811601	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45811601delT	uc001zvj.2	-						C15orf21_uc001zvk.2_RNA|C15orf21_uc010beg.1_Intron|C15orf21_uc010beh.1_Intron|C15orf21_uc010bei.1_Intron|C15orf21_uc010bej.1_Intron|C15orf21_uc001zvm.1_Intron|C15orf21_uc001zvn.1_Intron	NM_013309	NP_037441			solute carrier family 30 (zinc transporter),						regulation of sequestering of zinc ion|response to toxin	endosome membrane|integral to membrane|late endosome	zinc ion transmembrane transporter activity				0		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	45902837	45902838	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45902837_45902838delTT								PLDN (929 upstream) : SQRDL (20508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	47046695	47046696	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47046695_47046696insT								None (None upstream) : SEMA6D (429707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	47104837	47104846	+	IGR	DEL	CACACACACA	-	-	rs147623887		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47104837_47104846delCACACACACA								None (None upstream) : SEMA6D (371557 downstream)																																			---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	48064555	48064556	+	3'UTR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48064555_48064556delGT	uc010bek.2	+	19					SEMA6D_uc001zvw.2_3'UTR|SEMA6D_uc001zvy.2_3'UTR|SEMA6D_uc001zvz.2_3'UTR|SEMA6D_uc001zwa.2_3'UTR|SEMA6D_uc001zwb.2_3'UTR|SEMA6D_uc001zwc.2_3'UTR	NM_153618	NP_705871			semaphorin 6D isoform 4 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)														---	---	---	---
MYEF2	50804	broad.mit.edu	37	15	48449998	48449998	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48449998delA	uc001zwi.3	-						MYEF2_uc001zwj.3_Intron|MYEF2_uc001zwl.2_Intron	NM_016132	NP_057216			myelin expression factor 2						transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding|nucleotide binding|RNA binding			lung(2)|ovary(1)	3		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)														---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48812686	48812686	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48812686delT	uc001zwx.1	-							NM_000138	NP_000129			fibrillin 1 precursor						heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)														---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48845870	48845870	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48845870delT	uc001zwx.1	-							NM_000138	NP_000129			fibrillin 1 precursor						heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	49411864	49411864	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49411864delA								SECISBP2L (73234 upstream) : COPS2 (5609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	50060944	50060944	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50060944delT								DTWD1 (123612 upstream) : ATP8B4 (89492 downstream)																																			---	---	---	---
ATP8B4	79895	broad.mit.edu	37	15	50264705	50264706	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50264705_50264706delTT	uc001zxu.2	-						ATP8B4_uc010ber.2_Intron|ATP8B4_uc010ufd.1_Intron|ATP8B4_uc010ufe.1_Intron	NM_024837	NP_079113			ATPase class I type 8B member 4						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)														---	---	---	---
HDC	3067	broad.mit.edu	37	15	50555231	50555231	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50555231delA	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)													---	---	---	---
USP8	9101	broad.mit.edu	37	15	50772831	50772832	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50772831_50772832delTT	uc001zym.3	+						USP8_uc001zyk.1_Intron|USP8_uc001zyl.3_Intron|USP8_uc001zyn.3_Intron|USP8_uc010ufh.1_Intron|USP8_uc010bev.1_Intron	NM_001128611	NP_001122083			ubiquitin specific peptidase 8						cell cycle|cell proliferation|endosome organization|protein K48-linked deubiquitination|protein K63-linked deubiquitination|ubiquitin-dependent protein catabolic process	cytosol|early endosome|extrinsic to plasma membrane|nucleus	cysteine-type endopeptidase activity|SH3 domain binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(1)|central_nervous_system(1)	2				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	51102272	51102272	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51102272delA								SPPL2A (44362 upstream) : AP4E1 (98674 downstream)																																			---	---	---	---
AP4E1	23431	broad.mit.edu	37	15	51240537	51240540	+	Intron	DEL	TTTT	-	-	rs71729261		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51240537_51240540delTTTT	uc001zyx.1	+							NM_007347	NP_031373			adaptor-related protein complex 4, epsilon 1						intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)														---	---	---	---
AP4E1	23431	broad.mit.edu	37	15	51276506	51276507	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51276506_51276507delTT	uc001zyx.1	+							NM_007347	NP_031373			adaptor-related protein complex 4, epsilon 1						intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)														---	---	---	---
DMXL2	23312	broad.mit.edu	37	15	51745633	51745633	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51745633delT	uc002abf.2	-						DMXL2_uc002abd.2_Intron|DMXL2_uc010ufy.1_Intron|DMXL2_uc010bfa.2_Intron	NM_015263	NP_056078			Dmx-like 2							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	51830074	51830074	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51830074delA	uc002abf.2	-						DMXL2_uc010ufy.1_Intron|DMXL2_uc010bfa.2_Intron	NM_015263	NP_056078			Dmx-like 2							cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	52292307	52292308	+	IGR	DEL	TT	-	-	rs112632149		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52292307_52292308delTT								LEO1 (28349 upstream) : MAPK6 (19103 downstream)																																			---	---	---	---
MYO5A	4644	broad.mit.edu	37	15	52634556	52634556	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52634556delA	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010ugd.1_Intron|MYO5A_uc002abz.1_5'Flank|MYO5A_uc002aca.1_Intron|MYO5A_uc002acb.1_Intron|MYO5A_uc002acc.1_Intron	NM_000259	NP_000250			myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	53246688	53246689	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53246688_53246689delTT								ONECUT1 (164479 upstream) : WDR72 (559249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	53277556	53277557	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53277556_53277557delGT								ONECUT1 (195347 upstream) : WDR72 (528381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	53378202	53378202	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53378202delT								ONECUT1 (295993 upstream) : WDR72 (427736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	53382383	53382383	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53382383delA								ONECUT1 (300174 upstream) : WDR72 (423555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	53678399	53678399	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53678399delA								ONECUT1 (596190 upstream) : WDR72 (127539 downstream)																																			---	---	---	---
WDR72	256764	broad.mit.edu	37	15	54006846	54006846	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54006846delA	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	54885062	54885065	+	Intron	DEL	TTTT	-	-	rs148695701		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54885062_54885065delTTTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	54968582	54968582	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54968582delA								UNC13C (47777 upstream) : RSL24D1 (504939 downstream)																																			---	---	---	---
PIGB	9488	broad.mit.edu	37	15	55637455	55637455	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	55726958	55726958	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55726958delA	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)														---	---	---	---
DYX1C1	161582	broad.mit.edu	37	15	55759182	55759182	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55759182delT	uc002adc.2	-	5	951	c.583delA	c.(583-585)ATAfs	p.I195fs	CCPG1_uc002acy.2_5'UTR|DYX1C1_uc010ugh.1_RNA|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.2_Frame_Shift_Del_p.I195fs|DYX1C1_uc002add.2_Frame_Shift_Del_p.I195fs	NM_130810	NP_570722	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1 isoform a	195					neuron migration|regulation of estrogen receptor signaling pathway|regulation of proteasomal protein catabolic process	cytoplasm|nucleus	estrogen receptor binding			skin(1)	1				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)														---	---	---	---
RFX7	64864	broad.mit.edu	37	15	56417809	56417810	+	Intron	DEL	GT	-	-	rs72173431		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56417809_56417810delGT	uc010bfn.2	-							NM_022841	NP_073752			regulatory factor X domain containing 2						regulation of transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
RFX7	64864	broad.mit.edu	37	15	56527378	56527379	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56527378_56527379delTT	uc010bfn.2	-							NM_022841	NP_073752			regulatory factor X domain containing 2						regulation of transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	56916229	56916230	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56916229_56916230delAA	uc002ads.2	-											Homo sapiens cDNA clone IMAGE:5275275.																														---	---	---	---
ZNF280D	54816	broad.mit.edu	37	15	57107546	57107546	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57107546delA	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	57246029	57246029	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57246029delT	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	57305617	57305617	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57305617delT	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	57401849	57401849	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57401849delT	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	57484573	57484576	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57484573_57484576delTTTT	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								---	---	---	---
GCOM1	145781	broad.mit.edu	37	15	58000868	58000868	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58000868delA	uc002aem.2	+						GCOM1_uc002aeq.2_Intron|GCOM1_uc002aen.2_Intron|GCOM1_uc010bfy.2_Intron|GCOM1_uc002aeo.2_Intron|GCOM1_uc002aep.2_Intron|GCOM1_uc010bfx.2_Intron|GRINL1A_uc002aes.2_Intron|GRINL1A_uc002aev.1_Intron|GRINL1A_uc010ugu.1_Intron|GRINL1A_uc002aet.3_Intron|GRINL1A_uc002aeu.3_Intron	NM_001018090	NP_001018100			GRINL1A combined protein isoform 1						intracellular signal transduction	extrinsic to internal side of plasma membrane|I band				ovary(1)	1																		---	---	---	---
ADAM10	102	broad.mit.edu	37	15	59022203	59022203	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59022203delA	uc002afd.1	-						ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron|ADAM10_uc002afg.2_Intron	NM_001110	NP_001101			ADAM metallopeptidase domain 10 precursor						cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	59699491	59699491	+	IGR	DEL	T	-	-	rs35677105		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59699491delT								MYO1E (34420 upstream) : FAM81A (30881 downstream)																																			---	---	---	---
FAM81A	145773	broad.mit.edu	37	15	59811396	59811396	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59811396delT	uc002agc.2	+							NM_152450	NP_689663			hypothetical protein LOC145773											ovary(1)	1																		---	---	---	---
RORA	6095	broad.mit.edu	37	15	60931418	60931419	+	Intron	INS	-	T	T	rs78998110		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60931418_60931419insT	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	61115269	61115270	+	Intron	INS	-	CCTT	CCTT	rs143616698	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61115269_61115270insCCTT	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	61127099	61127099	+	Intron	DEL	T	-	-	rs76929717		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61127099delT	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	61511781	61511781	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61511781delA	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																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62336398	62336398	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62336398delA	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	63367902	63367903	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63367902_63367903delTT								TPM1 (3791 upstream) : LACTB (46129 downstream)																																			---	---	---	---
RAB8B	51762	broad.mit.edu	37	15	63498520	63498521	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63498520_63498521delTT	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																		---	---	---	---
RAB8B	51762	broad.mit.edu	37	15	63535920	63535920	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63535920delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	63698146	63698150	+	IGR	DEL	TGTTT	-	-	rs144832891	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63698146_63698150delTGTTT								CA12 (24071 upstream) : USP3 (98660 downstream)																																			---	---	---	---
USP3	9960	broad.mit.edu	37	15	63829779	63829779	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63829779delA	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)														---	---	---	---
FAM96A	84191	broad.mit.edu	37	15	64385734	64385734	+	Intron	DEL	A	-	-	rs77104671		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64385734delA	uc002amt.1	-						FAM96A_uc002amu.1_Intron|FAM96A_uc010uin.1_Intron|SNX1_uc010bgv.2_5'Flank|SNX1_uc010uio.1_5'Flank|SNX1_uc002amv.2_5'Flank|SNX1_uc002amw.2_5'Flank|SNX1_uc002amx.2_5'Flank|SNX1_uc002amy.2_5'Flank|SNX1_uc010bgw.2_5'Flank	NM_032231	NP_115607			family with sequence similarity 96, member A						chromosome segregation						0																		---	---	---	---
CSNK1G1	53944	broad.mit.edu	37	15	64494588	64494588	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64494588delT	uc002anf.2	-						CSNK1G1_uc002ane.2_Intron|CSNK1G1_uc002ang.1_Intron|CSNK1G1_uc002anh.1_Intron|CSNK1G1_uc002anj.2_Intron	NM_022048	NP_071331			casein kinase 1, gamma 1						Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0																		---	---	---	---
TRIP4	9325	broad.mit.edu	37	15	64686305	64686305	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64686305delA	uc002anm.2	+	2	305	c.262delA	c.(262-264)AAAfs	p.K88fs		NM_016213	NP_057297	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	88					positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ligand-dependent nuclear receptor binding|transcription coactivator activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
TRIP4	9325	broad.mit.edu	37	15	64687574	64687574	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64687574delT	uc002anm.2	+							NM_016213	NP_057297			thyroid hormone receptor interactor 4						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ligand-dependent nuclear receptor binding|transcription coactivator activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
ZNF609	23060	broad.mit.edu	37	15	64762725	64762725	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64762725delT	uc010bgy.2	+											SubName: Full=ZNF609 protein;							nucleus	zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
ZNF609	23060	broad.mit.edu	37	15	64839850	64839850	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64839850delT	uc002ann.2	+							NM_015042	NP_055857			zinc finger protein 609							nucleus	zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
RBPMS2	348093	broad.mit.edu	37	15	65046811	65046811	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65046811delA	uc002anq.2	-							NM_194272	NP_919248			RNA binding protein with multiple splicing 2								nucleic acid binding|nucleotide binding				0																		---	---	---	---
PDCD7	10081	broad.mit.edu	37	15	65428273	65428274	+	5'Flank	INS	-	TTGTTGTTGTTGTTG	TTGTTGTTGTTGTTG	rs141702187	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65428273_65428274insTTGTTGTTGTTGTTG	uc002aol.2	-							NM_005707	NP_005698			programmed cell death 7						apoptosis|induction of apoptosis|response to glucocorticoid stimulus	U12-type spliceosomal complex					0																		---	---	---	---
IGDCC4	57722	broad.mit.edu	37	15	65678319	65678319	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65678319delG	uc002aou.1	-	18	3240	c.3030delC	c.(3028-3030)CCCfs	p.P1010fs	IGDCC4_uc002aot.1_Frame_Shift_Del_p.P598fs	NM_020962	NP_066013	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member	1010	Cytoplasmic (Potential).					integral to membrane|plasma membrane				ovary(1)|pancreas(1)|skin(1)	3																OREG0023195	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	15	65732560	65732560	+	IGR	DEL	A	-	-	rs75604112		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65732560delA								IGDCC4 (17150 upstream) : DPP8 (5439 downstream)																																			---	---	---	---
C15orf44	81556	broad.mit.edu	37	15	65899821	65899823	+	Intron	DEL	AAT	-	-	rs3834547		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65899821_65899823delAAT	uc002apd.2	-						C15orf44_uc010uix.1_Intron|C15orf44_uc010uiz.1_Intron|C15orf44_uc010uja.1_Intron|C15orf44_uc010ujb.1_Intron|C15orf44_uc002ape.3_Intron|C15orf44_uc010uiy.1_Intron|C15orf44_uc010ujc.1_Intron	NM_030800	NP_110427			hypothetical protein LOC81556 isoform 2											ovary(1)	1																		---	---	---	---
DENND4A	10260	broad.mit.edu	37	15	65989151	65989151	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65989151delT	uc002aph.2	-						DENND4A_uc002api.2_Intron|DENND4A_uc002apj.3_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	66133850	66133850	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66133850delA								DENND4A (49219 upstream) : RAB11A (27946 downstream)																																			---	---	---	---
RAB11A	8766	broad.mit.edu	37	15	66180361	66180362	+	3'UTR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66180361_66180362insT	uc002apk.2	+	5					RAB11A_uc010ujk.1_3'UTR	NM_004663	NP_004654			Ras-related protein Rab-11A						cell cycle|cytokinesis|neuron projection development|plasma membrane to endosome transport|protein localization in plasma membrane|small GTPase mediated signal transduction|vesicle-mediated transport	cleavage furrow|plasma membrane|recycling endosome membrane|trans-Golgi network	GTP binding|GTPase activity|syntaxin binding				0																		---	---	---	---
DIS3L	115752	broad.mit.edu	37	15	66603786	66603787	+	Intron	INS	-	GT	GT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66603786_66603787insGT	uc010ujm.1	+						DIS3L_uc010ujl.1_Intron|DIS3L_uc002app.2_Intron|DIS3L_uc002apq.2_Intron|DIS3L_uc010bho.2_Intron	NM_001143688	NP_001137160			DIS3 mitotic control homolog (S.						rRNA catabolic process	cytoplasm|exosome (RNase complex)	exonuclease activity|protein binding|ribonuclease activity|RNA binding			ovary(2)	2																		---	---	---	---
SMAD3	4088	broad.mit.edu	37	15	67381265	67381265	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67381265delA	uc002aqj.2	+							NM_005902	NP_005893			mothers against decapentaplegic homolog 3						activation of caspase activity|cell cycle arrest|cell-cell junction organization|evasion of host defenses by virus|immune response|induction of apoptosis|negative regulation of cell growth|negative regulation of mitotic cell cycle|negative regulation of protein catabolic process|negative regulation of protein phosphorylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|protein stabilization|regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|transport|wound healing	cytosol|nuclear inner membrane|receptor complex	beta-catenin binding|co-SMAD binding|metal ion binding|protein homodimerization activity|protein kinase binding|R-SMAD binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor binding|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding			large_intestine(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)														---	---	---	---
AAGAB	79719	broad.mit.edu	37	15	67528577	67528577	+	Intron	DEL	A	-	-	rs35008448		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67528577delA	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																		---	---	---	---
MAP2K5	5607	broad.mit.edu	37	15	67915440	67915440	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67915440delA	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																		---	---	---	---
ANP32A	8125	broad.mit.edu	37	15	69072347	69072347	+	3'UTR	DEL	G	-	-	rs3214818		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69072347delG	uc002arl.2	-	7						NM_006305	NP_006296			acidic (leucine-rich) nuclear phosphoprotein 32						intracellular signal transduction|mRNA metabolic process|nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleoplasm|perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	70108585	70108585	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70108585delA								LOC145837 (244806 upstream) : C15orf50 (18988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70534887	70534888	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70534887_70534888insT								TLE3 (144631 upstream) : UACA (412007 downstream)																																			---	---	---	---
UACA	55075	broad.mit.edu	37	15	71004391	71004392	+	Intron	DEL	AT	-	-	rs66470788		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71004391_71004392delAT	uc002asr.2	-						UACA_uc010uke.1_Intron	NM_018003	NP_060473			uveal autoantigen with coiled-coil domains and							cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
UACA	55075	broad.mit.edu	37	15	71043171	71043171	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71043171delA	uc002asr.2	-						UACA_uc010uke.1_Intron	NM_018003	NP_060473			uveal autoantigen with coiled-coil domains and							cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
LRRC49	54839	broad.mit.edu	37	15	71175024	71175028	+	Intron	DEL	GACTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71175024_71175028delGACTT	uc002asu.2	+						THAP10_uc002asv.2_Intron	NM_017691	NP_060161			leucine rich repeat containing 49							cytoplasm|microtubule				ovary(1)	1																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71535607	71535608	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71535607_71535608insT	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	72112730	72112730	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72112730delT								NR2E3 (2135 upstream) : MYO9A (5639 downstream)																																			---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72243782	72243782	+	Intron	DEL	T	-	-	rs3830247		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72243782delT	uc002atl.3	-						MYO9A_uc010biq.2_Intron|MYO9A_uc002atn.1_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																		---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72289975	72289975	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72289975delA	uc002atl.3	-						MYO9A_uc010biq.2_Intron|MYO9A_uc002ato.2_Intron|MYO9A_uc002atn.1_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																		---	---	---	---
PKM2	5315	broad.mit.edu	37	15	72510473	72510473	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72510473delT	uc002atx.1	-						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)													---	---	---	---
BBS4	585	broad.mit.edu	37	15	73007603	73007603	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73007603delT	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	73290556	73290557	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73290556_73290557delTT								ADPGK (213889 upstream) : NEO1 (54318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	73323545	73323545	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73323545delA								ADPGK (246878 upstream) : NEO1 (21330 downstream)																																			---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73492865	73492868	+	Intron	DEL	AGAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73492865_73492868delAGAG	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	73558929	73558929	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73558929delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	73673512	73673514	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73673512_73673514delAAA								HCN4 (11907 upstream) : C15orf60 (61985 downstream)																																			---	---	---	---
C15orf60	283677	broad.mit.edu	37	15	73797381	73797381	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73797381delT	uc002avq.2	+						C15orf60_uc010bjb.2_Intron	NM_001042367	NP_001035826			hypothetical protein LOC283677											pancreas(1)	1																		---	---	---	---
CD276	80381	broad.mit.edu	37	15	74003465	74003465	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74003465delT	uc002avv.1	+						CD276_uc010bjd.1_Intron|CD276_uc002avu.1_Intron|CD276_uc002avw.1_Intron|CD276_uc010ulb.1_Intron|CD276_uc002avx.2_Intron	NM_001024736	NP_001019907			CD276 antigen isoform a						cell proliferation|immune response|positive regulation of interferon-gamma biosynthetic process|positive regulation of T cell proliferation|regulation of immune response|T cell activation	external side of plasma membrane|integral to membrane	receptor binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	74393230	74393230	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74393230delA								GOLGA6A (18339 upstream) : LOC283731 (25484 downstream)																																			---	---	---	---
CYP11A1	1583	broad.mit.edu	37	15	74649106	74649106	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74649106delC	uc002axt.2	-						CYP11A1_uc002axs.2_Intron|CYP11A1_uc010bjm.1_Intron|CYP11A1_uc010bjn.1_Intron|CYP11A1_uc010bjo.1_Intron|CYP11A1_uc010ulj.1_Intron|CYP11A1_uc010bjq.2_Intron|uc002axu.2_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)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	74822064	74822066	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74822064_74822066delTTT								UBL7 (68535 upstream) : ARID3B (11482 downstream)																																			---	---	---	---
ARID3B	10620	broad.mit.edu	37	15	74870037	74870038	+	Intron	INS	-	GT	GT	rs144994380	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74870037_74870038insGT	uc002aye.2	+						ARID3B_uc002ayd.2_Intron	NM_006465	NP_006456			AT rich interactive domain 3B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
EDC3	80153	broad.mit.edu	37	15	74979528	74979528	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74979528delA	uc002ayn.2	-						EDC3_uc002ayo.2_Intron|EDC3_uc002aym.2_Intron	NM_001142443	NP_001135915			enhancer of mRNA decapping 3						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			ovary(1)	1																		---	---	---	---
SCAMP5	192683	broad.mit.edu	37	15	75311041	75311041	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75311041delT	uc002azk.1	+						SCAMP5_uc002azl.1_Intron|SCAMP5_uc002azm.1_Intron|SCAMP5_uc002azn.1_Intron|SCAMP5_uc010uly.1_Intron	NM_138967	NP_620417			secretory carrier membrane protein 5						exocytosis|negative regulation of endocytosis|positive regulation of calcium ion-dependent exocytosis|positive regulation of cytokine secretion|protein transport|response to endoplasmic reticulum stress	cell junction|integral to membrane|recycling endosome membrane|synaptic vesicle membrane|trans-Golgi network membrane	protein binding			ovary(1)	1																		---	---	---	---
SIN3A	25942	broad.mit.edu	37	15	75706706	75706706	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
CSPG4	1464	broad.mit.edu	37	15	75999209	75999209	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75999209delA	uc002baw.2	-							NM_001897	NP_001888			chondroitin sulfate proteoglycan 4 precursor						angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3																		---	---	---	---
NRG4	145957	broad.mit.edu	37	15	76243229	76243229	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76243229delT	uc002bbo.2	-						NRG4_uc010bkm.1_Intron|NRG4_uc002bbn.2_Intron|NRG4_uc010bkn.2_Intron|NRG4_uc010bko.2_Intron	NM_138573	NP_612640			neuregulin 4							extracellular region|integral to membrane|plasma membrane	growth factor activity				0																		---	---	---	---
C15orf27	123591	broad.mit.edu	37	15	76365280	76365280	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76365280delT	uc002bbq.2	+						C15orf27_uc010bkp.2_Intron	NM_152335	NP_689548			hypothetical protein LOC123591							integral to membrane					0																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76929886	76929886	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76929886delT	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																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	77018799	77018799	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77018799delA	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron|SCAPER_uc002bca.1_Intron|SCAPER_uc002bcb.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																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	77167555	77167556	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77167555_77167556insA	uc002bby.2	-						SCAPER_uc002bbz.1_Intron|SCAPER_uc002bca.1_Intron|SCAPER_uc002bcb.1_Intron|SCAPER_uc002bcc.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																		---	---	---	---
RCN2	5955	broad.mit.edu	37	15	77239729	77239729	+	Intron	DEL	T	-	-	rs3215250		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77239729delT	uc002bcd.2	+						RCN2_uc002bce.2_Intron|RCN2_uc010bks.2_Intron	NM_002902	NP_002893			reticulocalbin 2 precursor							endoplasmic reticulum lumen	calcium ion binding				0																		---	---	---	---
PSTPIP1	9051	broad.mit.edu	37	15	77310786	77310786	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77310786delT	uc002bcf.2	+						PSTPIP1_uc010bkt.1_Intron|PSTPIP1_uc010umo.1_Intron|PSTPIP1_uc010bku.1_Intron|PSTPIP1_uc002bcg.2_Intron|PSTPIP1_uc010bkv.1_Intron|PSTPIP1_uc010bkw.1_Intron	NM_003978	NP_003969			proline-serine-threonine phosphatase interacting						cell adhesion|signal transduction	cleavage furrow|lamellipodium|perinuclear region of cytoplasm	catalytic activity			ovary(1)	1																		---	---	---	---
HMG20A	10363	broad.mit.edu	37	15	77753444	77753444	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77753444delA	uc002bcr.2	+						HMG20A_uc002bcq.1_Intron|HMG20A_uc002bcs.2_Intron	NM_018200	NP_060670			high-mobility group 20A						chromatin modification	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
LINGO1	84894	broad.mit.edu	37	15	77956509	77956514	+	Intron	DEL	GTGTGC	-	-	rs148569014	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77956509_77956514delGTGTGC	uc002bcu.1	-							NM_032808	NP_116197			leucine-rich repeat neuronal 6A						negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane				ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	78282902	78282903	+	IGR	INS	-	CTTAACCCTGAT	CTTAACCCTGAT	rs143794049	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78282902_78282903insCTTAACCCTGAT								LOC645752 (63714 upstream) : LOC91450 (2673 downstream)																																			---	---	---	---
CIB2	10518	broad.mit.edu	37	15	78407239	78407239	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78407239delA	uc002bdb.1	-						CIB2_uc002bdc.1_Intron|CIB2_uc010ums.1_Intron	NM_006383	NP_006374			DNA-dependent protein kinase catalytic								calcium ion binding				0																		---	---	---	---
IDH3A	3419	broad.mit.edu	37	15	78456697	78456700	+	Intron	DEL	TTTT	-	-	rs144772337		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78456697_78456700delTTTT	uc002bdd.2	+						IDH3A_uc010umt.1_Intron|IDH3A_uc010umu.1_Intron|IDH3A_uc002bde.2_Intron|IDH3A_uc010umv.1_Intron|IDH3A_uc002bdf.2_Intron|IDH3A_uc002bdg.2_Intron	NM_005530	NP_005521			isocitrate dehydrogenase 3 (NAD+) alpha						carbohydrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	isocitrate dehydrogenase (NAD+) activity|magnesium ion binding|NAD binding				0					NADH(DB00157)													---	---	---	---
IREB2	3658	broad.mit.edu	37	15	78758544	78758544	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	78842835	78842836	+	IGR	INS	-	T	T	rs144365532	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78842835_78842836insT								PSMA4 (1275 upstream) : CHRNA5 (15070 downstream)																																			---	---	---	---
MORF4L1	10933	broad.mit.edu	37	15	79172835	79172835	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79172835delT	uc002bel.2	+						MORF4L1_uc010bli.1_Intron|MORF4L1_uc010blj.1_Intron|MORF4L1_uc002bem.2_Intron|MORF4L1_uc010une.1_Intron	NM_206839	NP_996670			MORF-related gene 15 isoform 2						double-strand break repair via homologous recombination|histone deacetylation|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|Sin3 complex	protein N-terminus binding				0																		---	---	---	---
RASGRF1	5923	broad.mit.edu	37	15	79345065	79345065	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79345065delG	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	79817875	79817875	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79817875delT								KIAA1024 (53233 upstream) : MTHFS (319445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	79996915	79996915	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79996915delT								KIAA1024 (232273 upstream) : MTHFS (140405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80908263	80908263	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80908263delC								ARNT2 (17991 upstream) : FAM108C1 (79389 downstream)																																			---	---	---	---
MESDC2	23184	broad.mit.edu	37	15	81272982	81272982	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81272982delA	uc002bfy.1	-						MESDC2_uc002bfx.2_Intron|MESDC2_uc010uno.1_Intron	NM_015154	NP_055969			mesoderm development candidate 2						mesoderm development|protein folding|Wnt receptor signaling pathway	endoplasmic reticulum					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	81705818	81705818	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81705818delA								TMC3 (39400 upstream) : MEX3B (628310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	82039000	82039000	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82039000delT								TMC3 (372582 upstream) : MEX3B (295128 downstream)																																			---	---	---	---
GOLGA6L10	647042	broad.mit.edu	37	15	83014189	83014190	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83014189_83014190delAA	uc010unt.1	-						uc002bhl.2_Intron|uc002bhm.2_Intron|GOLGA6L10_uc010uny.1_Intron|GOLGA6L10_uc002bia.1_5'Flank					Homo sapiens cDNA FLJ40113 fis, clone TESTI2008621.												0																		---	---	---	---
CPEB1	64506	broad.mit.edu	37	15	83243976	83243977	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83243976_83243977insG	uc002bit.2	-						CPEB1_uc010uoe.1_5'Flank|CPEB1_uc002biu.2_Intron|CPEB1_uc010uof.1_Intron|CPEB1_uc002biv.2_Intron	NM_001079533	NP_001073001			cytoplasmic polyadenylation element binding						mRNA processing|regulation of translation	cell junction|cytoplasmic mRNA processing body|dendrite|postsynaptic density|postsynaptic membrane	nucleotide binding|RNA binding			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(143;0.229)															---	---	---	---
FSD2	123722	broad.mit.edu	37	15	83432427	83432428	+	Intron	INS	-	TT	TT	rs146376727	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83432427_83432428insTT	uc002bjd.2	-						FSD2_uc010uol.1_Intron|FSD2_uc010uom.1_Intron	NM_001007122	NP_001007123			fibronectin type III and SPRY domain containing											central_nervous_system(1)	1																		---	---	---	---
FSD2	123722	broad.mit.edu	37	15	83434691	83434691	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83434691delC	uc002bjd.2	-	10	1813	c.1646delG	c.(1645-1647)GGCfs	p.G549fs	FSD2_uc010uol.1_Frame_Shift_Del_p.G504fs|FSD2_uc010uom.1_Frame_Shift_Del_p.G504fs	NM_001007122	NP_001007123	A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing	549	Fibronectin type-III 2.|B30.2/SPRY.									central_nervous_system(1)	1																		---	---	---	---
TM6SF1	53346	broad.mit.edu	37	15	83805312	83805312	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83805312delT	uc002bjp.2	+	10	1110	c.1001delT	c.(1000-1002)CTTfs	p.L334fs	TM6SF1_uc010bmq.2_Frame_Shift_Del_p.L303fs|TM6SF1_uc002bjq.2_3'UTR|TM6SF1_uc010bmr.2_RNA|TM6SF1_uc002bjr.2_Frame_Shift_Del_p.L186fs	NM_023003	NP_075379	Q9BZW5	TM6S1_HUMAN	transmembrane 6 superfamily member 1 isoform 1	334	Helical; (Potential).					integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	84017272	84017273	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84017272_84017273delAA								BNC1 (63804 upstream) : SH3GL3 (98818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	84024616	84024616	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84024616delA								BNC1 (71148 upstream) : SH3GL3 (91475 downstream)																																			---	---	---	---
SH3GL3	6457	broad.mit.edu	37	15	84159018	84159018	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84159018delT	uc002bjw.2	+						SH3GL3_uc010bms.2_Intron|SH3GL3_uc010uot.1_Intron|SH3GL3_uc002bjx.2_Intron|SH3GL3_uc002bju.2_Intron|SH3GL3_uc002bjv.2_Intron	NM_003027	NP_003018			SH3-domain GRB2-like 3						central nervous system development|endocytosis|signal transduction	early endosome membrane	identical protein binding|lipid binding			pancreas(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84489830	84489830	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84489830delA	uc002bjz.3	+						ADAMTSL3_uc002bjy.1_Intron|ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400			ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84527645	84527646	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84527645_84527646insA	uc002bjz.3	+						ADAMTSL3_uc002bjy.1_Intron|ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400			ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
UBE2Q2P1	388165	broad.mit.edu	37	15	85109937	85109937	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85109937delA	uc002bkn.1	-							NR_003661				Homo sapiens cDNA FLJ43276 fis, clone KIDNE2011532, moderately similar to Homo sapiens melanoma-associated chondroitin sulfate proteoglycan 4.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	85121557	85121558	+	RNA	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85121557_85121558delAA	uc002bko.1	+	3		c.757_758delAA								Homo sapiens cDNA: FLJ22824 fis, clone KAIA3991.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	85126413	85126414	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85126413_85126414delAC								UBE2Q2P1 (12387 upstream) : ZSCAN2 (17835 downstream)																																			---	---	---	---
SEC11A	23478	broad.mit.edu	37	15	85254637	85254637	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85254637delA	uc002blb.1	-						SEC11A_uc002blc.1_Intron	NM_014300	NP_055115			SEC11-like 1						energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	endoplasmic reticulum membrane|integral to membrane|microsome	protein binding|serine-type peptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(143;0.199)															---	---	---	---
ALPK3	57538	broad.mit.edu	37	15	85388088	85388089	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85388088_85388089delAA	uc002ble.2	+							NM_020778	NP_065829			alpha-kinase 3						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)															---	---	---	---
SLC28A1	9154	broad.mit.edu	37	15	85449805	85449820	+	Intron	DEL	CTTCCTTCCTTCCTTC	-	-	rs62021373		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85449805_85449820delCTTCCTTCCTTCCTTC	uc002blg.2	+						SLC28A1_uc010upd.1_Intron|SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204			solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
SLC28A1	9154	broad.mit.edu	37	15	85459161	85459163	+	Intron	DEL	TGT	-	-	rs71466061		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85459161_85459163delTGT	uc002blg.2	+						SLC28A1_uc010upd.1_Intron|SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204			solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
SLC28A1	9154	broad.mit.edu	37	15	85472221	85472221	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85472221delC	uc002blg.2	+						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	85634360	85634360	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85634360delA	uc002blh.2	+	8	989	c.800delA	c.(799-801)GAAfs	p.E267fs	PDE8A_uc002bli.2_Intron|PDE8A_uc010bnc.2_Frame_Shift_Del_p.E20fs|PDE8A_uc010bnd.2_Frame_Shift_Del_p.E20fs|PDE8A_uc002blj.2_Intron|PDE8A_uc002blk.2_Intron	NM_002605	NP_002596	O60658	PDE8A_HUMAN	phosphodiesterase 8A isoform 1	267	PAS.				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	85785266	85785266	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85785266delT	uc010upj.1	+							NM_198181	NP_937824			golgi autoantigen, golgin subfamily a, 6D-like																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	85842954	85842955	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85842954_85842955delAA								PDE8A (160584 upstream) : AKAP13 (80916 downstream)																																			---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	86082434	86082434	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86082434delT	uc002blv.1	+						AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron	NM_007200	NP_009131			A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	86283954	86283955	+	Intron	INS	-	AC	AC	rs144018637	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86283954_86283955insAC	uc002blv.1	+						AKAP13_uc002blu.1_Intron|AKAP13_uc002blw.1_Intron|AKAP13_uc002blx.1_Intron	NM_007200	NP_009131			A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
KLHL25	64410	broad.mit.edu	37	15	86325283	86325283	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86325283delA	uc002bly.2	-							NM_022480	NP_071925			BTB/POZ KELCH domain protein							cytoplasm				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	86348633	86348633	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86348633delA								KLHL25 (10444 upstream) : AGBL1 (336609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	86447352	86447352	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86447352delA								KLHL25 (109163 upstream) : AGBL1 (237890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	86547657	86547658	+	IGR	INS	-	TGTG	TGTG	rs111846783		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86547657_86547658insTGTG								KLHL25 (209468 upstream) : AGBL1 (137584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	86561434	86561435	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86561434_86561435insA								KLHL25 (223245 upstream) : AGBL1 (123807 downstream)																																			---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	86778669	86778669	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86778669delA	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	86923509	86923510	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86923509_86923510delTT	uc002blz.1	+							NM_152336	NP_689549			ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	87928557	87928557	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87928557delT								AGBL1 (356274 upstream) : NCRNA00052 (191603 downstream)																																			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88423337	88423337	+	Intron	DEL	T	-	-	rs71851481		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88423337delT	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.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)			---	---	---	---
Unknown	0	broad.mit.edu	37	15	89001565	89001565	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89001565delA								NTRK3 (201904 upstream) : MRPL46 (1143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	89122935	89122935	+	IGR	DEL	A	-	-	rs34032513		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89122935delA								DET1 (33023 upstream) : MIR1179 (28403 downstream)																																			---	---	---	---
ABHD2	11057	broad.mit.edu	37	15	89644099	89644099	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89644099delA	uc002bnj.2	+						ABHD2_uc010ups.1_Intron|ABHD2_uc002bnk.2_Intron	NM_007011	NP_008942			alpha/beta hydrolase domain containing protein							integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)																	---	---	---	---
RLBP1	6017	broad.mit.edu	37	15	89767513	89767514	+	5'Flank	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89767513_89767514delTT	uc002bnl.2	-							NM_000326	NP_000317			retinaldehyde binding protein 1						response to stimulus|visual perception|vitamin A metabolic process	cytoplasm|soluble fraction	retinol binding|transporter activity			central_nervous_system(1)	1	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)													---	---	---	---
FANCI	55215	broad.mit.edu	37	15	89813049	89813050	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89813049_89813050delTT	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				---	---	---	---
POLG	5428	broad.mit.edu	37	15	89859551	89859551	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89859551delT	uc002bns.3	-	23					FANCI_uc010bnp.1_Intron|FANCI_uc002bnm.1_Intron|FANCI_uc002bnn.1_Intron|FANCI_uc002bnp.1_Intron|FANCI_uc002bnq.1_Intron|POLG_uc002bnr.3_3'UTR	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)					---	---	---	---
Unknown	0	broad.mit.edu	37	15	89893816	89893817	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89893816_89893817insT								POLG (15790 upstream) : LOC254559 (10993 downstream)																																			---	---	---	---
LOC254559	254559	broad.mit.edu	37	15	89931254	89931254	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89931254delT	uc002bnt.2	+						LOC254559_uc002bnv.2_Intron|LOC254559_uc002bnw.2_Intron					Homo sapiens cDNA FLJ30148 fis, clone BRACE2000267.												0																		---	---	---	---
AP3S2	10239	broad.mit.edu	37	15	90414601	90414601	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90414601delA	uc002boq.3	-						AP3S2_uc002bos.3_Intron|AP3S2_uc010bns.2_Intron|AP3S2_uc002bor.3_Intron|AP3S2_uc010bnt.2_Intron	NM_005829	NP_005820			adaptor-related protein complex 3, sigma 2						intracellular protein transport|vesicle-mediated transport	cytoplasmic vesicle membrane|Golgi apparatus|membrane coat	protein transporter activity				0	Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)															---	---	---	---
ZNF710	374655	broad.mit.edu	37	15	90617233	90617234	+	Intron	DEL	AA	-	-	rs11424945		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90617233_90617234delAA	uc002bov.1	+							NM_198526	NP_940928			zinc finger protein 710						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)															---	---	---	---
IDH2	3418	broad.mit.edu	37	15	90632138	90632144	+	Intron	DEL	ATTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90632138_90632144delATTTTTT	uc002box.2	-						IDH2_uc010uqb.1_Intron|IDH2_uc010uqc.1_Intron|IDH2_uc010bnu.2_Intron	NM_002168	NP_002159			isocitrate dehydrogenase 2 (NADP+),						2-oxoglutarate metabolic process|glyoxylate cycle|isocitrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding			haematopoietic_and_lymphoid_tissue(621)|central_nervous_system(80)|bone(7)|skin(3)	711	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)					M		GBM								---	---	---	---
C15orf58	390637	broad.mit.edu	37	15	90781533	90781533	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90781533delA	uc002bpc.2	+							NM_001013657	NP_001013679			hypothetical protein LOC390637						glucose metabolic process	cytoplasm	GDP-D-glucose phosphorylase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	90868742	90868742	+	IGR	DEL	A	-	-	rs78745053	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90868742delA								TTLL13 (53299 upstream) : GABARAPL3 (21023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	90875715	90875716	+	IGR	DEL	TT	-	-	rs35040546		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90875715_90875716delTT								TTLL13 (60272 upstream) : GABARAPL3 (14049 downstream)																																			---	---	---	---
CRTC3	64784	broad.mit.edu	37	15	91116868	91116868	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91116868delT	uc002bpp.2	+						CRTC3_uc002bpn.2_Intron|CRTC3_uc002bpo.2_Intron	NM_022769	NP_073606			transducer of regulated CREB protein 3 isoform						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus			CRTC3/MAML2(26)	salivary_gland(26)|ovary(1)	27	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)					T	MAML2	salivary gland mucoepidermoid								---	---	---	---
CRTC3	64784	broad.mit.edu	37	15	91186961	91186961	+	3'UTR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91186961delG	uc002bpp.2	+	15					CRTC3_uc002bpo.2_3'UTR	NM_022769	NP_073606			transducer of regulated CREB protein 3 isoform						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus			CRTC3/MAML2(26)	salivary_gland(26)|ovary(1)	27	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)					T	MAML2	salivary gland mucoepidermoid								---	---	---	---
Unknown	0	broad.mit.edu	37	15	91370809	91370810	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91370809_91370810delTT								BLM (12125 upstream) : FURIN (41075 downstream)																																			---	---	---	---
MAN2A2	4122	broad.mit.edu	37	15	91465145	91465145	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91465145delA	uc002bqc.2	+	22					MAN2A2_uc010uql.1_3'UTR|MAN2A2_uc010uqm.1_3'UTR	NM_006122	NP_006113			mannosidase, alpha, class 2A, member 2						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			large_intestine(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)															---	---	---	---
VPS33B	26276	broad.mit.edu	37	15	91567301	91567301	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91567301delT	uc002bqp.1	-						VPS33B_uc002bqq.1_5'Flank|VPS33B_uc010uqu.1_5'Flank|uc002bqr.1_Intron|uc002bqs.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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	15	92164408	92164408	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92164408delA								SV2B (325760 upstream) : SLCO3A1 (232530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	92217364	92217364	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92217364delA								SV2B (378716 upstream) : SLCO3A1 (179574 downstream)																																			---	---	---	---
SLCO3A1	28232	broad.mit.edu	37	15	92409449	92409449	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92409449delA	uc002bqx.2	+						SLCO3A1_uc002bqy.2_Intron|SLCO3A1_uc010boc.1_Intron|SLCO3A1_uc002bqz.1_Intron	NM_013272	NP_037404			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)															---	---	---	---
ST8SIA2	8128	broad.mit.edu	37	15	92999576	92999577	+	Intron	INS	-	C	C	rs148255959	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92999576_92999577insC	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)															---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93536457	93536457	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93536457delT	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)															---	---	---	---
RGMA	56963	broad.mit.edu	37	15	93619048	93619048	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93619048delT	uc002bss.1	-						RGMA_uc002bsq.1_5'Flank|RGMA_uc010boi.1_5'Flank|RGMA_uc002bsr.1_5'Flank|RGMA_uc010urc.1_5'Flank	NM_020211	NP_064596			RGM domain family, member A precursor						axon guidance	anchored to membrane|endoplasmic reticulum|plasma membrane					0	Lung NSC(78;0.0542)|all_lung(78;0.0786)		BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	93786744	93786745	+	IGR	INS	-	TG	TG	rs149546481	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93786744_93786745insTG								RGMA (154311 upstream) : MCTP2 (988056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	93882126	93882126	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93882126delG	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	94607274	94607274	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94607274delT								RGMA (974841 upstream) : MCTP2 (167527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95354806	95354807	+	IGR	DEL	AT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95354806_95354807delAT								MCTP2 (327626 upstream) : LOC145820 (621515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95500125	95500125	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95500125delC								MCTP2 (472945 upstream) : LOC145820 (476197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95830956	95830958	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95830956_95830958delAAA	uc002btm.2	-											Homo sapiens hypothetical gene supported by BC040875, mRNA (cDNA clone IMAGE:5721930).																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	96996371	96996372	+	IGR	INS	-	GT	GT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96996371_96996372insGT								NR2F2 (112881 upstream) : SPATA8 (330307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97170610	97170610	+	IGR	DEL	C	-	-	rs79611327		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97170610delC								NR2F2 (287120 upstream) : SPATA8 (156069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97216253	97216254	+	IGR	DEL	AA	-	-	rs35122809		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97216253_97216254delAA								NR2F2 (332763 upstream) : SPATA8 (110425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97369796	97369796	+	IGR	DEL	T	-	-	rs75338337		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97369796delT								SPATA8 (40952 upstream) : LOC91948 (916050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97846380	97846380	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97846380delT								SPATA8 (517536 upstream) : LOC91948 (439466 downstream)																																			---	---	---	---
ARRDC4	91947	broad.mit.edu	37	15	98514138	98514138	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98514138delT	uc010bom.2	+						ARRDC4_uc002bui.3_Intron	NM_183376	NP_899232			arrestin domain containing 4						signal transduction						0	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)															---	---	---	---
PGPEP1L	145814	broad.mit.edu	37	15	99512588	99512588	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99512588delG	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	99590280	99590281	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99590280_99590281insT								PGPEP1L (39256 upstream) : SYNM (55005 downstream)																																			---	---	---	---
TTC23	64927	broad.mit.edu	37	15	99778338	99778338	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99778338delT	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	100089509	100089514	+	IGR	DEL	TTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100089509_100089514delTTTTTT								LRRC28 (162229 upstream) : MEF2A (16619 downstream)																																			---	---	---	---
MEF2A	4205	broad.mit.edu	37	15	100134081	100134081	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100134081delA	uc002bve.2	+						MEF2A_uc010urv.1_Intron|MEF2A_uc010bos.2_Intron|MEF2A_uc002bvf.2_Intron|MEF2A_uc002bvg.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)															---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100544571	100544572	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100544571_100544572insC	uc002bvv.1	-							NM_139057	NP_620688			ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)														---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100598546	100598547	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100598546_100598547insT	uc002bvv.1	-							NM_139057	NP_620688			ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)														---	---	---	---
ALDH1A3	220	broad.mit.edu	37	15	101448785	101448785	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101448785delC	uc002bwn.3	+						ALDH1A3_uc010bpb.2_Intron|uc002bwo.1_Intron	NM_000693	NP_000684			aldehyde dehydrogenase 1A3						retinal metabolic process	cytoplasm	aldehyde dehydrogenase|protein homodimerization activity			central_nervous_system(2)|lung(1)|pancreas(1)	4	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		NADH(DB00157)|Vitamin A(DB00162)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	101629674	101629677	+	IGR	DEL	TGTT	-	-	rs142907577	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101629674_101629677delTGTT								LRRK1 (19359 upstream) : CHSY1 (86255 downstream)																																	OREG0023523	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	15	101799913	101799914	+	IGR	INS	-	G	G	rs113269205		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101799913_101799914insG								CHSY1 (7787 upstream) : SELS (11300 downstream)																																			---	---	---	---
PCSK6	5046	broad.mit.edu	37	15	101991763	101991763	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101991763delA	uc002bwy.2	-						PCSK6_uc010bpe.2_Intron|PCSK6_uc002bxa.2_Intron|PCSK6_uc002bxb.2_Intron|PCSK6_uc002bxc.1_Intron|PCSK6_uc002bxd.1_Intron|PCSK6_uc002bxe.2_Intron|PCSK6_uc002bxg.1_Intron	NM_002570	NP_002561			paired basic amino acid cleaving system 4						glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	102112387	102112387	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102112387delA								PCSK6 (82200 upstream) : TM2D3 (60793 downstream)																																			---	---	---	---
TM2D3	80213	broad.mit.edu	37	15	102185369	102185369	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
MRPL28	10573	broad.mit.edu	37	16	418761	418762	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:418761_418762insC	uc002cgr.1	-						MRPL28_uc010bqu.1_Intron|MRPL28_uc002cgs.1_Intron|MRPL28_uc002cgt.1_Intron	NM_006428	NP_006419			mitochondrial ribosomal protein L28 precursor						translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)																---	---	---	---
RAB11FIP3	9727	broad.mit.edu	37	16	521162	521162	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:521162delC	uc002chf.2	+							NM_014700	NP_055515			rab11-family interacting protein 3 isoform 1						cell cycle|cytokinesis|endocytic recycling|protein transport	centrosome|cleavage furrow|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		Hepatocellular(16;0.0218)														OREG0003708	type=REGULATORY REGION|Gene=BC009036|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
SOLH	6650	broad.mit.edu	37	16	588947	588947	+	Intron	DEL	T	-	-	rs113024162		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:588947delT	uc002chi.2	+						SOLH_uc002chg.2_RNA|SOLH_uc002chh.1_Intron	NM_005632	NP_005623			small optic lobes						proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)	2		Hepatocellular(780;0.00335)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	634792	634793	+	5'Flank	DEL	CT	-	-	rs59164425		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:634792_634793delCT	uc010uuj.1	-											SubName: Full=cDNA FLJ56783;																														---	---	---	---
LMF1	64788	broad.mit.edu	37	16	920134	920134	+	Intron	DEL	G	-	-	rs111946394		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:920134delG	uc002ckj.2	-						LMF1_uc010brg.2_5'Flank|LMF1_uc010brh.2_Intron|LMF1_uc010bri.2_Intron|LMF1_uc002ckk.2_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	1075451	1075474	+	IGR	DEL	GGTGTGGAGGGTGCTGAGGTCCCC	-	-	rs72269290	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1075451_1075474delGGTGTGGAGGGTGCTGAGGTCCCC								SOX8 (38473 upstream) : LOC146336 (38610 downstream)																																			---	---	---	---
LOC146336	146336	broad.mit.edu	37	16	1117764	1117765	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1117764_1117765insT	uc002cko.2	-							NR_027242				SubName: Full=cDNA FLJ32252 fis, clone PROST1000167, weakly similar to SYNAPSIN I;												0																		---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1228416	1228417	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1228416_1228417insC	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	1314535	1314538	+	IGR	DEL	TGTA	-	-	rs10578636		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1314535_1314538delTGTA								TPSD1 (6041 upstream) : UBE2I (44642 downstream)																																			---	---	---	---
UBE2I	7329	broad.mit.edu	37	16	1357753	1357756	+	5'Flank	DEL	GAAT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1357753_1357756delGAAT	uc002clc.1	+						uc010uuy.1_RNA|UBE2I_uc002cld.1_5'Flank|UBE2I_uc002cle.1_5'Flank|UBE2I_uc002clf.1_5'Flank|UBE2I_uc002clg.1_5'Flank	NM_194261	NP_919237			ubiquitin-conjugating enzyme E2I						cell division|chromosome segregation|interspecies interaction between organisms|mitosis|negative regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|protein sumoylation	cytoplasm|PML body|synaptonemal complex	ATP binding|enzyme binding|ubiquitin-protein ligase activity			breast(1)|skin(1)	2		Hepatocellular(780;0.00369)																---	---	---	---
GNPTG	84572	broad.mit.edu	37	16	1411645	1411645	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1411645delA	uc002clm.2	+							NM_032520	NP_115909			N-acetylglucosamine-1-phosphotransferase, gamma							extracellular region|Golgi apparatus	protein binding			central_nervous_system(1)	1		Hepatocellular(780;0.0893)																---	---	---	---
UNKL	64718	broad.mit.edu	37	16	1417261	1417263	+	In_Frame_Del	DEL	CTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1417261_1417263delCTT	uc010brn.1	-	8	1015_1017	c.997_999delAAG	c.(997-999)AAGdel	p.K333del	UNKL_uc002cln.2_In_Frame_Del_p.K125del|UNKL_uc002clo.2_In_Frame_Del_p.K122del|UNKL_uc002clp.2_In_Frame_Del_p.K125del			Q9H9P5	UNKL_HUMAN	SubName: Full=Putative ubiquitin-protein ligase;          EC=6.3.2.19; Flags: Fragment;	623						cytoplasm|nucleus	ligase activity|nucleic acid binding|zinc ion binding				0		Hepatocellular(780;0.0893)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	1528131	1528131	+	IGR	DEL	A	-	-	rs113910908		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1528131delA								CLCN7 (3046 upstream) : PTX4 (7810 downstream)																																			---	---	---	---
HN1L	90861	broad.mit.edu	37	16	1744692	1744692	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1744692delT	uc002cmg.2	+						HN1L_uc010uvi.1_Intron|HN1L_uc010brt.2_Intron|HN1L_uc010bru.2_Intron|HN1L_uc010uvj.1_Intron|HN1L_uc010uvk.1_Intron	NM_144570	NP_653171			hematological and neurological expressed 1-like							cytoplasm|nucleus				upper_aerodigestive_tract(1)	1																		---	---	---	---
C16orf73	254528	broad.mit.edu	37	16	1885264	1885264	+	Intron	DEL	A	-	-	rs75808584		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1885264delA	uc002cne.2	-						FAHD1_uc002cnd.2_Intron|FAHD1_uc010brz.2_Intron|C16orf73_uc010uvq.1_Intron|C16orf73_uc010uvr.1_Intron	NM_152764	NP_689977			hypothetical protein LOC254528 isoform 2						meiosis	cytoplasm					0																		---	---	---	---
PKD1	5310	broad.mit.edu	37	16	2166583	2166583	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2166583delG	uc002cos.1	-	8	1878	c.1669delC	c.(1669-1671)CTGfs	p.L557fs	PKD1_uc002cot.1_Frame_Shift_Del_p.L557fs	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	557	Extracellular (Potential).				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																		---	---	---	---
TRAF7	84231	broad.mit.edu	37	16	2211168	2211168	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2211168delC	uc002cow.2	+							NM_032271	NP_115647			TNF receptor-associated factor 7						activation of MAPKKK activity|apoptosis|regulation of apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic membrane-bounded vesicle|ubiquitin ligase complex	identical protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3																		---	---	---	---
DCI	1632	broad.mit.edu	37	16	2290222	2290224	+	Intron	DEL	TTA	-	-	rs26843	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2290222_2290224delTTA	uc002cpr.2	-						DCI_uc002cps.2_Intron	NM_001919	NP_001910			dodecenoyl-Coenzyme A delta isomerase precursor						fatty acid beta-oxidation	mitochondrial matrix	dodecenoyl-CoA delta-isomerase activity				0																		---	---	---	---
TBC1D24	57465	broad.mit.edu	37	16	2566646	2566646	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2566646delT	uc002cqm.2	+						ATP6V0C_uc002cqn.2_Intron|ATP6V0C_uc002cqo.2_5'Flank	NM_020705	NP_065756			TBC1 domain family, member 24						neuron projection development	cytoplasm	protein binding|Rab GTPase activator activity				0																		---	---	---	---
LOC652276	652276	broad.mit.edu	37	16	2660450	2660451	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2660450_2660451delTT	uc002cqx.2	+						LOC652276_uc002cqy.3_Intron					Homo sapiens cDNA FLJ39075 fis, clone NT2RP7016911.												0																		---	---	---	---
SRRM2	23524	broad.mit.edu	37	16	2819161	2819163	+	In_Frame_Del	DEL	TCT	-	-	rs149101693	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2819161_2819163delTCT	uc002crk.2	+	12	8446_8448	c.7897_7899delTCT	c.(7897-7899)TCTdel	p.S2648del		NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	2648	Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
TCEB2	6923	broad.mit.edu	37	16	2821616	2821616	+	3'UTR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2821616delG	uc002crn.2	-	4					TCEB2_uc002crm.2_Intron	NM_007108	NP_009039			elongin B isoform a						positive regulation of viral transcription|protein complex assembly|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|nucleoplasm	protein binding				0																		---	---	---	---
PKMYT1	9088	broad.mit.edu	37	16	3031648	3031648	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3031648delA	uc002csn.2	-						PKMYT1_uc002csm.2_5'Flank|PKMYT1_uc002cso.2_5'Flank|PKMYT1_uc002csp.2_5'Flank|PKMYT1_uc002csq.2_5'Flank	NM_004203	NP_004194			protein kinase Myt1 isoform 1						G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis	endoplasmic reticulum membrane|Golgi membrane|membrane fraction|nucleoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)	1																		---	---	---	---
HCFC1R1	54985	broad.mit.edu	37	16	3073537	3073537	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3073537delA	uc002csx.1	-						HCFC1R1_uc002csy.1_Intron|HCFC1R1_uc002csz.1_Intron|THOC6_uc002ctb.2_5'Flank|THOC6_uc002ctd.2_5'Flank|THOC6_uc002ctc.2_5'Flank|THOC6_uc002cta.2_5'Flank	NM_001002018	NP_001002018			host cell factor C1 regulator 1 (XPO1 dependant)							cytoplasm|nucleus					0																		---	---	---	---
CLUAP1	23059	broad.mit.edu	37	16	3569691	3569691	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3569691delA	uc002cvk.1	+						CLUAP1_uc002cvj.1_Intron|CLUAP1_uc002cvl.1_Intron|CLUAP1_uc002cvm.1_Intron	NM_015041	NP_055856			clusterin associated protein 1 isoform 1							nucleus	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	3669676	3669676	+	IGR	DEL	A	-	-	rs112990379		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3669676delA								BTBD12 (8091 upstream) : DNASE1 (33264 downstream)																																			---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3816054	3816055	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3816054_3816055delTT	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	3884844	3884845	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3884844_3884845insA	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	3950455	3950455	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3950455delA								CREBBP (20334 upstream) : ADCY9 (62198 downstream)																																			---	---	---	---
ADCY9	115	broad.mit.edu	37	16	4159636	4159637	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4159636_4159637insC	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																		---	---	---	---
DNAJA3	9093	broad.mit.edu	37	16	4493689	4493689	+	Intron	DEL	T	-	-	rs34123742		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4493689delT	uc002cwk.2	+						DNAJA3_uc002cwl.2_Intron|DNAJA3_uc010uxk.1_Intron	NM_005147	NP_005138			DnaJ (Hsp40) homolog, subfamily A, member 3						activation of caspase activity|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of cell proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein kinase activity|neuromuscular junction development|positive regulation of apoptosis|positive regulation of protein ubiquitination|protein folding|protein folding|protein stabilization|response to heat|response to interferon-gamma	cytosol|mitochondrial matrix|mitochondrial nucleoid|nucleus	ATP binding|heat shock protein binding|interferon-gamma receptor binding|metal ion binding|NF-kappaB binding|protein kinase binding			ovary(2)|breast(2)	4																		---	---	---	---
GLYR1	84656	broad.mit.edu	37	16	4871252	4871252	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4871252delC	uc002cxx.3	-						GLYR1_uc002cxy.2_Intron|GLYR1_uc002cxz.1_Intron|GLYR1_uc002cya.2_Intron|GLYR1_uc010uxv.1_Intron	NM_032569	NP_115958			cytokine-like nuclear factor n-pac						pentose-phosphate shunt	nucleus	coenzyme binding|DNA binding|methylated histone residue binding|phosphogluconate dehydrogenase (decarboxylating) activity				0																		---	---	---	---
UBN1	29855	broad.mit.edu	37	16	4917403	4917406	+	Intron	DEL	CTAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4917403_4917406delCTAA	uc002cyb.2	+						UBN1_uc010uxw.1_Intron|UBN1_uc002cyc.2_Intron	NM_001079514	NP_001072982			ubinuclein 1						chromatin modification|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter	PML body|tight junction	DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)	2																		---	---	---	---
SEC14L5	9717	broad.mit.edu	37	16	5051941	5051941	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5051941delT	uc002cye.2	+							NM_014692	NP_055507			SEC14-like 5							integral to membrane|intracellular	transporter activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	5153515	5153515	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5153515delT								FAM86A (5726 upstream) : A2BP1 (915617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	5683854	5683855	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5683854_5683855delAA								FAM86A (536065 upstream) : A2BP1 (385277 downstream)																																			---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6085684	6085684	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6085684delC	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	6219580	6219580	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6219580delA	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	6247562	6247563	+	Intron	INS	-	C	C	rs146423116	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6247562_6247563insC	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	6363180	6363180	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6363180delG	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	6833318	6833318	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6833318delT	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	7249911	7249913	+	Intron	DEL	AAC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7249911_7249913delAAC	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	7612022	7612022	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7612022delA	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	8155347	8155348	+	IGR	DEL	AG	-	-	rs34789756		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8155347_8155348delAG								A2BP1 (392007 upstream) : TMEM114 (464155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8353163	8353163	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8353163delA								A2BP1 (589823 upstream) : TMEM114 (266340 downstream)																																			---	---	---	---
PMM2	5373	broad.mit.edu	37	16	8909076	8909079	+	Intron	DEL	TTTT	-	-	rs112569962		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8909076_8909079delTTTT	uc002czf.3	+						PMM2_uc010uyf.1_Intron|PMM2_uc010uyg.1_Intron|PMM2_uc010uyh.1_Intron|PMM2_uc010buj.2_Intron|PMM2_uc010uyi.1_Intron	NM_000303	NP_000294			phosphomannomutase 2						dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	cytosol	phosphomannomutase activity			ovary(1)	1																		---	---	---	---
USP7	7874	broad.mit.edu	37	16	9055361	9055363	+	Intron	DEL	AGG	-	-	rs111608726		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9055361_9055363delAGG	uc002czl.2	-							NM_003470	NP_003461			ubiquitin specific peptidase 7						interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	9493489	9493489	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9493489delA								C16orf72 (279944 upstream) : GRIN2A (353778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9719604	9719610	+	IGR	DEL	TTTTTTT	-	-	rs79691055		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9719604_9719610delTTTTTTT								C16orf72 (506059 upstream) : GRIN2A (127657 downstream)																																			---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	9945182	9945183	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9945182_9945183delAC	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)													---	---	---	---
FAM18A	780776	broad.mit.edu	37	16	10867203	10867203	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10867203delA	uc010buo.1	-	5	691	c.420delT	c.(418-420)TTTfs	p.F140fs	FAM18A_uc010uyr.1_RNA|FAM18A_uc010uys.1_RNA|FAM18A_uc010uyt.1_RNA|FAM18A_uc010bun.2_RNA|FAM18A_uc010uyu.1_RNA|FAM18A_uc002dad.3_RNA|FAM18A_uc002daf.1_RNA|FAM18A_uc002dae.1_Frame_Shift_Del_p.F76fs	NM_001079512	NP_001072980	A6NH52	FA18A_HUMAN	hypothetical protein LOC780776	140	Helical; (Potential).					integral to membrane					0																		---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11066725	11066725	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	11575186	11575186	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11575186delT	uc002dax.1	-											Homo sapiens cDNA FLJ44575 fis, clone UTERU3018154.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	11580125	11580128	+	Intron	DEL	GGAG	-	-	rs71662682		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11580125_11580128delGGAG	uc002dax.1	-											Homo sapiens cDNA FLJ44575 fis, clone UTERU3018154.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	11841775	11841775	+	IGR	DEL	A	-	-	rs78892811		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11841775delA								TXNDC11 (5127 upstream) : ZC3H7A (2668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	11904387	11904387	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11904387delG								ZC3H7A (13299 upstream) : BCAR4 (9307 downstream)																																			---	---	---	---
GSPT1	2935	broad.mit.edu	37	16	12002949	12002949	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12002949delT	uc002dbt.2	-						GSPT1_uc002dbu.2_Intron|GSPT1_uc010bux.2_Intron	NM_002094	NP_002085			G1 to S phase transition 1 isoform 1						G1/S transition of mitotic cell cycle|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|protein methylation	intracellular	GTP binding|GTPase activity|protein binding|translation release factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12172308	12172308	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12172308delA	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	12182966	12182984	+	Intron	DEL	AGAGAGAGAGAGAGAGAAA	-	-	rs139548374	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12182966_12182984delAGAGAGAGAGAGAGAGAAA	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	12412560	12412560	+	Intron	DEL	T	-	-	rs77974083		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12412560delT	uc002dby.3	+							NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
CPPED1	55313	broad.mit.edu	37	16	12877582	12877582	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12877582delA	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	12972348	12972353	+	IGR	DEL	AAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12972348_12972353delAAAAAA								CPPED1 (74604 upstream) : SHISA9 (23124 downstream)																																			---	---	---	---
SHISA9	729993	broad.mit.edu	37	16	13171101	13171103	+	Intron	DEL	TTT	-	-	rs11320901		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13171101_13171103delTTT	uc010uyy.1	+							NM_001145204	NP_001138676			shisa homolog 9 isoform 1						regulation of short-term neuronal synaptic plasticity	cell junction|dendritic spine membrane|ionotropic glutamate receptor complex|synapse					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	13729595	13729597	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13729595_13729597delAAA								SHISA9 (395323 upstream) : ERCC4 (284417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13770317	13770317	+	IGR	DEL	A	-	-	rs138960911		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13770317delA								SHISA9 (436045 upstream) : ERCC4 (243697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13950269	13950269	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13950269delT								SHISA9 (615997 upstream) : ERCC4 (63745 downstream)																																			---	---	---	---
ERCC4	2072	broad.mit.edu	37	16	14016109	14016110	+	Intron	INS	-	T	T	rs113434368		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14016109_14016110insT	uc002dce.2	+						ERCC4_uc010bva.2_Intron	NM_005236	NP_005227			excision repair cross-complementing rodent						double-strand break repair via homologous recombination|meiotic mismatch repair|negative regulation of telomere maintenance|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|nucleotide-excision repair, DNA incision, 5'-to lesion|resolution of meiotic recombination intermediates|telomere maintenance via telomere shortening|transcription-coupled nucleotide-excision repair	nuclear chromosome, telomeric region|nucleoplasm|nucleotide-excision repair factor 1 complex	damaged DNA binding|protein C-terminus binding|protein N-terminus binding|single-stranded DNA binding|single-stranded DNA specific endodeoxyribonuclease activity			lung(4)|ovary(3)|skin(2)|pancreas(1)	10								Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
MKL2	57496	broad.mit.edu	37	16	14255360	14255360	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14255360delA	uc010uza.1	+						MKL2_uc002dcg.2_Intron	NM_014048	NP_054767			megakaryoblastic leukemia 2 protein						cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	14483766	14483767	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14483766_14483767delTT								MIR365-1 (80538 upstream) : PARN (45792 downstream)																																			---	---	---	---
PARN	5073	broad.mit.edu	37	16	14674917	14674917	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14674917delT	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																		---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15189974	15189974	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15189974delT	uc002ddc.2	+						RRN3_uc002dde.2_5'Flank|RRN3_uc010uzq.1_5'Flank|RRN3_uc002ddf.1_5'Flank|uc010bve.1_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)													---	---	---	---
MPV17L	255027	broad.mit.edu	37	16	15497628	15497629	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15497628_15497629delAA	uc002ddn.2	+						MPV17L_uc002ddm.2_Intron	NM_001128423	NP_001121895			MPV17 mitochondrial membrane protein-like							integral to membrane|peroxisomal membrane					0																		---	---	---	---
C16orf45	89927	broad.mit.edu	37	16	15616289	15616290	+	Intron	DEL	CA	-	-	rs113409761		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15616289_15616290delCA	uc002ddo.2	+						C16orf45_uc002ddp.2_Intron	NM_033201	NP_149978			hypothetical protein LOC89927 isoform 1											ovary(1)	1																		---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15870961	15870962	+	Intron	INS	-	AC	AC	rs140901109	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15870961_15870962insAC	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002dea.1_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								---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15932640	15932640	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15932640delG	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002deb.3_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	15989477	15989477	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15989477delA								C16orf63 (7030 upstream) : ABCC1 (53957 downstream)																																			---	---	---	---
ABCC1	4363	broad.mit.edu	37	16	16133067	16133068	+	Intron	DEL	TG	-	-	rs113288233		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16133067_16133068delTG	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron|ABCC1_uc002del.3_Intron|ABCC1_uc010bvn.2_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)													---	---	---	---
NOMO3	408050	broad.mit.edu	37	16	16361286	16361286	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16361286delT	uc002deq.2	+						NOMO3_uc002dep.2_Intron|NOMO3_uc010bvp.1_Intron	NM_001004067	NP_001004067			nodal modulator 3 precursor							integral to membrane	carbohydrate binding|carboxypeptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	17145546	17145546	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17145546delT								LOC339047 (701109 upstream) : XYLT1 (50637 downstream)																																			---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17375640	17375640	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17375640delC	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	18065820	18065822	+	IGR	DEL	AAA	-	-	rs112979283		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18065820_18065822delAAA								XYLT1 (501082 upstream) : NOMO2 (445361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18332828	18332828	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18332828delA								XYLT1 (768090 upstream) : NOMO2 (178355 downstream)																																			---	---	---	---
NOMO2	283820	broad.mit.edu	37	16	18531693	18531696	+	Intron	DEL	CATC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18531693_18531696delCATC	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	18844064	18844064	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18844064delT	uc002dfm.2	-						SMG1_uc010bwb.2_Intron|SMG1_uc010bwa.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																		---	---	---	---
TMC7	79905	broad.mit.edu	37	16	19020932	19020932	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19020932delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	19138224	19138224	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19138224delA								ITPRIPL2 (5276 upstream) : SYT17 (41414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	19148699	19148699	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19148699delC								ITPRIPL2 (15751 upstream) : SYT17 (30939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	19391555	19391556	+	IGR	INS	-	A	A	rs149971006	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19391555_19391556insA								LOC728276 (75839 upstream) : TMC5 (30305 downstream)																																			---	---	---	---
C16orf62	57020	broad.mit.edu	37	16	19665869	19665869	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19665869delA	uc002dgn.1	+						C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Intron	NM_020314	NP_064710			hypothetical protein LOC57020							integral to membrane				ovary(1)	1																		---	---	---	---
C16orf88	400506	broad.mit.edu	37	16	19726906	19726906	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19726906delT	uc002dgq.2	-						IQCK_uc002dgr.2_5'Flank|IQCK_uc002dgs.2_5'Flank|IQCK_uc010vat.1_5'Flank|IQCK_uc010bwc.2_5'Flank|IQCK_uc010vau.1_5'Flank	NM_001012991	NP_001013009			hypothetical protein LOC400506							nucleolus					0																		---	---	---	---
IQCK	124152	broad.mit.edu	37	16	19795327	19795327	+	Intron	DEL	A	-	-	rs34122713		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19795327delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	19998989	19998989	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19998989delT								GPRC5B (102157 upstream) : GPR139 (44054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	20342196	20342196	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20342196delA								GP2 (3361 upstream) : UMOD (2178 downstream)																																			---	---	---	---
UMOD	7369	broad.mit.edu	37	16	20352314	20352316	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20352314_20352316delAAA	uc002dgz.2	-						UMOD_uc002dha.2_Intron|UMOD_uc002dhb.2_Intron	NM_003361	NP_003352			uromodulin precursor						cellular defense response|negative regulation of cell proliferation	anchored to membrane|apical plasma membrane|basolateral plasma membrane|cilium membrane|extrinsic to membrane|primary cilium|spindle pole	calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
UMOD	7369	broad.mit.edu	37	16	20358206	20358221	+	Intron	DEL	AGAAAGAAAGAAAGAA	-	-	rs149973371		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20358206_20358221delAGAAAGAAAGAAAGAA	uc002dgz.2	-						UMOD_uc002dha.2_Intron|UMOD_uc002dhb.2_Intron	NM_003361	NP_003352			uromodulin precursor						cellular defense response|negative regulation of cell proliferation	anchored to membrane|apical plasma membrane|basolateral plasma membrane|cilium membrane|extrinsic to membrane|primary cilium|spindle pole	calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
LOC81691	81691	broad.mit.edu	37	16	20832606	20832606	+	Intron	DEL	T	-	-	rs113292563		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20832606delT	uc002dhv.2	+						ERI2_uc002dht.3_Intron|LOC81691_uc002dhx.2_Intron|LOC81691_uc002dhw.2_Intron|LOC81691_uc002dhy.3_Intron	NM_030941	NP_112203			exonuclease NEF-sp isoform 1							nucleolus	exonuclease activity|nucleotide binding|RNA binding			ovary(1)|kidney(1)	2																		---	---	---	---
LOC81691	81691	broad.mit.edu	37	16	20844527	20844527	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20844527delT	uc002dhv.2	+						ERI2_uc002dht.3_Intron|LOC81691_uc002dhx.2_Intron|LOC81691_uc002dhw.2_Intron|LOC81691_uc002dhy.3_Intron	NM_030941	NP_112203			exonuclease NEF-sp isoform 1							nucleolus	exonuclease activity|nucleotide binding|RNA binding			ovary(1)|kidney(1)	2																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21033224	21033225	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21033224_21033225insA	uc010vbe.1	-							NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21041322	21041322	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21041322delT	uc010vbe.1	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21464447	21464447	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21464447delT	uc002diq.3	+						LOC100271836_uc002diu.1_Intron|LOC100271836_uc002diz.1_Intron					Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21469994	21469994	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21469994delA	uc002diq.3	+						LOC100271836_uc002diu.1_Intron|LOC100271836_uc002diz.1_5'Flank					Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21580223	21580223	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21580223delA	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
OTOA	146183	broad.mit.edu	37	16	21725621	21725622	+	Intron	INS	-	CTTCCTTC	CTTCCTTC	rs34598445		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21725621_21725622insCTTCCTTC	uc002djh.2	+						uc002diq.3_Intron|OTOA_uc010vbj.1_Intron|OTOA_uc002dji.2_Intron|OTOA_uc010vbk.1_Intron	NM_144672	NP_653273			otoancorin isoform 1						sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(48;0.0414)														---	---	---	---
OTOA	146183	broad.mit.edu	37	16	21750351	21750352	+	Intron	INS	-	G	G	rs139527700	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21750351_21750352insG	uc002djh.2	+						uc002diq.3_Intron|OTOA_uc010vbj.1_Intron|OTOA_uc002dji.2_Intron|OTOA_uc010vbk.1_Intron	NM_144672	NP_653273			otoancorin isoform 1						sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(48;0.0414)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21902237	21902239	+	Intron	DEL	AAA	-	-	rs55836110		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21902237_21902239delAAA	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).																														---	---	---	---
PDZD9	255762	broad.mit.edu	37	16	22009713	22009714	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22009713_22009714insA	uc002dka.1	-							NM_173806	NP_776167			hypothetical protein LOC255762											pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	22645939	22645939	+	IGR	DEL	T	-	-	rs79378491		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22645939delT								LOC653786 (57753 upstream) : HS3ST2 (179921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22648732	22648733	+	IGR	DEL	TT	-	-	rs79744433		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22648732_22648733delTT								LOC653786 (60546 upstream) : HS3ST2 (177127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22696109	22696109	+	IGR	DEL	T	-	-	rs72233932		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22696109delT								LOC653786 (107923 upstream) : HS3ST2 (129751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22708660	22708660	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22708660delT								LOC653786 (120474 upstream) : HS3ST2 (117200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22745597	22745598	+	IGR	INS	-	GT	GT	rs149173783	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22745597_22745598insGT								LOC653786 (157411 upstream) : HS3ST2 (80262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22948648	22948649	+	IGR	DEL	TT	-	-	rs66955458		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22948648_22948649delTT								HS3ST2 (20991 upstream) : USP31 (124080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	23068941	23068941	+	IGR	DEL	T	-	-	rs78626905		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23068941delT								HS3ST2 (141284 upstream) : USP31 (3788 downstream)																																			---	---	---	---
USP31	57478	broad.mit.edu	37	16	23098403	23098403	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23098403delT	uc002dll.2	-						USP31_uc010bxm.2_5'Flank	NM_020718	NP_065769			ubiquitin specific peptidase 31						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(3)|lung(3)|breast(2)|pancreas(1)|skin(1)	10				GBM - Glioblastoma multiforme(48;0.0187)														---	---	---	---
COG7	91949	broad.mit.edu	37	16	23456980	23456980	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23456980delA	uc002dlo.2	-							NM_153603	NP_705831			component of oligomeric golgi complex 7						intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)														---	---	---	---
GGA2	23062	broad.mit.edu	37	16	23507957	23507958	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23507957_23507958insG	uc002dlq.2	-						GGA2_uc010bxo.1_Intron	NM_015044	NP_055859			ADP-ribosylation factor binding protein 2						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)														---	---	---	---
EARS2	124454	broad.mit.edu	37	16	23565511	23565512	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23565511_23565512insT	uc002dlt.3	-						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	23612149	23612149	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23612149delT								NDUFAB1 (4510 upstream) : PALB2 (2334 downstream)																																			---	---	---	---
DCTN5	84516	broad.mit.edu	37	16	23673373	23673376	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23673373_23673376delAAAA	uc002dly.1	+							NM_032486	NP_115875			dynactin 5							centrosome	transferase activity			upper_aerodigestive_tract(1)	1				GBM - Glioblastoma multiforme(48;0.0156)														---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24201251	24201251	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24201251delT	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	24395779	24395779	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24395779delT								CACNG3 (22043 upstream) : RBBP6 (153235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	24527422	24527422	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24527422delA								CACNG3 (153686 upstream) : RBBP6 (21592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25031294	25031294	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25031294delA								ARHGAP17 (4619 upstream) : LCMT1 (91753 downstream)																																			---	---	---	---
LCMT1	51451	broad.mit.edu	37	16	25176839	25176839	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25176839delT	uc002dnx.1	+						LCMT1_uc002dny.1_Intron|LCMT1_uc002dnz.1_Intron|LCMT1_uc002doa.1_Intron	NM_016309	NP_057393			leucine carboxyl methyltransferase 1 isoform a								protein binding|protein C-terminal carboxyl O-methyltransferase activity|S-adenosylmethionine-dependent methyltransferase activity				0				GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)													---	---	---	---
LCMT1	51451	broad.mit.edu	37	16	25178632	25178632	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25178632delT	uc002dnx.1	+						LCMT1_uc002dny.1_Intron|LCMT1_uc002dnz.1_Intron|LCMT1_uc002doa.1_Intron	NM_016309	NP_057393			leucine carboxyl methyltransferase 1 isoform a								protein binding|protein C-terminal carboxyl O-methyltransferase activity|S-adenosylmethionine-dependent methyltransferase activity				0				GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	25294902	25294902	+	IGR	DEL	A	-	-	rs7206821	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25294902delA								ZKSCAN2 (26047 upstream) : HS3ST4 (408445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25438463	25438463	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25438463delT								ZKSCAN2 (169608 upstream) : HS3ST4 (264884 downstream)																																			---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	25778335	25778335	+	Intron	DEL	A	-	-	rs35896337		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25778335delA	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)														---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	25884642	25884645	+	Intron	DEL	TCCT	-	-	rs56296232	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25884642_25884645delTCCT	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)														---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	25884699	25884700	+	Intron	INS	-	CATC	CATC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25884699_25884700insCATC	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	26162484	26162484	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26162484delA								HS3ST4 (13476 upstream) : C16orf82 (915735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26264925	26264925	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26264925delA								HS3ST4 (115917 upstream) : C16orf82 (813294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26272373	26272373	+	IGR	DEL	A	-	-	rs71387708		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26272373delA								HS3ST4 (123365 upstream) : C16orf82 (805846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26385676	26385677	+	IGR	INS	-	TAGA	TAGA	rs111483317		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26385676_26385677insTAGA								HS3ST4 (236668 upstream) : C16orf82 (692542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26424580	26424580	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26424580delA								HS3ST4 (275572 upstream) : C16orf82 (653639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26536950	26536950	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26536950delA								HS3ST4 (387942 upstream) : C16orf82 (541269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26661976	26661979	+	IGR	DEL	TTGT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26661976_26661979delTTGT								HS3ST4 (512968 upstream) : C16orf82 (416240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26762294	26762295	+	IGR	DEL	GT	-	-	rs34622429		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26762294_26762295delGT								HS3ST4 (613286 upstream) : C16orf82 (315924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27088704	27088705	+	IGR	INS	-	CTTT	CTTT	rs143025532	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27088704_27088705insCTTT								C16orf82 (8218 upstream) : JMJD5 (126102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27387770	27387770	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27387770delA								IL4R (11672 upstream) : IL21R (25953 downstream)																																			---	---	---	---
IL21R	50615	broad.mit.edu	37	16	27419215	27419215	+	Intron	DEL	A	-	-	rs66689006		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27419215delA	uc002doq.1	+						IL21R_uc002dor.1_Intron	NM_181078	NP_851564			interleukin 21 receptor precursor						natural killer cell activation	integral to membrane	interleukin-21 receptor activity			ovary(2)|lung(1)|breast(1)	4								T	BCL6	NHL								---	---	---	---
Unknown	0	broad.mit.edu	37	16	28082584	28082592	+	IGR	DEL	TGTTGTTGT	-	-	rs145167871		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28082584_28082592delTGTTGTTGT								GSG1L (7754 upstream) : XPO6 (26724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	28227681	28227682	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28227681_28227682insA								XPO6 (4491 upstream) : SBK1 (76158 downstream)																																			---	---	---	---
EIF3CL	728689	broad.mit.edu	37	16	28417204	28417205	+	5'Flank	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28417204_28417205delAC	uc010byb.2	-						EIF3C_uc002dpg.3_5'Flank|EIF3CL_uc010vcs.1_5'Flank|EIF3CL_uc010byc.2_Intron|EIF3CL_uc002dpi.3_5'Flank|EIF3C_uc002dph.3_5'Flank	NM_001099661	NP_001093131			eukaryotic translation initiation factor 3,							eukaryotic translation initiation factor 3 complex	translation initiation factor activity				0																		---	---	---	---
CLN3	1201	broad.mit.edu	37	16	28493534	28493534	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28493534delG	uc002dpo.2	-						uc010vct.1_Intron|CLN3_uc002dpl.2_Intron|CLN3_uc010vcu.1_Intron|CLN3_uc002dpn.2_Intron|CLN3_uc002dpm.2_Intron|CLN3_uc010vcv.1_Intron|CLN3_uc010byd.2_Intron|CLN3_uc002dpp.2_Intron|CLN3_uc002dpt.1_Intron|CLN3_uc002dpq.1_Intron|CLN3_uc010bye.1_Intron|CLN3_uc002dpr.1_Intron|CLN3_uc010byf.1_Intron|CLN3_uc002dps.1_Intron|CLN3_uc002dpu.1_Intron|CLN3_uc002dpw.1_Intron|CLN3_uc010vcw.1_3'UTR	NM_000086	NP_000077			ceroid-lipofuscinosis, neuronal 3						amyloid precursor protein catabolic process|arginine transport|associative learning|autophagic vacuole fusion|cell death|cellular amino acid metabolic process|cytosolic calcium ion homeostasis|galactosylceramide metabolic process|globoside metabolic process|glucosylceramide metabolic process|ionotropic glutamate receptor signaling pathway|lysosomal lumen acidification|lysosomal lumen pH elevation|negative regulation of catalytic activity|negative regulation of macroautophagy|negative regulation of neuron apoptosis|negative regulation of proteolysis|neuromuscular process controlling balance|neurotransmitter metabolic process|protein catabolic process|protein folding|protein processing|receptor-mediated endocytosis|regulation of action potential|sphingomyelin metabolic process|vacuolar transport	autophagic vacuole|caveola|cytosol|early endosome|Golgi membrane|Golgi stack|integral to endoplasmic reticulum membrane|late endosome|lysosomal membrane|membrane fraction|mitochondrion|neuron projection|nucleus|synaptic vesicle|trans-Golgi network	unfolded protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	28527742	28527742	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28527742delA	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	28560276	28560276	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28560276delT	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
SH2B1	25970	broad.mit.edu	37	16	28883088	28883088	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28883088delT	uc002dri.2	+						uc010vct.1_Intron|SH2B1_uc010vdc.1_Intron|SH2B1_uc002drj.2_Intron|SH2B1_uc002drk.2_Intron|SH2B1_uc002drl.2_Intron|SH2B1_uc010vdd.1_Intron|SH2B1_uc010vde.1_Intron|SH2B1_uc002drm.2_Intron	NM_001145795	NP_001139267			SH2B adaptor protein 1 isoform 1						blood coagulation|intracellular signal transduction	cytosol|membrane|nucleus	signal transducer activity			ovary(2)	2																		---	---	---	---
ATP2A1	487	broad.mit.edu	37	16	28910320	28910321	+	Intron	INS	-	AC	AC	rs142994822	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28910320_28910321insAC	uc002dro.1	+						uc010vct.1_Intron|ATP2A1_uc002drn.1_Intron|ATP2A1_uc002drp.1_Intron	NM_173201	NP_775293			ATPase, Ca++ transporting, fast twitch 1 isoform						apoptosis in response to endoplasmic reticulum stress|apoptotic mitochondrial changes|ATP biosynthetic process|calcium ion import|elevation of endoplasmic reticulum calcium ion concentration|elevation of mitochondrial calcium ion concentration|maintenance of mitochondrion location|negative regulation of striated muscle contraction|platelet activation|positive regulation of fast-twitch skeletal muscle fiber contraction|reduction of endoplasmic reticulum calcium ion concentration|relaxation of skeletal muscle|response to endoplasmic reticulum stress	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|H zone|I band|microsome|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum|sarcoplasmic reticulum membrane	ATP binding|ATP binding|calcium ion binding|calcium ion binding|calcium-transporting ATPase activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ATP2A1	487	broad.mit.edu	37	16	28915340	28915340	+	Intron	DEL	G	-	-	rs10718640		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28915340delG	uc002dro.1	+						uc010vct.1_Intron|ATP2A1_uc002drn.1_Intron|ATP2A1_uc002drp.1_Intron	NM_173201	NP_775293			ATPase, Ca++ transporting, fast twitch 1 isoform						apoptosis in response to endoplasmic reticulum stress|apoptotic mitochondrial changes|ATP biosynthetic process|calcium ion import|elevation of endoplasmic reticulum calcium ion concentration|elevation of mitochondrial calcium ion concentration|maintenance of mitochondrion location|negative regulation of striated muscle contraction|platelet activation|positive regulation of fast-twitch skeletal muscle fiber contraction|reduction of endoplasmic reticulum calcium ion concentration|relaxation of skeletal muscle|response to endoplasmic reticulum stress	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|H zone|I band|microsome|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum|sarcoplasmic reticulum membrane	ATP binding|ATP binding|calcium ion binding|calcium ion binding|calcium-transporting ATPase activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	29250431	29250431	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29250431delT	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	29349607	29349608	+	Intron	DEL	AA	-	-	rs76472264		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29349607_29349608delAA	uc010vct.1	-						RUNDC2C_uc010bys.1_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	29659612	29659613	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29659612_29659613delTT	uc010bzb.1	-						uc002dtf.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
PRRT2	112476	broad.mit.edu	37	16	29825016	29825016	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29825016delC	uc002due.3	+	2	942	c.641delC	c.(640-642)GCCfs	p.A214fs	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|uc002duc.1_5'Flank|PRRT2_uc002dud.2_Frame_Shift_Del_p.A214fs|PRRT2_uc002duf.1_Frame_Shift_Del_p.A214fs|C16orf53_uc002dug.3_5'Flank	NM_145239	NP_660282	Q7Z6L0	PRRT2_HUMAN	proline-rich transmembrane protein 2	214	Extracellular (Potential).|Pro-rich.			A -> AP (in Ref. 3; CAD38881).	response to biotic stimulus	integral to membrane					0																		---	---	---	---
SEZ6L2	26470	broad.mit.edu	37	16	29900761	29900762	+	Intron	DEL	AA	-	-	rs79310759		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29900761_29900762delAA	uc002duq.3	-						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Intron|SEZ6L2_uc002dur.3_Intron|SEZ6L2_uc002dus.3_Intron|SEZ6L2_uc010vec.1_Intron|SEZ6L2_uc010ved.1_Intron	NM_201575	NP_963869			seizure related 6 homolog (mouse)-like 2 isoform							endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
ALDOA	226	broad.mit.edu	37	16	30069797	30069797	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30069797delT	uc002dvw.2	+						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|ALDOA_uc010bzo.1_Intron|ALDOA_uc002dvx.2_Intron	NM_184043	NP_908932			fructose-bisphosphate aldolase A						actin filament organization|ATP biosynthetic process|fructose 1,6-bisphosphate metabolic process|gluconeogenesis|glycolysis|muscle cell homeostasis|platelet activation|platelet degranulation|protein homotetramerization|regulation of cell shape|striated muscle contraction	actin cytoskeleton|cytosol|extracellular vesicular exosome|I band|platelet alpha granule lumen	actin binding|fructose binding|fructose-bisphosphate aldolase activity|identical protein binding|tubulin binding			lung(1)	1																		---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	30154543	30154543	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30154543delA	uc010bzb.1	-						uc002dtf.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
ZNF48	197407	broad.mit.edu	37	16	30409310	30409310	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30409310delC	uc002dya.1	+	2	798	c.739delC	c.(739-741)CCCfs	p.P247fs	ZNF48_uc002dxz.1_Frame_Shift_Del_p.P124fs	NM_152652	NP_689865	Q96MX3	ZNF48_HUMAN	zinc finger protein 48	247					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	30460801	30460801	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30460801delT								SEPHS2 (3577 upstream) : ITGAL (23182 downstream)																																			---	---	---	---
ZNF768	79724	broad.mit.edu	37	16	30548073	30548073	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30548073delT	uc010vex.1	-						ZNF747_uc002dyn.2_5'Flank|ZNF747_uc002dyo.1_5'Flank|ZNF747_uc010vey.1_5'Flank|uc002dyp.1_RNA	NM_024671	NP_078947			zinc finger protein 768						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF689	115509	broad.mit.edu	37	16	30616641	30616641	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30616641delG	uc002dyx.2	-	3	767	c.447delC	c.(445-447)CCCfs	p.P149fs	ZNF689_uc010bzy.2_5'UTR	NM_138447	NP_612456	Q96CS4	ZN689_HUMAN	zinc finger protein HIT-39	149	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			Colorectal(24;0.198)															---	---	---	---
RNF40	9810	broad.mit.edu	37	16	30782044	30782044	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30782044delT	uc002dzq.2	+						RNF40_uc010caa.2_Intron|RNF40_uc010cab.2_Intron|RNF40_uc010vfa.1_Intron|RNF40_uc002dzr.2_Intron|RNF40_uc010vfb.1_Intron|RNF40_uc010vfc.1_Intron	NM_014771	NP_055586			ring finger protein 40						histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process	nucleus|synaptosome|ubiquitin ligase complex	protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding			central_nervous_system(1)	1			Colorectal(24;0.198)															---	---	---	---
SETD1A	9739	broad.mit.edu	37	16	30984175	30984177	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30984175_30984177delAAA	uc002ead.1	+							NM_014712	NP_055527			SET domain containing 1A						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																		---	---	---	---
PRSS36	146547	broad.mit.edu	37	16	31158893	31158893	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31158893delC	uc002ebd.2	-						PRSS36_uc010vff.1_Intron|PRSS36_uc010vfg.1_Intron|PRSS36_uc010vfh.1_Intron	NM_173502	NP_775773			protease, serine, 36 precursor						proteolysis	cytoplasm|proteinaceous extracellular matrix	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
ITGAM	3684	broad.mit.edu	37	16	31331140	31331140	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31331140delT	uc002ebq.2	+						ITGAM_uc002ebr.2_Intron|ITGAM_uc010cam.1_Intron|ITGAM_uc010can.2_Intron|ITGAM_uc002ebs.1_5'Flank	NM_000632	NP_000623			integrin alpha M isoform 2 precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	31345826	31345829	+	IGR	DEL	CCTT	-	-	rs12932165		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31345826_31345829delCCTT								ITGAM (1615 upstream) : ITGAX (20680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	31399657	31399657	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31399657delA								ITGAX (5339 upstream) : ITGAD (4976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	31665728	31665729	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31665728_31665729delAA								CSDAP1 (84883 upstream) : KIAA0664P3 (46205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32364636	32364638	+	IGR	DEL	TTT	-	-	rs138997860		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32364636_32364638delTTT								HERC2P4 (200762 upstream) : TP53TG3B (320203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32407001	32407002	+	IGR	INS	-	T	T	rs140894241		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32407001_32407002insT								HERC2P4 (243127 upstream) : TP53TG3B (277839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32615646	32615646	+	IGR	DEL	C	-	-	rs72173161		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32615646delC								HERC2P4 (451772 upstream) : TP53TG3B (69195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32651985	32651985	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32651985delT								HERC2P4 (488111 upstream) : TP53TG3B (32856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32819048	32819050	+	IGR	DEL	TCA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32819048_32819050delTCA								TP53TG3B (130170 upstream) : SLC6A10P (69747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33537022	33537029	+	IGR	DEL	TCCAACAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33537022_33537029delTCCAACAA								SLC6A10P (640559 upstream) : MIR1826 (428479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33920371	33920371	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33920371delT								None (None upstream) : MIR1826 (45137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33955276	33955277	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33955276_33955277insTG								None (None upstream) : MIR1826 (10231 downstream)																																			---	---	---	---
MIR1826	100302162	broad.mit.edu	37	16	33964913	33964914	+	5'Flank	DEL	CG	-	-	rs78287706	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33964913_33964914delCG	hsa-mir-1826|MI0008194	+																							0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	34686678	34686678	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34686678delT								LOC283914 (60594 upstream) : LOC146481 (25107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	35201075	35201075	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35201075delT								LOC146481 (486108 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	46490972	46490972	+	IGR	DEL	G	-	-	rs76837012	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46490972delG								None (None upstream) : ANKRD26P1 (12277 downstream)																																			---	---	---	---
VPS35	55737	broad.mit.edu	37	16	46697194	46697195	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46697194_46697195delTC	uc002eef.3	-						VPS35_uc002eed.2_Intron|VPS35_uc002eee.2_Intron	NM_018206	NP_060676			vacuolar protein sorting 35						protein transport|retrograde transport, endosome to Golgi	cytosol|endosome|membrane	protein binding				0		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)																---	---	---	---
GPT2	84706	broad.mit.edu	37	16	46950267	46950267	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46950267delA	uc002eel.2	+						GPT2_uc002eem.2_Intron	NM_133443	NP_597700			glutamic pyruvate transaminase 2 isoform 1						2-oxoglutarate metabolic process|cellular amino acid biosynthetic process|L-alanine metabolic process	mitochondrial matrix	L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
GPT2	84706	broad.mit.edu	37	16	46959140	46959140	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46959140delT	uc002eel.2	+						GPT2_uc002eem.2_Intron|GPT2_uc002een.2_Intron	NM_133443	NP_597700			glutamic pyruvate transaminase 2 isoform 1						2-oxoglutarate metabolic process|cellular amino acid biosynthetic process|L-alanine metabolic process	mitochondrial matrix	L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	46967457	46967457	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46967457delA								GPT2 (2257 upstream) : DNAJA2 (21817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	47058397	47058398	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47058397_47058398delTT								DNAJA2 (50772 upstream) : NETO2 (57044 downstream)																																			---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47189556	47189557	+	3'UTR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47189556_47189557insT	uc002eet.2	-	18					ITFG1_uc010vgg.1_3'UTR|ITFG1_uc010vgh.1_3'UTR	NM_030790	NP_110417			integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)																---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47292700	47292700	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47292700delA	uc002eet.2	-						ITFG1_uc010vgg.1_Intron|ITFG1_uc010vgh.1_Intron	NM_030790	NP_110417			integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)																---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47308174	47308174	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47308174delA	uc002eet.2	-						ITFG1_uc010vgg.1_Intron|ITFG1_uc010vgh.1_Intron	NM_030790	NP_110417			integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)																---	---	---	---
PHKB	5257	broad.mit.edu	37	16	47576361	47576361	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47576361delT	uc002eev.3	+						PHKB_uc010vgi.1_Intron|PHKB_uc002eeu.3_Intron	NM_000293	NP_000284			phosphorylase kinase, beta isoform a						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)																---	---	---	---
LONP2	83752	broad.mit.edu	37	16	48346273	48346274	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48346273_48346274delTT	uc002efi.1	+						LONP2_uc010vgm.1_Intron|LONP2_uc002efj.1_Intron	NM_031490	NP_113678			peroxisomal LON protease-like						misfolded or incompletely synthesized protein catabolic process|protein targeting to peroxisome|signal peptide processing	nucleoid|peroxisomal matrix	ATP binding|ATP-dependent peptidase activity|enzyme binding|sequence-specific DNA binding|serine-type endopeptidase activity				0																		---	---	---	---
LONP2	83752	broad.mit.edu	37	16	48377607	48377608	+	Intron	DEL	AA	-	-	rs112146880		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48377607_48377608delAA	uc002efi.1	+						LONP2_uc010vgm.1_Intron|LONP2_uc002efj.1_Intron	NM_031490	NP_113678			peroxisomal LON protease-like						misfolded or incompletely synthesized protein catabolic process|protein targeting to peroxisome|signal peptide processing	nucleoid|peroxisomal matrix	ATP binding|ATP-dependent peptidase activity|enzyme binding|sequence-specific DNA binding|serine-type endopeptidase activity				0																		---	---	---	---
SIAH1	6477	broad.mit.edu	37	16	48439281	48439281	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48439281delA	uc002efl.2	-											Homo sapiens SIAH1 mRNA for seven in absentia homolog 1 isoform a, complete cds, clone: FLJ08065AAAN.						axon guidance|cell cycle|neuron apoptosis|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	beta-catenin destruction complex|cytosol|nucleus	protein C-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)																---	---	---	---
N4BP1	9683	broad.mit.edu	37	16	48579939	48579942	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48579939_48579942delAAAA	uc002efp.2	-							NM_153029	NP_694574			Nedd4 binding protein 1						negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination	nucleolus|PML body					0		all_cancers(37;0.179)|all_lung(18;0.11)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	48736682	48736713	+	IGR	DEL	CTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTT	-	-	rs71134568		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48736682_48736713delCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTT								N4BP1 (92562 upstream) : CBLN1 (575498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	48990633	48990634	+	IGR	INS	-	AT	AT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48990633_48990634insAT								N4BP1 (346513 upstream) : CBLN1 (321577 downstream)																																			---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49767125	49767126	+	Intron	DEL	AA	-	-	rs74751716		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49767125_49767126delAA	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	50073419	50073422	+	IGR	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50073419_50073422delAAAA								TMEM188 (2421 upstream) : HEATR3 (26459 downstream)																																			---	---	---	---
HEATR3	55027	broad.mit.edu	37	16	50107881	50107881	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50107881delT	uc002efw.2	+						HEATR3_uc002efx.2_Intron	NM_182922	NP_891552			HEAT repeat containing 3								binding			ovary(1)|skin(1)	2																		---	---	---	---
PAPD5	64282	broad.mit.edu	37	16	50207593	50207594	+	Intron	INS	-	TTG	TTG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50207593_50207594insTTG	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	50347347	50347347	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50347347delA	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	50451223	50451224	+	IGR	INS	-	TG	TG	rs9933683		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50451223_50451224insTG								BRD7 (48394 upstream) : NKD1 (131017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	50527019	50527019	+	IGR	DEL	T	-	-	rs67330375		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50527019delT								BRD7 (124190 upstream) : NKD1 (55222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51189454	51189454	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51189454delG								SALL1 (4271 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51501005	51501005	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51501005delT								SALL1 (315822 upstream) : TOX3 (970913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51729825	51729825	+	IGR	DEL	C	-	-	rs8048664	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51729825delC								SALL1 (544642 upstream) : TOX3 (742093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	52233367	52233368	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52233367_52233368delCA								None (None upstream) : TOX3 (238550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	52335714	52335715	+	IGR	INS	-	AC	AC	rs140529919	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52335714_52335715insAC								None (None upstream) : TOX3 (136203 downstream)																																			---	---	---	---
TOX3	27324	broad.mit.edu	37	16	52562321	52562321	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52562321delT	uc002egw.2	-						TOX3_uc010vgt.1_Intron|TOX3_uc010vgu.1_Intron	NM_001080430	NP_001073899			TOX high mobility group box family member 3						apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity				0																		---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53265548	53265548	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53265548delT	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002eha.1_Intron|CHD9_uc002ehc.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	53325577	53325577	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53325577delT	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-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
RPGRIP1L	23322	broad.mit.edu	37	16	53709561	53709561	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53709561delA	uc002ehp.2	-						RPGRIP1L_uc002eho.3_Intron|RPGRIP1L_uc010vgy.1_Intron|RPGRIP1L_uc010cbx.2_Intron|RPGRIP1L_uc010vgz.1_Intron|RPGRIP1L_uc002ehq.1_Intron	NM_015272	NP_056087			RPGRIP1-like isoform a						negative regulation of G-protein coupled receptor protein signaling pathway	cell-cell junction|centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)																---	---	---	---
RPGRIP1L	23322	broad.mit.edu	37	16	53734649	53734649	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53734649delA	uc002ehp.2	-						RPGRIP1L_uc002eho.3_Intron|RPGRIP1L_uc010vgy.1_Intron|RPGRIP1L_uc010cbx.2_Intron|RPGRIP1L_uc010vgz.1_Intron|RPGRIP1L_uc002ehq.1_Intron|RPGRIP1L_uc010cby.1_Intron	NM_015272	NP_056087			RPGRIP1-like isoform a						negative regulation of G-protein coupled receptor protein signaling pathway	cell-cell junction|centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)																---	---	---	---
FTO	79068	broad.mit.edu	37	16	53748081	53748081	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53748081delT	uc002ehr.2	+						FTO_uc010vha.1_Intron	NM_001080432	NP_001073901			fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
FTO	79068	broad.mit.edu	37	16	54141566	54141567	+	Intron	INS	-	T	T	rs140923176	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54141566_54141567insT	uc002ehr.2	+						FTO_uc010vha.1_Intron|FTO_uc010cbz.2_Intron|FTO_uc002ehs.2_Intron	NM_001080432	NP_001073901			fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	54200084	54200084	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54200084delA								FTO (51706 upstream) : IRX3 (117128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54435072	54435074	+	IGR	DEL	AAA	-	-	rs11439556		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54435072_54435074delAAA								IRX3 (114694 upstream) : IRX5 (530037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55241475	55241475	+	IGR	DEL	G	-	-	rs111359989		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55241475delG								IRX5 (273082 upstream) : IRX6 (116996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55485875	55485876	+	IGR	INS	-	TTG	TTG	rs142913330	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55485875_55485876insTTG								IRX6 (121204 upstream) : MMP2 (27205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55776076	55776077	+	IGR	DEL	AC	-	-	rs141799220		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55776076_55776077delAC								SLC6A2 (38378 upstream) : CES4 (18434 downstream)																																			---	---	---	---
CES1	1066	broad.mit.edu	37	16	55851562	55851563	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55851562_55851563delGT	uc002eim.2	-						CES1_uc010ccf.2_5'Flank|CES1_uc002eil.2_Intron|CES1_uc002ein.2_Intron	NM_001025194	NP_001020365			carboxylesterase 1 isoform b precursor						response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)													---	---	---	---
LOC283856	283856	broad.mit.edu	37	16	56161913	56161915	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56161913_56161915delTTT	uc002eis.1	-							NR_027078				Homo sapiens hypothetical protein LOC283856, mRNA (cDNA clone IMAGE:5263025).												0																		---	---	---	---
BBS2	583	broad.mit.edu	37	16	56526867	56526867	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56526867delA	uc002ejd.2	-							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				---	---	---	---
Unknown	0	broad.mit.edu	37	16	56889061	56889062	+	IGR	DEL	AC	-	-	rs6499856	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56889061_56889062delAC								NUP93 (10385 upstream) : MIR138-2 (3368 downstream)																																			---	---	---	---
SLC12A3	6559	broad.mit.edu	37	16	56897621	56897622	+	5'Flank	DEL	TA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56897621_56897622delTA	uc010ccm.2	+						SLC12A3_uc002ekd.3_5'Flank|SLC12A3_uc010ccn.2_5'Flank	NM_001126108	NP_001119580			solute carrier family 12, member 3 isoform 3						sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)													---	---	---	---
NLRC5	84166	broad.mit.edu	37	16	57021570	57021570	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57021570delC	uc002ekk.1	+							NM_032206	NP_115582			nucleotide-binding oligomerization domains 27						defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)																---	---	---	---
ARL2BP	23568	broad.mit.edu	37	16	57279941	57279941	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57279941delT	uc002elf.1	+						ARL2BP_uc010ccy.1_Intron|ARL2BP_uc010vhl.1_Intron	NM_012106	NP_036238			binder of Arl Two						maintenance of protein location in nucleus|positive regulation of tyrosine phosphorylation of Stat3 protein|signal transduction	centrosome|midbody|mitochondrial intermembrane space|nucleus|spindle	protein binding|small GTPase regulator activity|transcription coactivator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	57376882	57376883	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57376882_57376883insG								PLLP (58311 upstream) : CCL22 (15835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	57434881	57434881	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57434881delA								CX3CL1 (15927 upstream) : CCL17 (3798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	57724790	57724790	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57724790delA								GPR97 (1502 upstream) : CCDC135 (3923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	57904009	57904009	+	IGR	DEL	A	-	-	rs148359286		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57904009delA								KIFC3 (7276 upstream) : CNGB1 (12235 downstream)																																			---	---	---	---
NDRG4	65009	broad.mit.edu	37	16	58517272	58517272	+	Intron	DEL	A	-	-	rs35447648		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58517272delA	uc002enm.2	+						NDRG4_uc002enk.2_Intron|NDRG4_uc010vif.1_Intron	NM_001130487	NP_001123959			NDRG family member 4 isoform 2						cell differentiation|cell growth|multicellular organismal development|response to stress	cytoplasm				skin(1)	1																		---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58555109	58555110	+	In_Frame_Ins	INS	-	TAC	TAC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58555109_58555110insTAC	uc002env.2	-	48	7322_7323	c.7029_7030insGTA	c.(7027-7032)insGTA	p.2343_2344insV	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_In_Frame_Ins_p.2338_2339insV|CNOT1_uc002ent.2_In_Frame_Ins_p.281_282insV|CNOT1_uc010vik.1_In_Frame_Ins_p.1300_1301insV	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	2343_2344					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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	58670625	58670626	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58670625_58670626insT								CNOT1 (6875 upstream) : SLC38A7 (29672 downstream)																																			---	---	---	---
SLC38A7	55238	broad.mit.edu	37	16	58703575	58703575	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58703575delA	uc002eod.1	-						SLC38A7_uc002eob.1_Intron|SLC38A7_uc002eoc.1_Intron|SLC38A7_uc010vil.1_Intron	NM_018231	NP_060701			solute carrier family 38, member 7						amino acid transport|sodium ion transport	integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	58778130	58778130	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58778130delT								GOT2 (9884 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	58862360	58862362	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58862360_58862362delAAA								GOT2 (94114 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	58902640	58902640	+	IGR	DEL	T	-	-	rs61151258		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58902640delT								GOT2 (134394 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	58944205	58944205	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58944205delA								GOT2 (175959 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	58952106	58952106	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58952106delT								GOT2 (183860 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59011062	59011063	+	IGR	INS	-	AGA	AGA	rs140687964	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59011062_59011063insAGA								GOT2 (242816 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59360042	59360042	+	IGR	DEL	A	-	-	rs1364203	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59360042delA								GOT2 (591796 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59417538	59417539	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59417538_59417539insA								GOT2 (649292 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59653669	59653669	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59653669delT								GOT2 (885423 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59760423	59760426	+	IGR	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59760423_59760426delAAAA								GOT2 (992177 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60517682	60517683	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60517682_60517683delGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60528323	60528324	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60528323_60528324insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60892391	60892392	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60892391_60892392delAG								None (None upstream) : CDH8 (794843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61372809	61372810	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61372809_61372810insA								None (None upstream) : CDH8 (314425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61528043	61528043	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61528043delA								None (None upstream) : CDH8 (159192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61645966	61645966	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61645966delA								None (None upstream) : CDH8 (41269 downstream)																																			---	---	---	---
CDH8	1006	broad.mit.edu	37	16	61888034	61888035	+	Intron	DEL	AC	-	-	rs5817315		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61888034_61888035delAC	uc002eog.1	-						CDH8_uc002eoh.2_Intron	NM_001796	NP_001787			cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
CDH8	1006	broad.mit.edu	37	16	61892263	61892263	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61892263delG	uc002eog.1	-						CDH8_uc002eoh.2_5'Flank	NM_001796	NP_001787			cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	62429115	62429115	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62429115delT								CDH8 (359079 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	62666300	62666300	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62666300delT								CDH8 (596264 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63627305	63627312	+	IGR	DEL	CACACACA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63627305_63627312delCACACACA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63720558	63720559	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63720558_63720559delGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64294575	64294575	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64294575delA								None (None upstream) : CDH11 (686110 downstream)																																			---	---	---	---
CDH11	1009	broad.mit.edu	37	16	65002243	65002243	+	Intron	DEL	T	-	-	rs74510343		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65002243delT	uc002eoi.2	-						CDH11_uc010cdn.2_Intron|CDH11_uc002eoj.2_Intron|CDH11_uc010vin.1_Intron	NM_001797	NP_001788			cadherin 11, type 2 preproprotein						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)			---	---	---	---
CDH11	1009	broad.mit.edu	37	16	65078361	65078361	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65078361delT	uc002eoi.2	-						CDH11_uc002eoj.2_Intron|CDH11_uc010vin.1_Intron|CDH11_uc010vio.1_Intron	NM_001797	NP_001788			cadherin 11, type 2 preproprotein						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)			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65283596	65283599	+	IGR	DEL	AAGT	-	-	rs140006855		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65283596_65283599delAAGT								CDH11 (127677 upstream) : LOC283867 (34803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65950727	65950732	+	IGR	DEL	GTGTGC	-	-	rs56911318		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65950727_65950732delGTGTGC								LOC283867 (340524 upstream) : CDH5 (449793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	66203427	66203432	+	IGR	DEL	AAAGAA	-	-	rs142904820	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66203427_66203432delAAAGAA								LOC283867 (593224 upstream) : CDH5 (197093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	66205965	66205966	+	IGR	INS	-	A	A	rs143404337	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66205965_66205966insA								LOC283867 (595762 upstream) : CDH5 (194559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	66290226	66290226	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66290226delA								LOC283867 (680023 upstream) : CDH5 (110299 downstream)																																			---	---	---	---
CMTM4	146223	broad.mit.edu	37	16	66651271	66651271	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66651271delA	uc002epz.2	-						CMTM4_uc002eqa.2_3'UTR	NM_178818	NP_848933			chemokine-like factor superfamily 4 isoform 1						chemotaxis	extracellular space|integral to membrane	cytokine activity			pancreas(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)														---	---	---	---
CCDC79	283847	broad.mit.edu	37	16	66819754	66819754	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66819754delT	uc010viv.1	-	9	897	c.635delA	c.(634-636)AATfs	p.N212fs	CCDC79_uc002eqc.1_RNA|CCDC79_uc002eqd.1_Frame_Shift_Del_p.N212fs	NM_001136505	NP_001129977	Q8NA31	CCD79_HUMAN	coiled-coil domain containing 79	212					regulation of transcription, DNA-dependent		DNA binding				0																		---	---	---	---
CES3	23491	broad.mit.edu	37	16	67000964	67000964	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
HSF4	3299	broad.mit.edu	37	16	67203836	67203837	+	3'UTR	DEL	TT	-	-	rs3215366		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67203836_67203837delTT	uc002erl.1	+	15					HSF4_uc002erm.1_3'UTR|HSF4_uc002ern.1_RNA|HSF4_uc010cec.1_RNA|NOL3_uc010vjc.1_5'Flank	NM_001040667	NP_001035757			heat shock transcription factor 4 isoform b						response to stress	nucleus	sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)												OREG0023873	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ATP6V0D1	9114	broad.mit.edu	37	16	67500230	67500237	+	Intron	DEL	ACACACAC	-	-	rs68126652		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67500230_67500237delACACACAC	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)														---	---	---	---
ACD	65057	broad.mit.edu	37	16	67693253	67693253	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67693253delC	uc002etq.3	-						ACD_uc002etp.3_Intron|ACD_uc002etr.3_Intron|ACD_uc010vjt.1_3'UTR|PARD6A_uc002ets.2_5'Flank|PARD6A_uc002ett.2_5'Flank|PARD6A_uc002etu.2_5'Flank	NM_001082486	NP_001075955			adrenocortical dysplasia homolog isoform 1						intracellular protein transport|negative regulation of telomere maintenance via telomerase|positive regulation of single-stranded telomeric DNA binding|positive regulation of telomerase activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|telomere assembly	nuclear telomere cap complex|nucleoplasm	DNA binding|DNA polymerase binding			pancreas(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)														---	---	---	---
GFOD2	81577	broad.mit.edu	37	16	67719395	67719395	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67719395delG	uc002eub.2	-	2	519	c.224delC	c.(223-225)CCTfs	p.P75fs	GFOD2_uc002euc.2_Intron|GFOD2_uc010cen.2_Frame_Shift_Del_p.P75fs	NM_030819	NP_110446	Q3B7J2	GFOD2_HUMAN	glucose-fructose oxidoreductase domain	75						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)														---	---	---	---
TSNAXIP1	55815	broad.mit.edu	37	16	67854645	67854645	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67854645delA	uc002euj.2	+						TSNAXIP1_uc010cep.2_Intron|TSNAXIP1_uc010vjz.1_Intron|TSNAXIP1_uc002euf.3_Intron|TSNAXIP1_uc010vka.1_Intron|TSNAXIP1_uc010vkb.1_Intron|TSNAXIP1_uc002eug.3_Intron|TSNAXIP1_uc002euh.3_Intron|TSNAXIP1_uc002eui.3_Intron|TSNAXIP1_uc002euk.2_5'Flank	NM_018430	NP_060900			translin-associated factor X interacting protein						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)														---	---	---	---
CENPT	80152	broad.mit.edu	37	16	67869732	67869732	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67869732delT	uc002eun.3	-						CENPT_uc002eum.3_5'Flank|CENPT_uc010vkc.1_5'Flank|CENPT_uc010vkd.1_5'Flank|CENPT_uc010vke.1_5'Flank	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	67950825	67950825	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67950825delC	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)														---	---	---	---
PSKH1	5681	broad.mit.edu	37	16	67955877	67955877	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67955877delT	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)														---	---	---	---
DPEP2	64174	broad.mit.edu	37	16	68030596	68030596	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68030596delT	uc002eve.2	-						DPEP2_uc002evf.2_Intron|DPEP2_uc002evg.2_Intron	NM_022355	NP_071750			dipeptidase 2 precursor						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|proteolysis	anchored to membrane|plasma membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)														---	---	---	---
SLC7A6OS	84138	broad.mit.edu	37	16	68339958	68339958	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68339958delA	uc002evw.1	-							NM_032178	NP_115554			solute carrier family 7, member 6 opposite						protein transport	cytoplasm|nucleus				ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)														---	---	---	---
SMPD3	55512	broad.mit.edu	37	16	68474901	68474901	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68474901delC	uc002ewa.2	-							NM_018667	NP_061137			neutral sphingomyelin phosphodiesterase 3						cell cycle|multicellular organismal development|sphingomyelin catabolic process	Golgi membrane|integral to membrane|plasma membrane	metal ion binding|sphingomyelin phosphodiesterase activity			skin(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	68664189	68664190	+	IGR	DEL	TT	-	-	rs112287693		TCGA-BR-4292-01	TCGA-BR-4292-01									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	68707819	68707819	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68707819delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	68749325	68749326	+	IGR	INS	-	A	A	rs144657689	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68749325_68749326insA								CDH3 (16368 upstream) : CDH1 (21869 downstream)														p.?(1)																					---	---	---	---
CDH1	999	broad.mit.edu	37	16	68832151	68832151	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68832151delT	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	68958391	68958391	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68958391delA	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)														---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	69042546	69042546	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69042546delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	69130897	69130897	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69130897delA								TMCO7 (11814 upstream) : HAS3 (8570 downstream)																																			---	---	---	---
CIRH1A	84916	broad.mit.edu	37	16	69190058	69190060	+	Intron	DEL	TTT	-	-	rs72463058		TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
SNTB2	6645	broad.mit.edu	37	16	69304762	69304762	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69304762delT	uc002ewu.2	+							NM_006750	NP_006741			basic beta 2 syntrophin							cell junction|dystrophin-associated glycoprotein complex|membrane fraction|microtubule|transport vesicle membrane	actin binding|calmodulin binding|protein binding				0		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)														---	---	---	---
NFAT5	10725	broad.mit.edu	37	16	69718776	69718777	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69718776_69718777insT	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																		---	---	---	---
NOB1	28987	broad.mit.edu	37	16	69790410	69790411	+	5'Flank	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69790410_69790411insT	uc002exs.2	-							NM_014062	NP_054781			nin one binding protein							nucleus	metal ion binding|protein binding				0																		---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69824478	69824478	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69824478delT	uc002exu.1	+						WWP2_uc002ext.2_Intron|WWP2_uc002exv.1_Intron	NM_007014	NP_008945			WW domain containing E3 ubiquitin protein ligase						entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6																		---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69923049	69923050	+	Intron	INS	-	AC	AC	rs143311481	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69923049_69923050insAC	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																		---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70123382	70123382	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70123382delT	uc002exy.2	+							NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	70227259	70227259	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70227259delA								CLEC18C (6463 upstream) : EXOSC6 (56875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	70253714	70253714	+	Intron	DEL	T	-	-	rs62049377		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70253714delT	uc002eyl.1	-											Homo sapiens cDNA FLJ46379 fis, clone THYMU2003803, moderately similar to Homo sapiens PI-3-kinase-related kinase SMG-1 (SMG1).																														---	---	---	---
ST3GAL2	6483	broad.mit.edu	37	16	70422805	70422806	+	Intron	DEL	AA	-	-	rs11304215		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70422805_70422806delAA	uc002eyw.2	-						ST3GAL2_uc002eyx.2_Intron	NM_006927	NP_008858			ST3 beta-galactoside alpha-2,3-sialyltransferase						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)																---	---	---	---
MTSS1L	92154	broad.mit.edu	37	16	70710944	70710944	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70710944delC	uc002ezj.2	-						MTSS1L_uc002ezk.1_Intron	NM_138383	NP_612392			metastasis suppressor 1-like						filopodium assembly|signal transduction		actin binding|cytoskeletal adaptor activity|SH3 domain binding			central_nervous_system(1)	1																		---	---	---	---
VAC14	55697	broad.mit.edu	37	16	70825292	70825292	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70825292delT	uc002ezm.2	-						VAC14_uc010cfw.2_Intron|VAC14_uc002ezn.2_Intron	NM_018052	NP_060522			Vac14 homolog						interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)|skin(1)	2		Ovarian(137;0.0699)																---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	70964222	70964222	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70964222delA	uc002ezr.2	-							NM_032821	NP_116210			hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	71463747	71463747	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71463747delA								CALB2 (39408 upstream) : ZNF23 (17766 downstream)																																			---	---	---	---
MARVELD3	91862	broad.mit.edu	37	16	71668441	71668442	+	Frame_Shift_Ins	INS	-	G	G	rs150498655	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71668441_71668442insG	uc002fat.2	+	3	1004_1005	c.941_942insG	c.(940-942)GCGfs	p.A314fs	MARVELD3_uc002fau.2_Intron|MARVELD3_uc010cge.2_Intron	NM_052858	NP_443090	Q96A59	MALD3_HUMAN	MARVEL domain containing 3 isoform 2	314	MARVEL.|Helical; (Potential).					integral to membrane				skin(1)	1		Ovarian(137;0.125)																---	---	---	---
PHLPP2	23035	broad.mit.edu	37	16	71682687	71682687	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71682687delA	uc002fax.2	-	18					PHLPP2_uc002fav.2_Intron|PHLPP2_uc010cgf.2_3'UTR	NM_015020	NP_055835			PH domain and leucine rich repeat protein							cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
AP1G1	164	broad.mit.edu	37	16	71779706	71779706	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71779706delA	uc010cgg.2	-						AP1G1_uc002fba.2_Intron|AP1G1_uc002fbb.2_Intron|AP1G1_uc002faz.2_Intron	NM_001128	NP_001119			adaptor-related protein complex 1, gamma 1						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)																---	---	---	---
AP1G1	164	broad.mit.edu	37	16	71795578	71795579	+	Intron	DEL	AA	-	-	rs142639197	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71795578_71795579delAA	uc010cgg.2	-						AP1G1_uc002fba.2_Intron|AP1G1_uc002fbb.2_Intron|AP1G1_uc010vmg.1_Intron	NM_001128	NP_001119			adaptor-related protein complex 1, gamma 1						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)																---	---	---	---
AP1G1	164	broad.mit.edu	37	16	71803187	71803187	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71803187delA	uc010cgg.2	-						AP1G1_uc002fba.2_Intron|AP1G1_uc002fbb.2_Intron|AP1G1_uc010vmg.1_Intron|AP1G1_uc010vmh.1_Intron	NM_001128	NP_001119			adaptor-related protein complex 1, gamma 1						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)																---	---	---	---
PKD1L3	342372	broad.mit.edu	37	16	71963643	71963643	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71963643delA	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0																		---	---	---	---
PKD1L3	342372	broad.mit.edu	37	16	71982957	71982957	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71982957delC	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0																		---	---	---	---
PKD1L3	342372	broad.mit.edu	37	16	72006583	72006583	+	Intron	DEL	A	-	-	rs76727112		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72006583delA	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0																		---	---	---	---
DHODH	1723	broad.mit.edu	37	16	72050827	72050827	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72050827delT	uc002fbp.2	+						DHODH_uc010cgk.2_Intron	NM_001361	NP_001352			dihydroorotate dehydrogenase precursor						'de novo' pyrimidine base biosynthetic process|pyrimidine nucleoside biosynthetic process|UMP biosynthetic process	integral to membrane|mitochondrial inner membrane	dihydroorotate oxidase activity				0		Ovarian(137;0.125)			Atovaquone(DB01117)|Leflunomide(DB01097)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	72489951	72489951	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72489951delT	uc002fci.1	+											Homo sapiens cDNA FLJ38299 fis, clone FCBBF3017255.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	72600487	72600487	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72600487delA								PMFBP1 (394138 upstream) : ZFHX3 (216301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	72656838	72656839	+	IGR	DEL	AA	-	-	rs5817812		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72656838_72656839delAA								PMFBP1 (450489 upstream) : ZFHX3 (159949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	72791053	72791054	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72791053_72791054delTT	uc002fcj.1	+											Homo sapiens cDNA FLJ11501 fis, clone HEMBA1002100.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	72793670	72793670	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72793670delT	uc002fcj.1	+											Homo sapiens cDNA FLJ11501 fis, clone HEMBA1002100.																														---	---	---	---
HTA	283902	broad.mit.edu	37	16	73124625	73124627	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73124625_73124627delAAA	uc010vmq.1	+							NR_027756				Homo sapiens cDNA clone IMAGE:4544545, partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	73132586	73132586	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73132586delT								HTA (4916 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73663276	73663276	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73663276delA								HTA (535606 upstream) : PSMD7 (667405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73673757	73673757	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73673757delA								HTA (546087 upstream) : PSMD7 (656924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73945605	73945605	+	IGR	DEL	A	-	-	rs143465667		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73945605delA								HTA (817935 upstream) : PSMD7 (385076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74476551	74476551	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74476551delT								CLEC18B (20902 upstream) : GLG1 (4777 downstream)																																			---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74496163	74496163	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74496163delA	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139			golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2																		---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74514458	74514459	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74514458_74514459insT	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139			golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2																		---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74526833	74526833	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74526833delA	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139			golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	74648012	74648013	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74648012_74648013insT								GLG1 (6970 upstream) : RFWD3 (7285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74648255	74648256	+	IGR	INS	-	A	A	rs143011146	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74648255_74648256insA								GLG1 (7213 upstream) : RFWD3 (7042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74893340	74893342	+	IGR	DEL	TTT	-	-	rs111756314		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74893340_74893342delTTT								FA2H (84619 upstream) : WDR59 (14129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	75244416	75244417	+	IGR	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75244416_75244417insCA								CTRB2 (3344 upstream) : CTRB1 (8467 downstream)																																			---	---	---	---
CFDP1	10428	broad.mit.edu	37	16	75408551	75408551	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75408551delA	uc002fdy.2	-						CFDP1_uc002fdz.2_Intron	NM_006324	NP_006315			craniofacial development protein 1						multicellular organismal development					upper_aerodigestive_tract(1)	1																		---	---	---	---
CFDP1	10428	broad.mit.edu	37	16	75435669	75435672	+	Intron	DEL	GAAA	-	-	rs112379322		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75435669_75435672delGAAA	uc002fdy.2	-						CFDP1_uc002fdz.2_Intron|CFDP1_uc002fea.1_Intron	NM_006324	NP_006315			craniofacial development protein 1						multicellular organismal development					upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	75555082	75555082	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75555082delA								CHST6 (26156 upstream) : CHST5 (7348 downstream)																																			---	---	---	---
TERF2IP	54386	broad.mit.edu	37	16	75690320	75690320	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75690320delA	uc002fet.1	+	3	1108	c.1011delA	c.(1009-1011)CTAfs	p.L337fs		NM_018975	NP_061848	Q9NYB0	TE2IP_HUMAN	telomeric repeat binding factor 2, interacting	337					negative regulation of DNA recombination at telomere|negative regulation of telomere maintenance|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|regulation of double-strand break repair via homologous recombination|telomere maintenance via telomerase|transcription, DNA-dependent	cytoplasm|nuclear telomere cap complex|nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	76226954	76226955	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76226954_76226955insTG								TERF2IP (535626 upstream) : CNTNAP4 (84221 downstream)																																			---	---	---	---
CNTNAP4	85445	broad.mit.edu	37	16	76330541	76330542	+	Intron	INS	-	AG	AG	rs150169301	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76330541_76330542insAG	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron	NM_033401	NP_207837			cell recognition protein CASPR4 isoform 1						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	77193828	77193828	+	IGR	DEL	T	-	-	rs68066912		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77193828delT								CNTNAP4 (600693 upstream) : MON1B (31008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	77302351	77302352	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77302351_77302352insT								SYCE1L (55375 upstream) : ADAMTS18 (13674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	77309505	77309505	+	IGR	DEL	G	-	-	rs12926676	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77309505delG								SYCE1L (62529 upstream) : ADAMTS18 (6521 downstream)																																			---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77356311	77356311	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77356311delA	uc002ffc.3	-	14	2504	c.2085delT	c.(2083-2085)TTTfs	p.F695fs	ADAMTS18_uc010chc.1_Frame_Shift_Del_p.F283fs|ADAMTS18_uc002ffe.1_Frame_Shift_Del_p.F391fs	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	695	Cys-rich.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding	p.A696fs*18(2)		large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18																		---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77369410	77369411	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77369410_77369411insT	uc002ffc.3	-						ADAMTS18_uc010chc.1_Intron|ADAMTS18_uc002ffe.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																		---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77456438	77456438	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77456438delA	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	77657401	77657401	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77657401delT								ADAMTS18 (188390 upstream) : NUDT7 (99010 downstream)																																			---	---	---	---
VAT1L	57687	broad.mit.edu	37	16	77850683	77850683	+	Intron	DEL	A	-	-	rs71884745		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77850683delA	uc002ffg.1	+							NM_020927	NP_065978			vesicle amine transport protein 1 homolog (T.								oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
VAT1L	57687	broad.mit.edu	37	16	77949825	77949825	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77949825delA	uc002ffg.1	+							NM_020927	NP_065978			vesicle amine transport protein 1 homolog (T.								oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78332840	78332840	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78332840delT	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	78412028	78412028	+	Intron	DEL	T	-	-	rs7189441	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78412028delT	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	78930652	78930653	+	Intron	DEL	GT	-	-	rs145919325		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78930652_78930653delGT	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	79029461	79029462	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79029461_79029462insA	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	79526589	79526589	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79526589delA								WWOX (280026 upstream) : MAF (101157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	79731465	79731466	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79731465_79731466delTC								MAF (96843 upstream) : DYNLRB2 (843388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	79819021	79819025	+	IGR	DEL	AAAAA	-	-	rs72079109		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79819021_79819025delAAAAA								MAF (184399 upstream) : DYNLRB2 (755829 downstream)																																			---	---	---	---
CDYL2	124359	broad.mit.edu	37	16	80668215	80668215	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80668215delA	uc002ffs.2	-							NM_152342	NP_689555			chromodomain protein, Y-like 2							nucleus	catalytic activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
CDYL2	124359	broad.mit.edu	37	16	80805627	80805628	+	Intron	INS	-	A	A	rs148874788	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80805627_80805628insA	uc002ffs.2	-							NM_152342	NP_689555			chromodomain protein, Y-like 2							nucleus	catalytic activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
BCMO1	53630	broad.mit.edu	37	16	81285440	81285441	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81285440_81285441delCA	uc002fgn.1	+						BCMO1_uc002fgm.1_Intron|BCMO1_uc010vnp.1_Intron	NM_017429	NP_059125			beta-carotene 15,15'-monooxygenase						retinoid metabolic process|steroid metabolic process	cytosol	beta-carotene 15,15'-monooxygenase activity|metal ion binding|monooxygenase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	81448414	81448414	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81448414delA								GAN (34613 upstream) : CMIP (30361 downstream)																																			---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81508809	81508809	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81508809delA	uc002fgp.2	+							NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81570359	81570359	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81570359delT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	82056960	82056960	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82056960delT								SDR42E1 (11867 upstream) : HSD17B2 (11898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	82356429	82356429	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82356429delT								MPHOSPH6 (152600 upstream) : CDH13 (304149 downstream)																																			---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83179799	83179801	+	Intron	DEL	AAA	-	-	rs35303928		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83179799_83179801delAAA	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	83807981	83807981	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83807981delT	uc002fgx.2	+						CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
OSGIN1	29948	broad.mit.edu	37	16	83983256	83983256	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83983256delC	uc002fha.2	+						OSGIN1_uc002fhb.2_Intron	NM_013370	NP_037502			oxidative stress induced growth inhibitor 1						cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0																		---	---	---	---
NECAB2	54550	broad.mit.edu	37	16	84035269	84035288	+	Intron	DEL	CCTGGGCACCCCCTCACCTT	-	-	rs3215187		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84035269_84035288delCCTGGGCACCCCCTCACCTT	uc002fhd.2	+						NECAB2_uc002fhe.2_Intron	NM_019065	NP_061938			neuronal calcium-binding protein 2						antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity|protein binding			ovary(2)	2																		---	---	---	---
KIAA1609	57707	broad.mit.edu	37	16	84532335	84532336	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84532335_84532336insA	uc002fib.2	-						KIAA1609_uc010vod.1_Intron|KIAA1609_uc002fic.2_Intron	NM_020947	NP_065998			hypothetical protein LOC57707								protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	84660811	84660811	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84660811delT								COTL1 (9142 upstream) : KLHL36 (21320 downstream)																																			---	---	---	---
USP10	9100	broad.mit.edu	37	16	84775289	84775290	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84775289_84775290insA	uc002fii.2	+						USP10_uc010voe.1_Intron|USP10_uc010vof.1_Intron|USP10_uc002fij.2_Intron	NM_005153	NP_005144			ubiquitin specific protease 10						DNA damage response, signal transduction by p53 class mediator|DNA repair|protein deubiquitination|ubiquitin-dependent protein catabolic process	early endosome|intermediate filament cytoskeleton|nucleus	cystic fibrosis transmembrane conductance regulator binding|p53 binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0																		---	---	---	---
CRISPLD2	83716	broad.mit.edu	37	16	84883387	84883390	+	Intron	DEL	TTAG	-	-	rs145157300		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84883387_84883390delTTAG	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																		---	---	---	---
CRISPLD2	83716	broad.mit.edu	37	16	84900431	84900431	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84900431delT	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	85171527	85171528	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85171527_85171528delTC								FAM92B (25413 upstream) : KIAA0182 (473501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85321846	85321846	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85321846delA								FAM92B (175732 upstream) : KIAA0182 (323183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85444655	85444655	+	IGR	DEL	A	-	-	rs67937762		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85444655delA								FAM92B (298541 upstream) : KIAA0182 (200374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85608298	85608299	+	IGR	INS	-	T	T	rs141547524	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85608298_85608299insT								FAM92B (462184 upstream) : KIAA0182 (36730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85973732	85973732	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85973732delC								IRF8 (17523 upstream) : LOC732275 (391724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86038217	86038218	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86038217_86038218delTT								IRF8 (82008 upstream) : LOC732275 (327238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	87201906	87201906	+	Intron	DEL	T	-	-	rs78452854		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87201906delT	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	87217954	87217954	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87217954delA	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	87313271	87313271	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87313271delT	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																														---	---	---	---
MAP1LC3B	81631	broad.mit.edu	37	16	87432620	87432621	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87432620_87432621insT	uc002fjx.2	+						MAP1LC3B_uc010chs.2_Intron	NM_022818	NP_073729			microtubule-associated proteins 1A/1B light						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule	protein binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0249)														---	---	---	---
CA5A	763	broad.mit.edu	37	16	87947268	87947268	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87947268delT	uc002fkn.1	-							NM_001739	NP_001730			carbonic anhydrase VA, mitochondrial precursor						one-carbon metabolic process	mitochondrial matrix	carbonate dehydratase activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0513)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	88514351	88514351	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88514351delA								ZNF469 (7186 upstream) : ZFPM1 (5663 downstream)																																			---	---	---	---
ZFPM1	161882	broad.mit.edu	37	16	88593209	88593211	+	Intron	DEL	CCT	-	-	rs111670467	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88593209_88593211delCCT	uc002fkv.2	+							NM_153813	NP_722520			zinc finger protein, multitype 1						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|transcription factor binding|zinc ion binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0478)														---	---	---	---
ZNF778	197320	broad.mit.edu	37	16	89288779	89288779	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89288779delT	uc002fmv.2	+						ZNF778_uc010vpf.1_Intron|ZNF778_uc002fmw.1_Intron|ZNF778_uc010vpg.1_Intron	NM_182531	NP_872337			zinc finger protein 778						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0269)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	89750933	89750933	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89750933delT	uc002fnz.3	-						CDK10_uc002foa.2_5'Flank|CDK10_uc010cip.2_5'Flank|CDK10_uc010vpl.1_5'Flank|CDK10_uc002fob.2_5'Flank|CDK10_uc002fod.2_5'Flank|CDK10_uc002foe.2_5'Flank|CDK10_uc002fof.2_5'Flank|CDK10_uc010cio.2_5'Flank|CDK10_uc002fog.3_5'Flank|CDK10_uc002foh.3_5'Flank					Homo sapiens cDNA clone IMAGE:5172262, with apparent retained intron.																														---	---	---	---
SPATA2L	124044	broad.mit.edu	37	16	89767029	89767029	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89767029delC	uc002foj.2	-						SPATA2L_uc002fok.2_Intron	NM_152339	NP_689552			spermatogenesis associated 2-like												0		Lung NSC(15;0.00043)|all_lung(18;0.000665)|all_hematologic(23;0.0355)		BRCA - Breast invasive adenocarcinoma(80;0.0272)														---	---	---	---
FANCA	2175	broad.mit.edu	37	16	89880215	89880218	+	Intron	DEL	TGTG	-	-	rs67781268		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89880215_89880218delTGTG	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				---	---	---	---
RPH3AL	9501	broad.mit.edu	37	17	66205	66208	+	Intron	DEL	GAGA	-	-	rs141443761		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66205_66208delGAGA	uc002frd.1	-						RPH3AL_uc010vpy.1_Intron|RPH3AL_uc002fre.1_Intron|RPH3AL_uc002frf.1_Intron|RPH3AL_uc010cjl.1_Intron	NM_006987	NP_008918			rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)														---	---	---	---
RPH3AL	9501	broad.mit.edu	37	17	95191	95192	+	Intron	INS	-	GT	GT	rs145270784		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:95191_95192insGT	uc002frd.1	-						RPH3AL_uc010vpy.1_Intron|RPH3AL_uc002fre.1_Intron|RPH3AL_uc002frf.1_Intron|RPH3AL_uc010cjl.1_Intron	NM_006987	NP_008918			rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)														---	---	---	---
RPH3AL	9501	broad.mit.edu	37	17	166905	166905	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:166905delA	uc002frd.1	-						RPH3AL_uc010vpy.1_Intron|RPH3AL_uc002fre.1_Intron|RPH3AL_uc002frf.1_Intron|RPH3AL_uc010cjl.1_Intron	NM_006987	NP_008918			rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)														---	---	---	---
RPH3AL	9501	broad.mit.edu	37	17	168173	168174	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:168173_168174insG	uc002frd.1	-						RPH3AL_uc010vpy.1_Intron|RPH3AL_uc002fre.1_Intron|RPH3AL_uc002frf.1_Intron|RPH3AL_uc010cjl.1_Intron	NM_006987	NP_008918			rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)														---	---	---	---
RPH3AL	9501	broad.mit.edu	37	17	203465	203465	+	5'Flank	DEL	A	-	-	rs11356210		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:203465delA	uc002fre.1	-						RPH3AL_uc002frf.1_5'Flank|RPH3AL_uc010cjl.1_5'Flank	NM_006987	NP_008918			rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)														---	---	---	---
VPS53	55275	broad.mit.edu	37	17	526098	526099	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:526098_526099delTT	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)														---	---	---	---
VPS53	55275	broad.mit.edu	37	17	544101	544102	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:544101_544102insT	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)														---	---	---	---
VPS53	55275	broad.mit.edu	37	17	567323	567324	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:567323_567324insT	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)														---	---	---	---
FAM57A	79850	broad.mit.edu	37	17	637056	637056	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:637056delT	uc002frp.2	+						FAM57A_uc002frq.2_Intron|FAM57A_uc002frr.2_Intron	NM_024792	NP_079068			family with sequence similarity 57, member A							integral to membrane|plasma membrane					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0217)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	646138	646138	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:646138delT								FAM57A (64 upstream) : GEMIN4 (1523 downstream)																																			---	---	---	---
RNMTL1	55178	broad.mit.edu	37	17	691505	691505	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:691505delA	uc002frw.2	+							NM_018146	NP_060616			RNA methyltransferase like 1						RNA processing		protein binding|RNA binding|RNA methyltransferase activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0219)														---	---	---	---
ABR	29	broad.mit.edu	37	17	1050486	1050487	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1050486_1050487delTT	uc002fsd.2	-						ABR_uc002fse.2_Intron	NM_021962	NP_068781			active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)														---	---	---	---
TUSC5	286753	broad.mit.edu	37	17	1201529	1201529	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1201529delT	uc002fsi.1	+							NM_172367	NP_758955			LOST1						response to biotic stimulus	integral to membrane				skin(2)	2				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)														---	---	---	---
YWHAE	7531	broad.mit.edu	37	17	1262446	1262446	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1262446delA	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	1387335	1387336	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1387335_1387336delAA	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)														---	---	---	---
SMYD4	114826	broad.mit.edu	37	17	1684221	1684221	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1684221delT	uc002ftm.3	-	11						NM_052928	NP_443160			SET and MYND domain containing 4								zinc ion binding			skin(3)|kidney(2)	5																		---	---	---	---
RTN4RL1	146760	broad.mit.edu	37	17	1904548	1904548	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1904548delT	uc002ftp.2	-							NM_178568	NP_848663			reticulon 4 receptor-like 1 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
SMG6	23293	broad.mit.edu	37	17	2020136	2020136	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2020136delA	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	2041447	2041447	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2041447delA	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	2127217	2127217	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2127217delA	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	2162093	2162093	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2162093delA	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																		---	---	---	---
SRR	63826	broad.mit.edu	37	17	2213881	2213881	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2213881delT	uc002fue.1	+							NM_021947	NP_068766			serine racemase						D-serine biosynthetic process|L-serine metabolic process|protein homotetramerization|pyruvate biosynthetic process|response to lipopolysaccharide	cytoplasm|neuronal cell body|soluble fraction	ATP binding|calcium ion binding|D-serine ammonia-lyase activity|glycine binding|L-serine ammonia-lyase activity|magnesium ion binding|PDZ domain binding|protein homodimerization activity|pyridoxal phosphate binding|serine racemase activity|threonine racemase activity				0		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;3.24e-06)|READ - Rectum adenocarcinoma(1115;0.0649)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	2442903	2442904	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2442903_2442904delTC								METT10D (27703 upstream) : PAFAH1B1 (54019 downstream)																																			---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2790220	2790220	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2790220delG	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	2864512	2864512	+	Intron	DEL	A	-	-	rs113625406		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2864512delA	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	2909733	2909734	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2909733_2909734delTT	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																		---	---	---	---
TRPV3	162514	broad.mit.edu	37	17	3427202	3427203	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3427202_3427203delAC	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	3464820	3464821	+	IGR	DEL	AA	-	-	rs75940438		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3464820_3464821delAA								TRPV3 (3531 upstream) : TRPV1 (3920 downstream)																																			---	---	---	---
C17orf85	55421	broad.mit.edu	37	17	3752471	3752471	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3752471delT	uc010ckl.1	-						C17orf85_uc002fwq.2_5'Flank	NM_001114118	NP_001107590			ELG protein isoform a								nucleotide binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (3;0.0725)														---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3950937	3950937	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3950937delA	uc002fxe.2	-						ZZEF1_uc002fxh.2_Intron|ZZEF1_uc002fxi.2_Intron|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	3962780	3962781	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3962780_3962781delAG	uc002fxe.2	-						ZZEF1_uc002fxh.2_Intron|ZZEF1_uc002fxi.2_Intron|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	3976059	3976061	+	Intron	DEL	AGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3976059_3976061delAGA	uc002fxe.2	-						ZZEF1_uc002fxj.1_5'Flank	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	4017813	4017813	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4017813delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	4273509	4273509	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4273509delT								UBE2G1 (3540 upstream) : SPNS3 (63710 downstream)																																			---	---	---	---
SMTNL2	342527	broad.mit.edu	37	17	4509421	4509421	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4509421delT	uc002fyf.1	+						SMTNL2_uc002fye.2_Intron	NM_001114974	NP_001108446			smoothelin-like 2 isoform 1												0				READ - Rectum adenocarcinoma(115;0.0325)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	4516733	4516733	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4516733delT	uc002fyg.1	+											Homo sapiens cDNA clone IMAGE:5176687.																														---	---	---	---
MINK1	50488	broad.mit.edu	37	17	4759733	4759733	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4759733delT	uc010vsl.1	+						MINK1_uc010vsk.1_Intron|MINK1_uc010vsm.1_Intron|MINK1_uc010vsn.1_Intron|MINK1_uc010vso.1_Intron	NM_153827	NP_722549			misshapen-like kinase 1 isoform 3						JNK cascade	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)|skin(1)	6																		---	---	---	---
RNF167	26001	broad.mit.edu	37	17	4844849	4844849	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4844849delA	uc002fzq.2	+						SLC25A11_uc002fzo.1_5'Flank|SLC25A11_uc002fzp.1_5'Flank|RNF167_uc002fzr.2_Intron|RNF167_uc002fzs.2_Intron|RNF167_uc002fzt.2_Intron|RNF167_uc002fzu.2_Intron|RNF167_uc002fzv.2_Intron|RNF167_uc002fzw.1_Intron|RNF167_uc002fzx.2_Intron|RNF167_uc002fzy.2_5'Flank	NM_015528	NP_056343			ring finger protein 167 precursor						negative regulation of cell cycle|protein polyubiquitination	cytoplasm|endomembrane system|integral to membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
KIF1C	10749	broad.mit.edu	37	17	4912482	4912482	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4912482delT	uc002gan.1	+							NM_006612	NP_006603			kinesin family member 1C						microtubule-based movement|retrograde vesicle-mediated transport, Golgi to ER	endoplasmic reticulum|Golgi apparatus|microtubule	ATP binding|microtubule motor activity			breast(2)	2																		---	---	---	---
GPR172B	55065	broad.mit.edu	37	17	4952759	4952759	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4952759delA	uc010ckx.2	-											SubName: Full=cDNA FLJ41572 fis, clone CTONG2009725, highly similar to Porcine endogenous retrovirus A receptor 2;							integral to plasma membrane	receptor activity|riboflavin transporter activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	4958886	4958886	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4958886delC								GPR172B (3582 upstream) : ZFP3 (22868 downstream)																																			---	---	---	---
ZNF232	7775	broad.mit.edu	37	17	5013191	5013191	+	Intron	DEL	T	-	-	rs72458339		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5013191delT	uc002gas.2	-						ZNF232_uc002gar.1_Intron|ZNF232_uc002gat.2_Intron|ZNF232_uc010vsv.1_Intron	NM_014519	NP_055334			zinc finger protein 232						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	5096766	5096766	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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.																														---	---	---	---
DHX33	56919	broad.mit.edu	37	17	5364627	5364627	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5364627delT	uc002gca.2	-						DHX33_uc002gbz.2_5'UTR|DHX33_uc002gcb.2_Intron|DHX33_uc010clf.2_Intron	NM_020162	NP_064547			DEAH (Asp-Glu-Ala-His) box polypeptide 33							nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|pancreas(1)	2																		---	---	---	---
WSCD1	23302	broad.mit.edu	37	17	5973117	5973122	+	Intron	DEL	GTGTGC	-	-	rs66521205		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5973117_5973122delGTGTGC	uc010cli.2	+						WSCD1_uc002gcn.2_5'Flank|WSCD1_uc002gco.2_5'Flank	NM_015253	NP_056068			WSC domain containing 1							integral to membrane	sulfotransferase activity				0																		---	---	---	---
WSCD1	23302	broad.mit.edu	37	17	5986217	5986217	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5986217delA	uc010cli.2	+						WSCD1_uc002gcn.2_Intron|WSCD1_uc002gco.2_Intron|WSCD1_uc010clj.2_Intron	NM_015253	NP_056068			WSC domain containing 1							integral to membrane	sulfotransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	6112068	6112068	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6112068delA								WSCD1 (84323 upstream) : AIPL1 (214992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	6122113	6122113	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6122113delT								WSCD1 (94368 upstream) : AIPL1 (204947 downstream)																																			---	---	---	---
FAM64A	54478	broad.mit.edu	37	17	6350599	6350599	+	Intron	DEL	T	-	-	rs113827676		TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
TXNDC17	84817	broad.mit.edu	37	17	6544520	6544520	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6544520delA	uc002gdf.3	+	1	299	c.118delA	c.(118-120)AAAfs	p.K40fs	KIAA0753_uc002gde.3_5'Flank|KIAA0753_uc010vte.1_5'Flank	NM_032731	NP_116120	Q9BRA2	TXD17_HUMAN	thioredoxin-like 5	40					tumor necrosis factor-mediated signaling pathway	cytosol	electron carrier activity|peroxidase activity|protein binding|protein-disulfide reductase activity			ovary(1)	1																		---	---	---	---
ALOX12	239	broad.mit.edu	37	17	6906085	6906086	+	Intron	INS	-	T	T	rs141247518	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6906085_6906086insT	uc002gdx.3	+						uc002gdy.1_Intron	NM_000697	NP_000688			arachidonate 12-lipoxygenase						anti-apoptosis|cellular component movement|fatty acid oxidation|leukotriene biosynthetic process|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of cell proliferation|superoxide anion generation	cytosol|sarcolemma	arachidonate 12-lipoxygenase activity|hepoxilin-epoxide hydrolase activity|iron ion binding|lipoxygenase activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
DLG4	1742	broad.mit.edu	37	17	7095639	7095639	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7095639delG	uc002get.3	-						DLG4_uc010vtm.1_Intron|DLG4_uc010vtn.1_Intron|DLG4_uc010cly.2_Intron|DLG4_uc010vto.1_Intron	NM_001365	NP_001356			post-synaptic density protein 95 isoform 1						axon guidance|learning|protein complex assembly|protein localization to synapse|signal transduction|synaptic transmission	cell junction|cortical cytoskeleton|endocytic vesicle membrane|neuron spine|postsynaptic density|postsynaptic membrane|synaptosome	protein binding|protein C-terminus binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	7171329	7171329	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7171329delA								CLDN7 (4817 upstream) : SLC2A4 (13725 downstream)																																			---	---	---	---
FXR2	9513	broad.mit.edu	37	17	7505245	7505245	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7505245delA	uc002gia.1	-						FXR2_uc010vud.1_Intron	NM_004860	NP_004851			fragile X mental retardation syndrome related							cytosolic large ribosomal subunit	protein binding|RNA binding	p.?(1)			0				READ - Rectum adenocarcinoma(115;0.17)														---	---	---	---
ATP1B2	482	broad.mit.edu	37	17	7557763	7557764	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7557763_7557764delTT	uc002gif.1	+							NM_001678	NP_001669			Na+/K+ -ATPase beta 2 subunit						ATP biosynthetic process|blood coagulation|leukocyte migration	integral to membrane|plasma membrane	protein binding|sodium:potassium-exchanging ATPase activity	p.0?(2)|p.?(1)		central_nervous_system(1)|pancreas(1)	2		all_cancers(10;0.000178)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;2.55e-06)|READ - Rectum adenocarcinoma(115;0.168)														---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7650467	7650467	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7650467delT	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	7703141	7703142	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7703141_7703142delAC	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	7737652	7737653	+	IGR	INS	-	C	C	rs111926373		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7737652_7737653insC								DNAH2 (594 upstream) : KDM6B (5582 downstream)																																			---	---	---	---
ALOX12B	242	broad.mit.edu	37	17	7990546	7990557	+	Intron	DEL	ACACACACAGAC	-	-	rs72449480		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7990546_7990557delACACACACAGAC	uc002gjy.1	-						hsa-mir-4314|MI0015846_5'Flank	NM_001139	NP_001130			arachidonate 12-lipoxygenase, 12R type						epidermis development|leukotriene biosynthetic process		arachidonate 12-lipoxygenase activity|iron ion binding|lipoxygenase activity				0															Multiple Myeloma(8;0.094)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	8102400	8102401	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8102400_8102401delAA								C17orf59 (8836 upstream) : AURKB (5649 downstream)																																			---	---	---	---
C17orf68	80169	broad.mit.edu	37	17	8134459	8134459	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8134459delA	uc002gkq.3	-						C17orf68_uc010cnv.2_Intron	NM_025099	NP_079375			alpha accessory factor 132						positive regulation of DNA replication|telomere maintenance	Stn1-Ten1 complex	protein binding|single-stranded DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	8237991	8237991	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8237991delT								ARHGEF15 (12163 upstream) : ODF4 (5197 downstream)																																			---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8455303	8455303	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8455303delA	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron|MYH10_uc010cny.1_Intron	NM_005964	NP_005955			myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8508327	8508327	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8508327delA	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron	NM_005964	NP_005955			myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	8571998	8571999	+	IGR	DEL	TT	-	-	rs112072129		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8571998_8571999delTT								MYH10 (37962 upstream) : CCDC42 (61248 downstream)																																			---	---	---	---
NTN1	9423	broad.mit.edu	37	17	8980531	8980532	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8980531_8980532insA	uc002glw.3	+							NM_004822	NP_004813			netrin 1 precursor						apoptosis|axon guidance		protein binding				0																		---	---	---	---
NTN1	9423	broad.mit.edu	37	17	9138790	9138791	+	Intron	INS	-	A	A	rs148501446	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9138790_9138791insA	uc002glw.3	+							NM_004822	NP_004813			netrin 1 precursor						apoptosis|axon guidance		protein binding				0																		---	---	---	---
USP43	124739	broad.mit.edu	37	17	9582040	9582040	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9582040delC	uc010cod.2	+						USP43_uc002gma.3_Intron|USP43_uc010vva.1_Intron|USP43_uc010coe.2_Intron	NM_153210	NP_694942			ubiquitin specific protease 43						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	10183437	10183440	+	IGR	DEL	AAAC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10183437_10183440delAAAC								GAS7 (81569 upstream) : MYH13 (20743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	10639155	10639155	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10639155delA								TMEM220 (5509 upstream) : PIRT (86638 downstream)																																			---	---	---	---
PIRT	644139	broad.mit.edu	37	17	10737071	10737072	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10737071_10737072delAA	uc010col.2	-							NM_001101387	NP_001094857			phosphoinositide-interacting regulator of							integral to membrane				ovary(1)	1																		---	---	---	---
MAP2K4	6416	broad.mit.edu	37	17	12014798	12014800	+	Intron	DEL	TTT	-	-	rs68086974		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12014798_12014800delTTT	uc002gnj.2	+						MAP2K4_uc002gnk.2_Intron|MAP2K4_uc010vvi.1_Intron|MAP2K4_uc010vvj.1_Intron	NM_003010	NP_003001			mitogen-activated protein kinase kinase 4						cellular response to mechanical stimulus|innate immune response|JNK cascade|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	ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.?(1)		large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1)	58		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)				D|Mis|N		pancreatic|breast|colorectal								---	---	---	---
ELAC2	60528	broad.mit.edu	37	17	12920063	12920069	+	Intron	DEL	AAAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12920063_12920069delAAAAAAA	uc002gnz.3	-						ELAC2_uc010vvp.1_Intron|ELAC2_uc010vvq.1_Intron|ELAC2_uc010vvr.1_Intron	NM_018127	NP_060597			elaC homolog 2 isoform 1						tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0														Hereditary_Prostate_Cancer				---	---	---	---
Unknown	0	broad.mit.edu	37	17	13034552	13034553	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13034552_13034553delCA								ELAC2 (113193 upstream) : HS3ST3A1 (364453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	13050873	13050873	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13050873delA								ELAC2 (129514 upstream) : HS3ST3A1 (348133 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	13511379	13511380	+	IGR	INS	-	A	A	rs111895592		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13511379_13511380insA								HS3ST3A1 (6135 upstream) : CDRT15P (416435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	13872920	13872922	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13872920_13872922delTTT								HS3ST3A1 (367676 upstream) : CDRT15P (54893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14269992	14269992	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14269992delG								HS3ST3B1 (20500 upstream) : PMP22 (863105 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14301497	14301498	+	IGR	INS	-	TG	TG	rs138584378	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14301497_14301498insTG								HS3ST3B1 (52005 upstream) : PMP22 (831599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14376904	14376905	+	IGR	INS	-	T	T	rs149511855	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14376904_14376905insT								HS3ST3B1 (127412 upstream) : PMP22 (756192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14851004	14851004	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14851004delT								HS3ST3B1 (601512 upstream) : PMP22 (282093 downstream)																																			---	---	---	---
FAM18B2	201158	broad.mit.edu	37	17	15409706	15409707	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15409706_15409707insA	uc002goq.2	-						CDRT4_uc010vvw.1_Intron|FAM18B2_uc010vvx.1_Intron	NM_145301	NP_660344			hypothetical protein LOC201158 isoform 1							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0872)|BRCA - Breast invasive adenocarcinoma(8;0.0581)|READ - Rectum adenocarcinoma(1115;0.0967)														---	---	---	---
TRIM16	10626	broad.mit.edu	37	17	15535699	15535699	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15535699delA	uc002gox.2	-						TRIM16_uc002gor.1_Intron|TRIM16_uc002gow.2_Intron|TRIM16_uc002goy.2_Intron	NM_006470	NP_006461			tripartite motif-containing 16						histone H3 acetylation|histone H4 acetylation|positive regulation of interleukin-1 beta secretion|positive regulation of keratinocyte differentiation|positive regulation of retinoic acid receptor signaling pathway|positive regulation of transcription, DNA-dependent|response to growth hormone stimulus|response to organophosphorus|response to retinoic acid	cytoplasm|plasma membrane|PML body	DNA binding|interleukin-1 binding|NACHT domain binding|zinc ion binding			ovary(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)														---	---	---	---
ZNF286A	57335	broad.mit.edu	37	17	15600809	15600809	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15600809delT	uc010cot.2	+						ZNF286A_uc002goz.3_5'Flank|ZNF286A_uc010vwa.1_5'Flank|ZNF286A_uc002gpa.2_5'Flank	NM_001130842	NP_001124314			zinc finger protein 286						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)														---	---	---	---
NCOR1	9611	broad.mit.edu	37	17	15938845	15938851	+	Intron	DEL	TTTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15938845_15938851delTTTTTTT	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	15961519	15961519	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15961519delA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpl.2_5'UTR|NCOR1_uc002gpm.2_Intron|NCOR1_uc010vwb.1_Intron|NCOR1_uc010coy.2_Intron|NCOR1_uc010vwc.1_Intron	NM_006311	NP_006302			nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)														---	---	---	---
NCOR1	9611	broad.mit.edu	37	17	15971440	15971440	+	Intron	DEL	A	-	-	rs71358388		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15971440delA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpm.2_Frame_Shift_Del_p.F24fs|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	16011664	16011664	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16011664delT	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpp.1_Intron|NCOR1_uc002gpr.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	16077246	16077246	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16077246delA	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	16143106	16143106	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16143106delT	uc002gpv.2	+						PIGL_uc010vwd.1_Intron	NM_004278	NP_004269			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminylphosphatidylinositol deacetylase activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)														---	---	---	---
PIGL	9487	broad.mit.edu	37	17	16178038	16178038	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16178038delA	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)														---	---	---	---
LOC162632	162632	broad.mit.edu	37	17	16689738	16689738	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16689738delC	uc010cpj.1	+						LOC162632_uc010cpk.1_5'Flank|LOC162632_uc010vwq.1_5'Flank|LOC162632_uc002gqm.2_5'Flank|FAM106C_uc002gqo.2_5'Flank					Homo sapiens mRNA for KIAA0565 protein, partial cds.												0																		---	---	---	---
MPRIP	23164	broad.mit.edu	37	17	17003745	17003746	+	Intron	INS	-	GT	GT	rs143235971	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17003745_17003746insGT	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	17046886	17046886	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17046886delC	uc002gqu.1	+	9	1108	c.1052delC	c.(1051-1053)GCCfs	p.A351fs	MPRIP_uc002gqv.1_Frame_Shift_Del_p.A351fs|MPRIP_uc002gqw.1_Intron	NM_201274	NP_958431	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein	351	Interaction with F-actin (By similarity).					cytoplasm|cytoskeleton	actin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	17502810	17502812	+	IGR	DEL	TTT	-	-	rs76744249		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17502810_17502812delTTT								PEMT (7816 upstream) : RAI1 (81975 downstream)																																			---	---	---	---
RAI1	10743	broad.mit.edu	37	17	17629738	17629738	+	Intron	DEL	A	-	-	rs11348931		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17629738delA	uc002grm.2	+							NM_030665	NP_109590			retinoic acid induced 1							cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)|skin(1)	2				READ - Rectum adenocarcinoma(1115;0.0276)														---	---	---	---
RAI1	10743	broad.mit.edu	37	17	17696624	17696624	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17696624delG	uc002grm.2	+	3	831	c.362delG	c.(361-363)TGGfs	p.W121fs	RAI1_uc002grn.1_Frame_Shift_Del_p.W121fs	NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	121						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	17720838	17720838	+	Intron	DEL	G	-	-	rs2282180	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17720838delG	uc002gru.1	-						SREBF1_uc002grp.1_Intron|SREBF1_uc002grq.1_Intron|SREBF1_uc002grr.1_Intron|SREBF1_uc002grs.1_Intron|SREBF1_uc002grt.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																		---	---	---	---
LRRC48	83450	broad.mit.edu	37	17	17916001	17916001	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17916001delA	uc010vxd.1	+						LRRC48_uc002gsb.2_Intron	NM_001130090	NP_001123562			leucine rich repeat containing 48 isoform a							cytoplasm				pancreas(1)	1	all_neural(463;0.228)																	---	---	---	---
ALKBH5	54890	broad.mit.edu	37	17	18098206	18098207	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18098206_18098207insC	uc010cpw.2	+						ALKBH5_uc010cpx.2_Intron	NM_017758	NP_060228			alkB, alkylation repair homolog 5							integral to membrane	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0	all_neural(463;0.228)																	---	---	---	---
SHMT1	6470	broad.mit.edu	37	17	18235238	18235238	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18235238delA	uc002gta.2	-						SHMT1_uc002gsz.2_Intron|SHMT1_uc002gtb.2_Intron|SHMT1_uc010cqb.2_Intron|SHMT1_uc010vxt.1_Intron|SHMT1_uc002gtc.1_3'UTR	NM_004169	NP_004160			serine hydroxymethyltransferase 1 (soluble)						carnitine biosynthetic process|folic acid metabolic process|L-serine catabolic process|one-carbon metabolic process|purine base biosynthetic process	cytosol|nucleus	glycine hydroxymethyltransferase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)	1					Glycine(DB00145)|Mimosine(DB01055)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)													---	---	---	---
SHMT1	6470	broad.mit.edu	37	17	18242880	18242880	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18242880delT	uc002gta.2	-						SHMT1_uc002gsz.2_Intron|SHMT1_uc002gtb.2_Intron|SHMT1_uc010cqb.2_Intron|SHMT1_uc010vxt.1_Intron|SHMT1_uc002gtd.1_Intron	NM_004169	NP_004160			serine hydroxymethyltransferase 1 (soluble)						carnitine biosynthetic process|folic acid metabolic process|L-serine catabolic process|one-carbon metabolic process|purine base biosynthetic process	cytosol|nucleus	glycine hydroxymethyltransferase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)	1					Glycine(DB00145)|Mimosine(DB01055)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)													---	---	---	---
CCDC144B	284047	broad.mit.edu	37	17	18498498	18498498	+	Intron	DEL	A	-	-	rs71844421		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18498498delA	uc002gub.1	-						CCDC144B_uc002gua.3_Intron|CCDC144B_uc010vyc.1_Intron	NM_182568	NP_872374			coiled-coil domain containing 144B											ovary(1)|skin(1)	2																		---	---	---	---
PRPSAP2	5636	broad.mit.edu	37	17	18758768	18758768	+	5'Flank	DEL	T	-	-	rs78283723		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18758768delT	uc002gup.1	+						PRPSAP2_uc002guo.1_5'Flank|PRPSAP2_uc010vyi.1_5'Flank|PRPSAP2_uc010vyj.1_5'Flank	NM_002767	NP_002758			phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1																		---	---	---	---
EPN2	22905	broad.mit.edu	37	17	19183060	19183060	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19183060delT	uc002gvd.3	+						EPN2_uc002gvc.2_Intron|EPN2_uc010vyn.1_Intron|EPN2_uc010cql.1_Intron|EPN2_uc002gve.3_Intron|EPN2_uc002gvf.3_Intron|EPN2_uc010vyo.1_Intron|EPN2_uc002gvg.1_5'Flank	NM_014964	NP_055779			epsin 2 isoform b						endocytosis		lipid binding			skin(1)	1	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	19526377	19526377	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19526377delT								SLC47A1 (44031 upstream) : ALDH3A2 (25687 downstream)																																			---	---	---	---
SLC47A2	146802	broad.mit.edu	37	17	19621026	19621028	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19621026_19621028delAAA	uc002gwe.3	-						SLC47A2_uc002gwg.3_5'Flank|SLC47A2_uc002gwf.3_5'Flank|SLC47A2_uc002gwh.3_5'Flank|SLC47A2_uc002gwi.2_Intron|SLC47A2_uc010cqs.1_5'Flank|SLC47A2_uc010cqt.1_5'Flank	NM_152908	NP_690872			solute carrier family 47, member 2 isoform 1							integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)																	---	---	---	---
CYTSB	92521	broad.mit.edu	37	17	20207266	20207266	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20207266delA	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																		---	---	---	---
CCDC144C	348254	broad.mit.edu	37	17	20239466	20239466	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20239466delA	uc010cqy.1	+							NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0																		---	---	---	---
CCDC144C	348254	broad.mit.edu	37	17	20244363	20244363	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20244363delA	uc010cqy.1	+							NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	20639184	20639185	+	IGR	DEL	TT	-	-	rs77940668		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20639184_20639185delTT								LGALS9B (268336 upstream) : CCDC144NL (127525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	20679710	20679711	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20679710_20679711delAA								LGALS9B (308862 upstream) : CCDC144NL (86999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21232781	21232781	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21232781delA								MAP2K3 (14232 upstream) : KCNJ12 (46918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21233115	21233115	+	IGR	DEL	A	-	-	rs113355841		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21233115delA								MAP2K3 (14566 upstream) : KCNJ12 (46584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21236359	21236360	+	IGR	INS	-	G	G	rs138211082	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21236359_21236360insG								MAP2K3 (17810 upstream) : KCNJ12 (43339 downstream)																																			---	---	---	---
KCNJ12	3768	broad.mit.edu	37	17	21301404	21301407	+	Intron	DEL	TGTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21301404_21301407delTGTG	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	21322608	21322611	+	3'UTR	DEL	GTGT	-	-	rs72373280		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21322608_21322611delGTGT	uc002gyv.1	+	3						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	21328023	21328023	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21328023delG								KCNJ12 (4844 upstream) : C17orf51 (103549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21328103	21328104	+	IGR	INS	-	A	A	rs144296496		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21328103_21328104insA								KCNJ12 (4924 upstream) : C17orf51 (103468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21339354	21339355	+	IGR	INS	-	GCAG	GCAG	rs34586616		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21339354_21339355insGCAG								KCNJ12 (16175 upstream) : C17orf51 (92217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21408394	21408395	+	IGR	DEL	AA	-	-	rs141315490		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21408394_21408395delAA								KCNJ12 (85215 upstream) : C17orf51 (23177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21542634	21542635	+	IGR	INS	-	A	A	rs143877611	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21542634_21542635insA								C17orf51 (64903 upstream) : FAM27L (282735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21551333	21551333	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21551333delT								C17orf51 (73602 upstream) : FAM27L (274037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21552489	21552490	+	IGR	INS	-	GACGGG	GACGGG	rs141238951		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21552489_21552490insGACGGG								C17orf51 (74758 upstream) : FAM27L (272880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21564432	21564433	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21564432_21564433delTC								C17orf51 (86701 upstream) : FAM27L (260937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21566237	21566237	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21566237delA								C17orf51 (88506 upstream) : FAM27L (259133 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21731489	21731489	+	3'UTR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21731489delC	uc002gyy.3	+	2										SubName: Full=cDNA FLJ51326, highly similar to Homo sapiens ubiquitin B (UBB), mRNA;																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	21753752	21753752	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21753752delT								C17orf51 (276021 upstream) : FAM27L (71618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25326703	25326703	+	IGR	DEL	T	-	-	rs66491132		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25326703delT								None (None upstream) : WSB1 (294403 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25335454	25335456	+	IGR	DEL	CAC	-	-	rs149731847		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25335454_25335456delCAC								None (None upstream) : WSB1 (285650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25773154	25773157	+	IGR	DEL	AGGC	-	-	rs55913500	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25773154_25773157delAGGC								WSB1 (132509 upstream) : KSR1 (25879 downstream)																																			---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25882538	25882539	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25882538_25882539delGT	uc010crg.2	+						KSR1_uc002gzj.1_Intron	NM_014238	NP_055053			kinase suppressor of ras						Ras protein signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(1)	4	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	26544082	26544082	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26544082delA								NLK (20680 upstream) : PYY2 (9507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	26602993	26602993	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26602993delT								PPY2 (27679 upstream) : FLJ40504 (615 downstream)																																			---	---	---	---
SLC46A1	113235	broad.mit.edu	37	17	26732681	26732681	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26732681delC	uc002hbf.1	-						SLC46A1_uc002hbg.1_Intron|SLC46A1_uc010wak.1_Intron	NM_080669	NP_542400			proton-coupled folate transporter						cellular iron ion homeostasis|folic acid metabolic process	apical plasma membrane|cytoplasm|integral to membrane	folic acid binding|folic acid transporter activity|heme transporter activity				0	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)													---	---	---	---
FOXN1	8456	broad.mit.edu	37	17	26846347	26846350	+	Intron	DEL	AAAA	-	-	rs77466483		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26846347_26846350delAAAA	uc010crm.2	+							NM_003593	NP_003584			forkhead box N1						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)																	---	---	---	---
PIGS	94005	broad.mit.edu	37	17	26882987	26882987	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26882987delA	uc002hbo.2	-						PIGS_uc002hbn.2_Intron|PIGS_uc010wap.1_Intron	NM_033198	NP_149975			phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			breast(2)|urinary_tract(1)|kidney(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
PIGS	94005	broad.mit.edu	37	17	26885332	26885332	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26885332delA	uc002hbo.2	-						PIGS_uc002hbn.2_Intron|PIGS_uc010wap.1_Intron	NM_033198	NP_149975			phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			breast(2)|urinary_tract(1)|kidney(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
SPAG5	10615	broad.mit.edu	37	17	26910824	26910824	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26910824delA	uc002hbq.2	-						SGK494_uc010waq.1_Intron	NM_006461	NP_006452			sperm associated antigen 5						cell division|mitosis|phosphatidylinositol-mediated signaling|spindle organization	condensed chromosome kinetochore|cytoplasm|spindle pole	protein binding			central_nervous_system(1)	1	Lung NSC(42;0.00431)																	---	---	---	---
C17orf63	55731	broad.mit.edu	37	17	27143135	27143135	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27143135delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	27176383	27176383	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27176383delT								C17orf63 (6542 upstream) : ERAL1 (5660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	27200856	27200857	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27200856_27200857insA								MIR144 (12220 upstream) : FLOT2 (5501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	27205177	27205177	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27205177delT								MIR144 (16541 upstream) : FLOT2 (1181 downstream)																																			---	---	---	---
PHF12	57649	broad.mit.edu	37	17	27249005	27249005	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27249005delA	uc002hdg.1	-						PHF12_uc010wbb.1_Intron|PHF12_uc002hdi.1_Intron|PHF12_uc002hdj.1_Intron|PHF12_uc010crw.1_Intron|PHF12_uc002hdh.1_Intron	NM_001033561	NP_001028733			PHD finger protein 12 isoform 1						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	protein binding|zinc ion binding			ovary(1)	1	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)															---	---	---	---
SEZ6	124925	broad.mit.edu	37	17	27296185	27296185	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27296185delT	uc002hdp.2	-						SEZ6_uc002hdm.2_Intron|SEZ6_uc010cry.1_Intron|SEZ6_uc002hdq.1_Intron|SEZ6_uc010crz.1_Intron	NM_178860	NP_849191			seizure related 6 homolog isoform 1							integral to membrane|plasma membrane				large_intestine(1)|central_nervous_system(1)	2	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	27390813	27390815	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27390813_27390815delAAA								PIPOX (6577 upstream) : MYO18A (9713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	27653810	27653810	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27653810delA								NUFIP2 (32644 upstream) : TAOK1 (64133 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	27674757	27674757	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27674757delT								NUFIP2 (53591 upstream) : TAOK1 (43186 downstream)																																			---	---	---	---
EFCAB5	374786	broad.mit.edu	37	17	28320516	28320517	+	Intron	DEL	AA	-	-	rs78216599		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28320516_28320517delAA	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																		---	---	---	---
CCDC55	84081	broad.mit.edu	37	17	28505167	28505167	+	Frame_Shift_Del	DEL	A	-	-	rs143842750	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28505167delA	uc002heu.2	+	4	278	c.250delA	c.(250-252)AAAfs	p.K84fs	CCDC55_uc002hev.2_Frame_Shift_Del_p.K30fs|CCDC55_uc010wbl.1_Frame_Shift_Del_p.K30fs|CCDC55_uc010wbm.1_Frame_Shift_Del_p.K30fs|CCDC55_uc002hex.2_Frame_Shift_Del_p.K30fs	NM_032141	NP_115517	Q9H0G5	NSRP1_HUMAN	coiled-coil domain containing 55 isoform 1	84					developmental process|nucleocytoplasmic transport|regulation of alternative nuclear mRNA splicing, via spliceosome	nuclear speck|ribonucleoprotein complex	mRNA binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	28671515	28671515	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28671515delT								TMIGD1 (10450 upstream) : CPD (34469 downstream)																																			---	---	---	---
ADAP2	55803	broad.mit.edu	37	17	29284439	29284439	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	29438234	29438235	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29438234_29438235delAA	uc002hgg.2	+						NF1_uc002hge.1_Intron|NF1_uc002hgf.1_Intron|NF1_uc002hgh.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.0?(5)|p.?(1)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
NF1	4763	broad.mit.edu	37	17	29505708	29505708	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29505708delA	uc002hgg.2	+						NF1_uc002hge.1_Intron|NF1_uc002hgf.1_Intron|NF1_uc002hgh.2_Intron|NF1_uc010csn.1_Intron	NM_001042492	NP_001035957			neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
NF1	4763	broad.mit.edu	37	17	29575850	29575850	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29575850delT	uc002hgg.2	+						NF1_uc002hgh.2_Intron|NF1_uc010csn.1_Intron|NF1_uc002hgi.1_Intron	NM_001042492	NP_001035957			neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
NF1	4763	broad.mit.edu	37	17	29610442	29610443	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29610442_29610443insA	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)			---	---	---	---
NF1	4763	broad.mit.edu	37	17	29610446	29610446	+	Intron	DEL	C	-	-	rs76746518		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29610446delC	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)			---	---	---	---
NF1	4763	broad.mit.edu	37	17	29661844	29661845	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29661844_29661845insT	uc002hgg.2	+						NF1_uc002hgh.2_Intron|NF1_uc010cso.2_Intron|NF1_uc010wbt.1_5'Flank|NF1_uc010wbu.1_5'Flank	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			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
NF1	4763	broad.mit.edu	37	17	29684298	29684298	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29684298delA	uc002hgg.2	+	54	8214	c.7881delA	c.(7879-7881)GTAfs	p.V2627fs	NF1_uc002hgh.2_Frame_Shift_Del_p.V2606fs|NF1_uc010cso.2_Frame_Shift_Del_p.V815fs|NF1_uc010wbt.1_Frame_Shift_Del_p.V105fs|NF1_uc010wbu.1_RNA	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2627					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	29905529	29905529	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29905529delT								MIR365-2 (2989 upstream) : C17orf79 (273356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	30114751	30114751	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30114751delA								MIR365-2 (212211 upstream) : C17orf79 (64134 downstream)																																			---	---	---	---
SUZ12	23512	broad.mit.edu	37	17	30267580	30267580	+	Intron	DEL	A	-	-	rs67854327		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30267580delA	uc002hgs.2	+						SUZ12_uc002hgt.2_Intron	NM_015355	NP_056170			joined to JAZF1						negative regulation of cell differentiation|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|methylated histone residue binding|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)						T	JAZF1	endometrial stromal tumours								---	---	---	---
Unknown	0	broad.mit.edu	37	17	30419127	30419128	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30419127_30419128delCA								LRRC37B (38610 upstream) : RHOT1 (50345 downstream)																																			---	---	---	---
RHBDL3	162494	broad.mit.edu	37	17	30643409	30643409	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30643409delA	uc002hhe.1	+						RHBDL3_uc010csw.1_Intron|RHBDL3_uc010csx.1_Intron|RHBDL3_uc010csy.1_Intron|RHBDL3_uc002hhf.1_Intron	NM_138328	NP_612201			rhomboid protease 3						proteolysis	integral to membrane	calcium ion binding|serine-type endopeptidase activity			ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	30766777	30766778	+	IGR	INS	-	TTTT	TTTT	rs150216387	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30766777_30766778insTTTT								ZNF207 (58802 upstream) : PSMD11 (4724 downstream)																																			---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	30871120	30871120	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30871120delT	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	31105719	31105719	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31105719delT	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	31275023	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31275023delT								TMEM98 (6358 upstream) : SPACA3 (43859 downstream)																																			---	---	---	---
ACCN1	40	broad.mit.edu	37	17	31636166	31636166	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31636166delT	uc002hhu.2	-							NM_001094	NP_001085			amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)													---	---	---	---
ACCN1	40	broad.mit.edu	37	17	32483870	32483870	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32483870delC	uc002hhu.2	-							NM_001094	NP_001085			amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)													---	---	---	---
CCL7	6354	broad.mit.edu	37	17	32597489	32597490	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32597489_32597490insT	uc002hhz.2	+						CCL7_uc010ctf.2_Intron	NM_006273	NP_006264			chemokine (C-C motif) ligand 7 precursor						cell-cell signaling|cellular calcium ion homeostasis|chemotaxis|immune response|inflammatory response|signal transduction	extracellular space	chemokine activity|heparin binding			ovary(1)	1	Breast(3;0.00224)	Breast(31;0.151)|Ovarian(249;0.17)		BRCA - Breast invasive adenocarcinoma(366;0.155)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	32707214	32707214	+	IGR	DEL	T	-	-	rs113503051		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32707214delT								CCL1 (16962 upstream) : C17orf102 (193928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	33148721	33148721	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33148721delA								TMEM132E (182385 upstream) : CCT6B (106219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	33298159	33298159	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33298159delT								ZNF830 (7956 upstream) : LIG3 (9379 downstream)																																			---	---	---	---
AP2B1	163	broad.mit.edu	37	17	34034153	34034154	+	Intron	INS	-	TTGTTG	TTGTTG	rs139100237	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34034153_34034154insTTGTTG	uc002hjr.2	+						AP2B1_uc002hjq.2_Intron|AP2B1_uc010wci.1_Intron|AP2B1_uc002hjs.2_Intron|AP2B1_uc002hjt.2_Intron|AP2B1_uc010ctv.2_Intron|AP2B1_uc010wcj.1_Intron	NM_001282	NP_001273			adaptor-related protein complex 2, beta 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|coated pit|cytosol|endocytic vesicle membrane|plasma membrane	clathrin binding|protein transporter activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)														---	---	---	---
TAF15	8148	broad.mit.edu	37	17	34165342	34165342	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34165342delA	uc002hkd.2	+						TAF15_uc010ctw.1_Intron|TAF15_uc002hkc.2_Intron	NM_139215	NP_631961			TBP-associated factor 15 isoform 1						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								---	---	---	---
C17orf66	256957	broad.mit.edu	37	17	34183107	34183108	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34183107_34183108delCT	uc002hke.1	-						C17orf66_uc010wck.1_Intron|C17orf66_uc010wcl.1_Intron	NM_152781	NP_689994			hypothetical protein LOC256957								binding			breast(2)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)														---	---	---	---
TBC1D3C	414060	broad.mit.edu	37	17	34729654	34729654	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34729654delA	uc002hll.1	-						TBC1D3G_uc010wcv.1_Intron|TBC1D3G_uc002hlm.2_Intron	NM_001040282	NP_001035372			TBC1 domain family, member 3G							intracellular	Rab GTPase activator activity				0		Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
GGNBP2	79893	broad.mit.edu	37	17	34937715	34937715	+	Intron	DEL	A	-	-	rs76574496		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34937715delA	uc002hnb.2	+						GGNBP2_uc002hna.2_Intron|GGNBP2_uc002hnc.1_Intron	NM_024835	NP_079111			zinc finger protein 403						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasmic membrane-bounded vesicle				ovary(2)	2		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)														---	---	---	---
GGNBP2	79893	broad.mit.edu	37	17	34942126	34942126	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34942126delA	uc002hnb.2	+						GGNBP2_uc002hna.2_3'UTR|GGNBP2_uc002hnc.1_Intron	NM_024835	NP_079111			zinc finger protein 403						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasmic membrane-bounded vesicle				ovary(2)	2		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)														---	---	---	---
AATF	26574	broad.mit.edu	37	17	35400341	35400342	+	Intron	DEL	TT	-	-	rs34084439		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35400341_35400342delTT	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	35512541	35512541	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35512541delA	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuy.2_Intron|ACACA_uc010wdc.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)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	36197746	36197747	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36197746_36197747delAA								HNF1B (92650 upstream) : LOC284100 (4826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	36304010	36304010	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36304010delA								TBC1D3 (8912 upstream) : MRPL45 (148988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	36331303	36331304	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36331303_36331304delCT								TBC1D3 (36205 upstream) : MRPL45 (121694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	36400830	36400830	+	Intron	DEL	A	-	-	rs146367173		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36400830delA	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	36476863	36476863	+	Intron	DEL	T	-	-	rs67792707		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36476863delT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	36818848	36818849	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36818848_36818849delTT								SRCIN1 (56665 upstream) : C17orf96 (9112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	36843012	36843012	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36843012delA								C17orf96 (11825 upstream) : MLLT6 (18861 downstream)																																			---	---	---	---
CACNB1	782	broad.mit.edu	37	17	37341810	37341810	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37341810delC	uc002hrm.1	-						CACNB1_uc002hrl.1_Intron|CACNB1_uc002hrn.2_Intron|CACNB1_uc002hro.2_Intron|CACNB1_uc002hrp.1_Intron	NM_000723	NP_000714			calcium channel, voltage-dependent, beta 1						axon guidance	voltage-gated calcium channel complex				large_intestine(1)|ovary(1)	2					Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	37772444	37772445	+	IGR	INS	-	TTCT	TTCT	rs144000382	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37772444_37772445insTTCT								NEUROD2 (8269 upstream) : PPP1R1B (10734 downstream)																																			---	---	---	---
STARD3	10948	broad.mit.edu	37	17	37818444	37818444	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37818444delG	uc002hsd.2	+						STARD3_uc010weh.1_Intron|STARD3_uc002hse.2_Intron|STARD3_uc010wei.1_Intron|STARD3_uc002hsf.2_Intron|STARD3_uc002hsg.2_Intron	NM_006804	NP_006795			StAR-related lipid transfer (START) domain						cholesterol metabolic process|mitochondrial transport|steroid biosynthetic process	integral to membrane|late endosome membrane	cholesterol binding|cholesterol transporter activity				0	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
ERBB2	2064	broad.mit.edu	37	17	37870012	37870013	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37870012_37870013delAA	uc002hso.2	+						ERBB2_uc002hsm.2_Intron|ERBB2_uc010cwa.2_Intron|ERBB2_uc002hsp.2_Intron|ERBB2_uc010cwb.2_Intron|ERBB2_uc010wek.1_Intron|ERBB2_uc002hsl.2_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)			---	---	---	---
ZPBP2	124626	broad.mit.edu	37	17	38028509	38028509	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38028509delT	uc002hte.2	+						ZPBP2_uc002htf.2_Intron	NM_199321	NP_955353			zona pellucida binding protein 2 isoform 2						binding of sperm to zona pellucida	extracellular region				ovary(1)	1	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	38101141	38101142	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38101141_38101142delTC								ORMDL3 (17287 upstream) : GSDMA (18084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	39215669	39215669	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39215669delT	uc002hvx.2	-	1						NM_033184	NP_149440			keratin associated protein 2-4																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	39477527	39477527	+	IGR	DEL	A	-	-	rs142778009		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39477527delA								KRTAP17-1 (5580 upstream) : KRT33A (24844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	39496440	39496443	+	IGR	DEL	CTTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39496440_39496443delCTTC								KRTAP17-1 (24493 upstream) : KRT33A (5928 downstream)																																			---	---	---	---
NT5C3L	115024	broad.mit.edu	37	17	39982408	39982408	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39982408delA	uc002hyc.3	-						NT5C3L_uc002hxx.3_Intron|NT5C3L_uc010wfu.1_Intron|NT5C3L_uc002hyb.3_Intron|NT5C3L_uc002hyd.3_Intron|NT5C3L_uc002hxy.3_Intron|NT5C3L_uc002hxz.3_Intron|NT5C3L_uc002hya.3_Intron	NM_052935	NP_443167			5'-nucleotidase, cytosolic III-like							cytoplasm	5'-nucleotidase activity|magnesium ion binding				0		Breast(137;0.000162)		BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	40593802	40593803	+	IGR	INS	-	TTTC	TTTC	rs150457536	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40593802_40593803insTTTC								PTRF (18528 upstream) : ATP6V0A1 (17059 downstream)																																			---	---	---	---
ATP6V0A1	535	broad.mit.edu	37	17	40642658	40642658	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40642658delA	uc002hzr.2	+						ATP6V0A1_uc002hzq.2_Intron|ATP6V0A1_uc002hzs.2_Intron|ATP6V0A1_uc010wgj.1_Intron|ATP6V0A1_uc010wgk.1_Intron|ATP6V0A1_uc010cyg.2_Intron|ATP6V0A1_uc010wgl.1_Intron	NM_001130021	NP_001123493			ATPase, H+ transporting, lysosomal V0 subunit a1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytoplasmic vesicle membrane|endosome membrane|Golgi apparatus|integral to membrane|melanosome|nucleus|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)														---	---	---	---
FAM134C	162427	broad.mit.edu	37	17	40733384	40733384	+	3'UTR	DEL	A	-	-	rs35248732		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40733384delA	uc002ial.2	-	9					FAM134C_uc010wgq.1_3'UTR|FAM134C_uc002iam.1_3'UTR|FAM134C_uc010cyk.1_3'UTR	NM_178126	NP_835227			hypothetical protein LOC162427							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.134)														---	---	---	---
CNTNAP1	8506	broad.mit.edu	37	17	40836955	40836955	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40836955delA	uc002iay.2	+						CNTNAP1_uc010wgs.1_Intron	NM_003632	NP_003623			contactin associated protein 1 precursor						axon guidance|cell adhesion	paranode region of axon	receptor activity|receptor binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(3)|breast(3)|upper_aerodigestive_tract(1)|lung(1)	8		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)														---	---	---	---
CNTNAP1	8506	broad.mit.edu	37	17	40849186	40849186	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40849186delC	uc002iay.2	+						CNTNAP1_uc010wgs.1_Intron	NM_003632	NP_003623			contactin associated protein 1 precursor						axon guidance|cell adhesion	paranode region of axon	receptor activity|receptor binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(3)|breast(3)|upper_aerodigestive_tract(1)|lung(1)	8		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)														---	---	---	---
RAMP2	10266	broad.mit.edu	37	17	40915045	40915045	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40915045delT	uc002ibg.2	+	4					LOC100190938_uc002ibd.1_5'Flank|LOC100190938_uc002ibe.3_5'Flank|LOC100190938_uc002ibf.3_5'Flank|RAMP2_uc010cyt.2_3'UTR|RAMP2_uc002ibh.2_3'UTR	NM_005854	NP_005845			receptor activity modifying protein 2 precursor						intracellular protein transport|receptor-mediated endocytosis|regulation of G-protein coupled receptor protein signaling pathway	coated pit|integral to plasma membrane|lysosome	protein transporter activity				0		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0741)	Pramlintide(DB01278)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	41075787	41075787	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41075787delT								G6PC (10401 upstream) : AARSD1 (26758 downstream)																																			---	---	---	---
RUNDC1	146923	broad.mit.edu	37	17	41137975	41137975	+	Intron	DEL	T	-	-	rs114387949	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41137975delT	uc002ici.1	+						RUNDC1_uc010whi.1_Intron	NM_173079	NP_775102			RUN domain containing 1												0		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)														---	---	---	---
BRCA1	672	broad.mit.edu	37	17	41217357	41217357	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41217357delA	uc002icq.2	-						BRCA1_uc010whp.1_Intron|BRCA1_uc010whl.1_Intron|BRCA1_uc010whm.1_Intron|BRCA1_uc002icp.3_Intron|BRCA1_uc002icu.2_Intron|BRCA1_uc010cyx.2_Intron|BRCA1_uc002ict.2_Intron|BRCA1_uc010whn.1_Intron|BRCA1_uc010who.1_Intron|BRCA1_uc010whq.1_Intron|BRCA1_uc002idc.1_Intron|BRCA1_uc010whr.1_Intron	NM_007294	NP_009225			breast cancer 1, early onset isoform 1						androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)	52		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)				D|Mis|N|F|S		ovarian	breast|ovarian		Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_BRCA1_type	TCGA Ovarian(2;0.000030)			---	---	---	---
BRCA1	672	broad.mit.edu	37	17	41297124	41297124	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41297124delA	uc010whp.1	-						NBR2_uc002idh.2_Intron	NM_007298	NP_009229			breast cancer 1, early onset isoform 4						androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)	52		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)				D|Mis|N|F|S		ovarian	breast|ovarian		Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_BRCA1_type	TCGA Ovarian(2;0.000030)			---	---	---	---
DHX8	1659	broad.mit.edu	37	17	41573761	41573761	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41573761delA	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-4292-01	TCGA-BR-4292-01									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								---	---	---	---
MPP2	4355	broad.mit.edu	37	17	41959741	41959741	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41959741delG	uc010wip.1	-	6	784	c.727delC	c.(727-729)CGCfs	p.R243fs	MPP2_uc002ien.1_Frame_Shift_Del_p.R215fs|MPP2_uc010wim.1_Frame_Shift_Del_p.R187fs|MPP2_uc002ieo.1_Frame_Shift_Del_p.R198fs|MPP2_uc010win.1_Frame_Shift_Del_p.R59fs|MPP2_uc010wio.1_Frame_Shift_Del_p.R187fs|MPP2_uc010czm.1_Frame_Shift_Del_p.R181fs	NM_005374	NP_005365	Q14168	MPP2_HUMAN	palmitoylated membrane protein 2	222	PDZ.				signal transduction	cell surface|integral to plasma membrane|membrane fraction	guanylate kinase activity				0		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	42025267	42025268	+	IGR	DEL	AA	-	-	rs112096102		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42025267_42025268delAA								PPY (5434 upstream) : PYY (4841 downstream)																																			---	---	---	---
HDAC5	10014	broad.mit.edu	37	17	42160345	42160345	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42160345delT	uc002ifd.1	-						HDAC5_uc002ife.1_Intron|HDAC5_uc002iff.1_Intron|HDAC5_uc010czp.1_Intron|HDAC5_uc002ifg.1_Intron|HDAC5_uc002ifh.2_Intron	NM_005474	NP_005465			histone deacetylase 5 isoform 1						B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)														---	---	---	---
C17orf53	78995	broad.mit.edu	37	17	42226623	42226624	+	Intron	DEL	TT	-	-	rs68174578		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42226623_42226624delTT	uc002ifi.1	+						C17orf53_uc010czq.1_Intron|C17orf53_uc002ifj.1_Intron|C17orf53_uc002ifk.1_Intron	NM_024032	NP_076937			hypothetical protein LOC78995												0		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	42306808	42306808	+	IGR	DEL	G	-	-	rs76811292	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42306808delG								UBTF (7814 upstream) : SLC4A1 (18951 downstream)																																			---	---	---	---
SLC4A1	6521	broad.mit.edu	37	17	42335599	42335599	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42335599delG	uc002igf.3	-						SLC4A1_uc002igg.3_Intron	NM_000342	NP_000333			solute carrier family 4, anion exchanger, member						bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	42370318	42370318	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42370318delT								SLC4A1 (24816 upstream) : RUNDC3A (15609 downstream)																																			---	---	---	---
GPATCH8	23131	broad.mit.edu	37	17	42489295	42489296	+	Intron	INS	-	A	A	rs113092631		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42489295_42489296insA	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	42512617	42512617	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42512617delA	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	42531300	42531300	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42531300delA	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	42541565	42541566	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42541565_42541566insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	42774805	42774805	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42774805delT								CCDC43 (7640 upstream) : DBF4B (11171 downstream)																																			---	---	---	---
EFTUD2	9343	broad.mit.edu	37	17	42939102	42939102	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42939102delA	uc002ihn.2	-						EFTUD2_uc010wje.1_Intron|EFTUD2_uc010wjf.1_Intron	NM_004247	NP_004238			elongation factor Tu GTP binding domain							Cajal body|catalytic step 2 spliceosome|cytoplasm|nuclear speck	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(33;0.109)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	43254625	43254625	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43254625delT								HEXIM2 (7219 upstream) : FMNL1 (44667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	43403821	43403821	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43403821delA								MAP3K14 (9407 upstream) : ARHGAP27 (67448 downstream)																																			---	---	---	---
CRHR1	1394	broad.mit.edu	37	17	43844387	43844387	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43844387delA	uc002ijp.2	+						CRHR1_uc010wjx.1_Intron					SubName: Full=cDNA FLJ60308, highly similar to Corticotropin-releasing factor receptor 1;						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)														---	---	---	---
LOC100128977	100128977	broad.mit.edu	37	17	43931858	43931863	+	Intron	DEL	AGAGAC	-	-	rs67988336		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43931858_43931863delAGAGAC	uc010wjz.1	-							NR_024559				Homo sapiens cDNA clone IMAGE:4819956.												0																		---	---	---	---
LOC100128977	100128977	broad.mit.edu	37	17	43969331	43969331	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43969331delA	uc010wjz.1	-						MAPT_uc010dau.2_5'Flank|MAPT_uc002ijr.3_5'Flank|MAPT_uc002ijs.3_5'Flank|MAPT_uc002ijx.3_5'Flank|MAPT_uc002ijt.3_5'Flank|MAPT_uc002iju.3_5'Flank|MAPT_uc002ijv.3_5'Flank	NR_024559				Homo sapiens cDNA clone IMAGE:4819956.												0																		---	---	---	---
MAPT	4137	broad.mit.edu	37	17	44092249	44092250	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44092249_44092250delAA	uc002ijr.3	+						MAPT_uc010dau.2_Intron|MAPT_uc002ijs.3_Intron|MAPT_uc002ijx.3_Intron|MAPT_uc002ijt.3_Intron|MAPT_uc002iju.3_Intron|MAPT_uc002ijv.3_Intron	NM_016835	NP_058519			microtubule-associated protein tau isoform 1						cellular component disassembly involved in apoptosis|microtubule cytoskeleton organization|negative regulation of microtubule depolymerization|positive regulation of axon extension|positive regulation of microtubule polymerization|regulation of autophagy	axon|cytosol|growth cone|microtubule|microtubule associated complex|nuclear periphery|plasma membrane|tubulin complex	apolipoprotein E binding|enzyme binding|identical protein binding|lipoprotein particle binding|microtubule binding|protein binding|SH3 domain binding|structural constituent of cytoskeleton			pancreas(1)	1		Melanoma(429;0.216)																---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44107957	44107958	+	3'UTR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44107957_44107958delAA	uc002ikb.2	-	14					KIAA1267_uc002ikc.2_3'UTR|KIAA1267_uc002ikd.2_3'UTR|KIAA1267_uc010dav.2_3'UTR|KIAA1267_uc010wkb.1_3'UTR|KIAA1267_uc010wkc.1_3'UTR	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	44173995	44173995	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44173995delT	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	44292022	44292022	+	Intron	DEL	A	-	-	rs67664361		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44292022delA	uc010dav.2	-							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	44316942	44316942	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44316942delT								KIAA1267 (14225 upstream) : ARL17B (46921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	44324687	44324687	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44324687delT								KIAA1267 (21970 upstream) : ARL17B (39176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	44340154	44340155	+	IGR	DEL	AA	-	-	rs72462108		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44340154_44340155delAA								KIAA1267 (37437 upstream) : ARL17B (23708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	44835368	44835369	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44835368_44835369delAA								NSF (535 upstream) : WNT3 (6318 downstream)																																			---	---	---	---
WNT3	7473	broad.mit.edu	37	17	44876413	44876418	+	Intron	DEL	AAAAAA	-	-	rs71908001		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44876413_44876418delAAAAAA	uc002ikv.2	-							NM_030753	NP_110380			wingless-type MMTV integration site family,						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)															---	---	---	---
GOSR2	9570	broad.mit.edu	37	17	45062886	45062888	+	Intron	DEL	AAA	-	-	rs71712116		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45062886_45062888delAAA	uc010wkh.1	+							NM_004287	NP_004278			golgi SNAP receptor complex member 2 isoform A						cellular membrane fusion|ER to Golgi vesicle-mediated transport|protein transport	Golgi membrane|integral to membrane	transporter activity			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(9;0.102)															---	---	---	---
NPEPPS	9520	broad.mit.edu	37	17	45679340	45679340	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45679340delA	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010wkv.1_Intron|NPEPPS_uc002ils.1_5'Flank	NM_006310	NP_006301			aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0																		---	---	---	---
KPNB1	3837	broad.mit.edu	37	17	45753078	45753079	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45753078_45753079insA	uc002ilt.1	+						KPNB1_uc010wkw.1_Intron|KPNB1_uc010wkx.1_Intron	NM_002265	NP_002256			karyopherin beta 1						DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|protein import into nucleus, translocation|ribosomal protein import into nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein domain specific binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	45762504	45762504	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45762504delC								KPNB1 (1500 upstream) : TBKBP1 (10126 downstream)																																			---	---	---	---
TBX21	30009	broad.mit.edu	37	17	45812769	45812769	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45812769delC	uc002ilv.1	+							NM_013351	NP_037483			T-box 21						lymphocyte migration|multicellular organismal development|positive regulation of transcription, DNA-dependent|response to virus	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	45954595	45954596	+	IGR	INS	-	GAGG	GAGG	rs139699416	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45954595_45954596insGAGG								SP6 (21355 upstream) : SP2 (18920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	46084038	46084038	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46084038delT								CDK5RAP3 (24892 upstream) : COPZ2 (19497 downstream)																																			---	---	---	---
SNX11	29916	broad.mit.edu	37	17	46191221	46191222	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46191221_46191222delTT	uc002inf.1	+						SNX11_uc010wlg.1_Intron|SNX11_uc010wlh.1_Intron|SNX11_uc010wli.1_Intron|SNX11_uc010wlj.1_Intron|SNX11_uc002ing.1_Intron|SNX11_uc002inh.1_Intron	NM_152244	NP_689450			sorting nexin 11						cell communication|protein transport	membrane	phosphatidylinositol binding				0																		---	---	---	---
SKAP1	8631	broad.mit.edu	37	17	46303710	46303710	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46303710delT	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717			src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0																		---	---	---	---
SKAP1	8631	broad.mit.edu	37	17	46441638	46441638	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46441638delT	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	46758683	46758683	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46758683delT								MIR196A1 (48762 upstream) : PRAC (40409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	46820762	46820762	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46820762delT								HOXB13 (14651 upstream) : TTLL6 (18832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	46900197	46900197	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46900197delT								TTLL6 (5728 upstream) : CALCOCO2 (8175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	46957362	46957363	+	IGR	INS	-	A	A	rs111340350		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46957362_46957363insA								CALCOCO2 (15134 upstream) : ATP5G1 (12785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	47165730	47165731	+	IGR	DEL	GA	-	-	rs3086729		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47165730_47165731delGA								IGF2BP1 (32225 upstream) : B4GALNT2 (44091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	47323719	47323719	+	5'Flank	DEL	A	-	-	rs79643109		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47323719delA	uc002iot.1	+											Homo sapiens cDNA FLJ40194 fis, clone TESTI2019481.																														---	---	---	---
ZNF652	22834	broad.mit.edu	37	17	47412141	47412142	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47412141_47412142insA	uc002iov.3	-						ZNF652_uc002iow.2_Intron|ZNF652_uc002iou.3_Intron	NM_001145365	NP_001138837			zinc finger protein 652						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	47543266	47543267	+	IGR	INS	-	T	T	rs143485644	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47543266_47543267insT								PHB (51024 upstream) : NGFR (29388 downstream)																																			---	---	---	---
SLC35B1	10237	broad.mit.edu	37	17	47783728	47783728	+	Intron	DEL	G	-	-	rs138147992		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47783728delG	uc002iph.1	-						SLC35B1_uc002ipi.1_Intron|SLC35B1_uc002ipj.1_Intron|SLC35B1_uc010wly.1_Intron	NM_005827	NP_005818			solute carrier family 35, member B1							endoplasmic reticulum membrane|integral to membrane|microsome	UDP-galactose transmembrane transporter activity				0																		---	---	---	---
SLC35B1	10237	broad.mit.edu	37	17	47783742	47783743	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47783742_47783743insG	uc002iph.1	-						SLC35B1_uc002ipi.1_Intron|SLC35B1_uc002ipj.1_Intron|SLC35B1_uc010wly.1_Intron	NM_005827	NP_005818			solute carrier family 35, member B1							endoplasmic reticulum membrane|integral to membrane|microsome	UDP-galactose transmembrane transporter activity				0																		---	---	---	---
MYST2	11143	broad.mit.edu	37	17	47878861	47878861	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47878861delT	uc002ipm.2	+						MYST2_uc002ipl.1_Intron|MYST2_uc010wma.1_Intron|MYST2_uc010wmb.1_Intron|MYST2_uc010wmc.1_Intron|MYST2_uc010wmd.1_Intron|MYST2_uc010wme.1_Intron	NM_007067	NP_008998			MYST histone acetyltransferase 2						DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	histone acetyltransferase activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
TAC4	255061	broad.mit.edu	37	17	47919111	47919111	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47919111delG	uc002ipo.1	-						TAC4_uc002ipp.1_Intron|TAC4_uc002ipq.1_Intron|TAC4_uc002ipr.1_Intron|TAC4_uc002ips.1_Intron	NM_170685	NP_733786			tachykinin 4 isoform alpha						regulation of blood pressure	extracellular region				breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	48065239	48065239	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48065239delG								DLX4 (12917 upstream) : DLX3 (2137 downstream)																																			---	---	---	---
PPP1R9B	84687	broad.mit.edu	37	17	48215989	48215989	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48215989delT	uc002iqh.3	-							NM_032595	NP_115984			protein phosphatase 1, regulatory subunit 9B						cell cycle arrest|cell differentiation|cell migration|filopodium assembly|negative regulation of cell growth|nervous system development|regulation of cell growth by extracellular stimulus|regulation of cell proliferation|regulation of exit from mitosis|RNA splicing	adherens junction|cytoskeleton|dendritic spine|filopodium|lamellipodium|nucleoplasm|protein phosphatase type 1 complex|ruffle membrane|synapse	actin binding|protein phosphatase 1 binding|protein phosphatase inhibitor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	48487895	48487896	+	IGR	DEL	AT	-	-	rs28380076		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48487895_48487896delAT								LRRC59 (13063 upstream) : ACSF2 (15623 downstream)																																			---	---	---	---
ACSF2	80221	broad.mit.edu	37	17	48500652	48500652	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48500652delT	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)															---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48684862	48684863	+	Intron	INS	-	A	A	rs146578006	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48684862_48684863insA	uc002irk.1	+						CACNA1G_uc002irj.1_Intron|CACNA1G_uc002irl.1_Intron|CACNA1G_uc002irm.1_Intron|CACNA1G_uc002irn.1_Intron|CACNA1G_uc002iro.1_Intron|CACNA1G_uc002irp.1_Intron|CACNA1G_uc002irq.1_Intron|CACNA1G_uc002irr.1_Intron|CACNA1G_uc002irs.1_Intron|CACNA1G_uc002irt.1_Intron|CACNA1G_uc002irv.1_Intron|CACNA1G_uc002irw.1_Intron|CACNA1G_uc002iru.1_Intron|CACNA1G_uc002irx.1_Intron|CACNA1G_uc002iry.1_Intron|CACNA1G_uc002irz.1_Intron|CACNA1G_uc002isa.1_Intron|CACNA1G_uc002isb.1_Intron|CACNA1G_uc002isc.1_Intron|CACNA1G_uc002isd.1_Intron|CACNA1G_uc002ise.1_Intron|CACNA1G_uc002isf.1_Intron|CACNA1G_uc002isg.1_Intron|CACNA1G_uc002ish.1_Intron|CACNA1G_uc002isi.1_Intron	NM_018896	NP_061496			voltage-dependent calcium channel alpha 1G						axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48695303	48695304	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48695303_48695304insG	uc002irk.1	+						CACNA1G_uc002irj.1_Intron|CACNA1G_uc002irl.1_Intron|CACNA1G_uc002irm.1_Intron|CACNA1G_uc002irn.1_Intron|CACNA1G_uc002iro.1_Intron|CACNA1G_uc002irp.1_Intron|CACNA1G_uc002irq.1_Intron|CACNA1G_uc002irr.1_Intron|CACNA1G_uc002irs.1_Intron|CACNA1G_uc002irt.1_Intron|CACNA1G_uc002irv.1_Intron|CACNA1G_uc002irw.1_Intron|CACNA1G_uc002iru.1_Intron|CACNA1G_uc002irx.1_Intron|CACNA1G_uc002iry.1_Intron|CACNA1G_uc002irz.1_Intron|CACNA1G_uc002isa.1_Intron|CACNA1G_uc002isb.1_Intron|CACNA1G_uc002isc.1_Intron|CACNA1G_uc002isd.1_Intron|CACNA1G_uc002ise.1_Intron|CACNA1G_uc002isf.1_Intron|CACNA1G_uc002isg.1_Intron|CACNA1G_uc002ish.1_Intron|CACNA1G_uc002isi.1_Intron	NM_018896	NP_061496			voltage-dependent calcium channel alpha 1G						axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49166159	49166159	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49166159delA	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
NME1-NME2	654364	broad.mit.edu	37	17	49247504	49247510	+	Intron	DEL	TTTTTTT	-	-	rs112707943		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49247504_49247510delTTTTTTT	uc002itk.2	+						NME1-NME2_uc002itj.2_Intron|NME2_uc002itl.2_Intron|NME2_uc002itm.2_Intron|NME2_uc002itn.2_Intron|NME2_uc002ito.2_Intron	NM_002512	NP_002503			nucleoside diphosphate kinase B						cell adhesion|CTP biosynthetic process|GTP biosynthetic process|negative regulation of apoptosis|nucleobase, nucleoside and nucleotide interconversion|positive regulation of epithelial cell proliferation|positive regulation of keratinocyte differentiation|UTP biosynthetic process	cytosol|lamellipodium|nucleus|ruffle	ATP binding|DNA binding|metal ion binding|nucleoside diphosphate kinase activity|protein binding|protein histidine kinase activity|sequence-specific DNA binding transcription factor activity				0			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)															---	---	---	---
UTP18	51096	broad.mit.edu	37	17	49362423	49362425	+	Intron	DEL	AAA	-	-	rs77002893		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49362423_49362425delAAA	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	50076220	50076221	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50076220_50076221delTC	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	50946376	50946376	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50946376delT								CA10 (708999 upstream) : KIF2B (953863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51775373	51775374	+	IGR	DEL	GC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51775373_51775374delGC								None (None upstream) : KIF2B (124865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	52084079	52084079	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52084079delA								KIF2B (181506 upstream) : TOM1L1 (893973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	52245122	52245123	+	IGR	DEL	TG	-	-	rs7502739		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52245122_52245123delTG								KIF2B (342549 upstream) : TOM1L1 (732929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	52506601	52506601	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52506601delA								KIF2B (604028 upstream) : TOM1L1 (471451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	52747860	52747860	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52747860delA								KIF2B (845287 upstream) : TOM1L1 (230192 downstream)																																			---	---	---	---
STXBP4	252983	broad.mit.edu	37	17	53076653	53076653	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53076653delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	53446581	53446581	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53446581delA								HLF (44155 upstream) : MMD (23394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	53458579	53458582	+	IGR	DEL	CTTT	-	-	rs10545207	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53458579_53458582delCTTT								HLF (56153 upstream) : MMD (11393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	53575945	53575945	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53575945delT								MMD (76604 upstream) : TMEM100 (221045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	53678733	53678733	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53678733delT								MMD (179392 upstream) : TMEM100 (118257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	54175800	54175803	+	IGR	DEL	CGCG	-	-	rs71974439		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54175800_54175803delCGCG								PCTP (321053 upstream) : ANKFN1 (55033 downstream)																																			---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54298484	54298485	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54298484_54298485delAG	uc002iun.1	+							NM_153228	NP_694960			ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2																		---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54328331	54328331	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54328331delT	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	54699859	54699860	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54699859_54699860delTT								NOG (26908 upstream) : C17orf67 (169415 downstream)																																			---	---	---	---
TRIM25	7706	broad.mit.edu	37	17	54976070	54976071	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54976070_54976071delAA	uc002iut.2	-						TRIM25_uc010dcj.2_Intron	NM_005082	NP_005073			tripartite motif-containing 25						innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|response to virus	cell junction|cytosol|nucleus	sequence-specific DNA binding transcription factor activity|ubiquitin-protein ligase activity|zinc ion binding			lung(1)|breast(1)|skin(1)	3	Breast(9;6.15e-08)																	---	---	---	---
SCPEP1	59342	broad.mit.edu	37	17	55067301	55067301	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55067301delA	uc002iuv.3	+						SCPEP1_uc010dcl.2_Intron|SCPEP1_uc010wnk.1_Intron	NM_021626	NP_067639			serine carboxypeptidase 1 precursor						proteolysis	extracellular region	serine-type carboxypeptidase activity			skin(1)	1	Breast(9;2.86e-08)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	55211375	55211375	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55211375delT								AKAP1 (12666 upstream) : MSI2 (121837 downstream)																																			---	---	---	---
MRPS23	51649	broad.mit.edu	37	17	55925715	55925715	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55925715delA	uc002ivc.2	-							NM_016070	NP_057154			mitochondrial ribosomal protein S23						translation	intermediate filament cytoskeleton|mitochondrion|nuclear membrane|ribosome	structural constituent of ribosome				0	Breast(9;8.75e-08)																	---	---	---	---
RNF43	54894	broad.mit.edu	37	17	56435161	56435161	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	56516632	56516632	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56516632delA	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)																	---	---	---	---
MTMR4	9110	broad.mit.edu	37	17	56590291	56590291	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56590291delC	uc002iwj.2	-	3	125	c.15delG	c.(13-15)GGGfs	p.G5fs	MTMR4_uc010dcx.1_Frame_Shift_Del_p.G19fs	NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	5						cytoplasm|membrane	metal ion binding|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56711330	56711331	+	Intron	DEL	AA	-	-	rs71367608		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56711330_56711331delAA	uc010dcz.1	-						TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron	NM_198393	NP_938207			testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
RAD51C	5889	broad.mit.edu	37	17	56781158	56781158	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56781158delA	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				---	---	---	---
PPM1E	22843	broad.mit.edu	37	17	57060352	57060352	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57060352delA	uc002iwx.2	+	7					PPM1E_uc010ddd.2_3'UTR|TRIM37_uc002iwy.3_Intron	NM_014906	NP_055721			protein phosphatase 1E						protein dephosphorylation	cytoplasm|nucleolus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(3)|lung(1)|skin(1)	5	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)															---	---	---	---
TRIM37	4591	broad.mit.edu	37	17	57148405	57148405	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57148405delA	uc002iwy.3	-						TRIM37_uc002iwz.3_Intron|TRIM37_uc002ixa.3_Intron|TRIM37_uc010woc.1_Intron	NM_001005207	NP_001005207			tripartite motif-containing 37 protein							perinuclear region of cytoplasm|peroxisome	ligase activity|protein binding|zinc ion binding			lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1)	7	Medulloblastoma(34;0.0922)|all_neural(34;0.101)													Mulibrey_Nanism				---	---	---	---
Unknown	0	broad.mit.edu	37	17	57539309	57539309	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57539309delA								YPEL2 (60214 upstream) : DHX40 (103577 downstream)																																			---	---	---	---
CLTC	1213	broad.mit.edu	37	17	57722572	57722572	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57722572delT	uc002ixq.1	+						CLTC_uc002ixp.2_Intron|CLTC_uc002ixr.1_Intron	NM_004859	NP_004850			clathrin heavy chain 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)							T	ALK|TFE3	ALCL|renal 								---	---	---	---
CLTC	1213	broad.mit.edu	37	17	57770003	57770003	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57770003delT	uc002ixq.1	+						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 								---	---	---	---
TMEM49	81671	broad.mit.edu	37	17	57901112	57901112	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57901112delA	uc002ixu.3	+						TMEM49_uc010wog.1_Intron|TMEM49_uc010woh.1_Intron|TMEM49_uc010woi.1_Intron|TMEM49_uc010woj.1_Intron	NM_030938	NP_112200			transmembrane protein 49						autophagy|cell adhesion	endoplasmic reticulum|ER-Golgi intermediate compartment membrane|integral to membrane|plasma membrane|vacuolar membrane					0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;1.15e-09)|all cancers(12;1.15e-08)															---	---	---	---
TUBD1	51174	broad.mit.edu	37	17	57963602	57963602	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57963602delA	uc002ixw.1	-						TUBD1_uc010ddf.1_Intron|TUBD1_uc010ddg.1_Intron|TUBD1_uc010ddh.1_Intron|TUBD1_uc010wok.1_Intron|TUBD1_uc002ixx.1_Intron|TUBD1_uc010wol.1_Intron|TUBD1_uc010ddi.1_Intron	NM_016261	NP_057345			delta-tubulin						cell differentiation|microtubule-based movement|multicellular organismal development|protein polymerization|spermatogenesis	centriole|microtubule|nucleus	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)															---	---	---	---
RPS6KB1	6198	broad.mit.edu	37	17	57991981	57991981	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57991981delT	uc002ixy.2	+						RPS6KB1_uc010ddj.1_Intron|RPS6KB1_uc010wom.1_Intron|RPS6KB1_uc010won.1_Intron|RPS6KB1_uc010woo.1_Intron	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)															---	---	---	---
RPS6KB1	6198	broad.mit.edu	37	17	57992192	57992192	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57992192delA	uc002ixy.2	+						RPS6KB1_uc010ddj.1_Intron|RPS6KB1_uc010wom.1_Intron|RPS6KB1_uc010won.1_Intron|RPS6KB1_uc010woo.1_Intron	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)															---	---	---	---
USP32	84669	broad.mit.edu	37	17	58335007	58335007	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58335007delA	uc002iyo.1	-						USP32_uc002iyn.1_5'Flank|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)															---	---	---	---
USP32	84669	broad.mit.edu	37	17	58335158	58335158	+	Intron	DEL	T	-	-	rs115654059	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58335158delT	uc002iyo.1	-						USP32_uc002iyn.1_5'Flank|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)															---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	58766177	58766179	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58766177_58766179delAAA	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron	NM_001099432	NP_001092902			breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)															---	---	---	---
TBX2	6909	broad.mit.edu	37	17	59480289	59480308	+	Intron	DEL	GATAGAGAGAGAGAGAGAGA	-	-	rs72277883		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59480289_59480308delGATAGAGAGAGAGAGAGAGA	uc010wox.1	+						TBX2_uc002ize.2_Intron|TBX2_uc002izg.2_Intron	NM_005994	NP_005985			T-box 2						cell aging|positive regulation of cell proliferation		sequence-specific DNA binding				0																		---	---	---	---
MED13	9969	broad.mit.edu	37	17	60052501	60052504	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60052501_60052504delAAAA	uc002izo.2	-							NM_005121	NP_005112			mediator complex subunit 13						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	60313925	60313925	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60313925delA								MED13 (171282 upstream) : TBC1D3P2 (28144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	60339221	60339221	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60339221delC								MED13 (196578 upstream) : TBC1D3P2 (2848 downstream)																																			---	---	---	---
EFCAB3	146779	broad.mit.edu	37	17	60449588	60449588	+	Intron	DEL	T	-	-	rs66511931		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60449588delT	uc010wpc.1	+							NM_001144933	NP_001138405			EF-hand calcium binding domain 3 isoform a								calcium ion binding			skin(1)	1			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)															---	---	---	---
EFCAB3	146779	broad.mit.edu	37	17	60460528	60460528	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60460528delA	uc002izu.1	+						EFCAB3_uc010wpc.1_Intron	NM_173503	NP_775774			EF-hand calcium binding domain 3 isoform b								calcium ion binding			skin(1)	1			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)															---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60598118	60598118	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60598118delT	uc010ddp.2	+						TLK2_uc002izx.3_Intron|TLK2_uc002izz.3_Intron|TLK2_uc002jaa.3_Intron|TLK2_uc010wpd.1_Intron	NM_006852	NP_006843			tousled-like kinase 2 isoform A						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																		---	---	---	---
STRADA	92335	broad.mit.edu	37	17	61791012	61791013	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61791012_61791013delTT	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	61833945	61833946	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61833945_61833946insA	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																		---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61870025	61870025	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61870025delT	uc002jbu.2	+						DDX42_uc002jbv.2_Intron|DDX42_uc002jbw.1_Intron	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																		---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61888619	61888619	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61888619delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	61943446	61943449	+	IGR	DEL	ACAA	-	-	rs148727270		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61943446_61943449delACAA								TCAM1P (1708 upstream) : GH2 (5924 downstream)																																			---	---	---	---
SCN4A	6329	broad.mit.edu	37	17	62049213	62049213	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62049213delG	uc002jds.1	-							NM_000334	NP_000325			voltage-gated sodium channel type 4 alpha						muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)													---	---	---	---
POLG2	11232	broad.mit.edu	37	17	62489544	62489544	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62489544delA	uc002jei.2	-						POLG2_uc010deg.1_Intron	NM_007215	NP_009146			DNA polymerase subunit gamma-2, mitochondrial						DNA repair|DNA-dependent DNA replication|glycyl-tRNA aminoacylation	mitochondrial chromosome	ATP binding|DNA-directed DNA polymerase activity|glycine-tRNA ligase activity|identical protein binding|single-stranded DNA binding			central_nervous_system(1)	1	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)															---	---	---	---
POLG2	11232	broad.mit.edu	37	17	62492629	62492630	+	Frame_Shift_Del	DEL	AG	-	-	rs149446102		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62492629_62492630delAG	uc002jei.2	-	1	540_541	c.457_458delCT	c.(457-459)CTAfs	p.L153fs	POLG2_uc010deg.1_Frame_Shift_Del_p.L153fs	NM_007215	NP_009146	Q9UHN1	DPOG2_HUMAN	DNA polymerase subunit gamma-2, mitochondrial	153					DNA repair|DNA-dependent DNA replication|glycyl-tRNA aminoacylation	mitochondrial chromosome	ATP binding|DNA-directed DNA polymerase activity|glycine-tRNA ligase activity|identical protein binding|single-stranded DNA binding			central_nervous_system(1)	1	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)															---	---	---	---
LOC146880	146880	broad.mit.edu	37	17	62752363	62752363	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62752363delA	uc010wqc.1	-							NR_026899				Homo sapiens cDNA FLJ30780 fis, clone FEBRA2000856.												0																		---	---	---	---
LOC146880	146880	broad.mit.edu	37	17	62759677	62759677	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62759677delA	uc010wqd.1	-						LOC146880_uc010wqc.1_Intron|LOC146880_uc002jet.1_Intron					Homo sapiens cDNA FLJ30780 fis, clone FEBRA2000856.												0																		---	---	---	---
RGS9	8787	broad.mit.edu	37	17	63186049	63186049	+	Intron	DEL	T	-	-	rs112552969		TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
RGS9	8787	broad.mit.edu	37	17	63197219	63197220	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63197219_63197220delAC	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																		---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	63689421	63689421	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63689421delT	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron|CCDC46_uc002jfk.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	64106795	64106796	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64106795_64106796delAA	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)															---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	64150296	64150296	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64150296delA	uc002jfl.2	-						CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64333674	64333674	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64333674delT	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	64455191	64455191	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64455191delA	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	64641111	64641111	+	Intron	DEL	A	-	-	rs3217111		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64641111delA	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)													---	---	---	---
CACNG5	27091	broad.mit.edu	37	17	64840804	64840806	+	Intron	DEL	ATG	-	-	rs35328992		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64840804_64840806delATG	uc010wqi.1	+							NM_145811	NP_665810			voltage-dependent calcium channel gamma-5						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|postsynaptic density|postsynaptic membrane	voltage-gated calcium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)															---	---	---	---
HELZ	9931	broad.mit.edu	37	17	65156546	65156546	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65156546delA	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)																	---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65424655	65424655	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65424655delA	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65592511	65592511	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65592511delA	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
BPTF	2186	broad.mit.edu	37	17	65897421	65897421	+	Intron	DEL	A	-	-	rs143897652		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65897421delA	uc002jgf.2	+						BPTF_uc002jge.2_Intron|BPTF_uc010wqm.1_Intron	NM_182641	NP_872579			bromodomain PHD finger transcription factor						brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	66092900	66092900	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66092900delT								KPNA2 (49931 upstream) : LOC651250 (4796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66464023	66464023	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66464023delT								WIPI1 (10370 upstream) : PRKAR1A (44087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66483020	66483020	+	IGR	DEL	T	-	-	rs34344732		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66483020delT								WIPI1 (29367 upstream) : PRKAR1A (25090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66647892	66647895	+	IGR	DEL	CCAT	-	-	rs10534468		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66647892_66647895delCCAT								FAM20A (50797 upstream) : ABCA8 (215538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66653378	66653378	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66653378delT								FAM20A (56283 upstream) : ABCA8 (210055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66659558	66659558	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66659558delT								FAM20A (62463 upstream) : ABCA8 (203875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66774948	66774948	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66774948delT								FAM20A (177853 upstream) : ABCA8 (88485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66822526	66822527	+	IGR	INS	-	TGTGTGTG	TGTGTGTG	rs112741515		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66822526_66822527insTGTGTGTG								FAM20A (225431 upstream) : ABCA8 (40906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66964648	66964649	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66964648_66964649delTT								ABCA8 (13115 upstream) : ABCA9 (6125 downstream)																																			---	---	---	---
ABCA6	23460	broad.mit.edu	37	17	67092949	67092949	+	Intron	DEL	A	-	-	rs80020819		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67092949delA	uc002jhw.1	-							NM_080284	NP_525023			ATP-binding cassette, sub-family A, member 6						transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)																	---	---	---	---
ABCA5	23461	broad.mit.edu	37	17	67294448	67294451	+	Intron	DEL	AGAG	-	-	rs72245536		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67294448_67294451delAGAG	uc002jif.2	-						ABCA5_uc002jie.2_Intron|ABCA5_uc002jig.2_Intron|ABCA5_uc002jih.2_Intron|ABCA5_uc010dfe.2_Intron	NM_018672	NP_061142			ATP-binding cassette, sub-family A , member 5						cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)																	---	---	---	---
MAP2K6	5608	broad.mit.edu	37	17	67494792	67494793	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67494792_67494793delCA	uc002jij.2	+						MAP2K6_uc002jii.2_Intron	NM_002758	NP_002749			mitogen-activated protein kinase kinase 6						activation of MAPK activity|cell cycle arrest|DNA damage induced protein phosphorylation|innate immune response|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of muscle cell differentiation|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|pancreas(1)	5	Breast(10;6.05e-10)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	67595167	67595167	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67595167delT	uc002jil.2	+											Homo sapiens cDNA clone IMAGE:30336294.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	67703569	67703569	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67703569delA								MAP2K6 (165107 upstream) : KCNJ16 (367857 downstream)																																			---	---	---	---
KCNJ16	3773	broad.mit.edu	37	17	68091413	68091414	+	Intron	INS	-	T	T	rs141950683	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68091413_68091414insT	uc002jin.2	+						KCNJ16_uc002jio.2_Intron	NM_018658	NP_061128			potassium inwardly-rectifying channel J16						synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(1)|central_nervous_system(1)|skin(1)	3	Breast(10;2.96e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	68132754	68132754	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68132754delA								KCNJ16 (1010 upstream) : KCNJ2 (32060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68744561	68744561	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68744561delA								KCNJ2 (568380 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69724419	69724419	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69724419delT								None (None upstream) : SOX9 (392742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69824977	69824977	+	IGR	DEL	C	-	-	rs111461727		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69824977delC								None (None upstream) : SOX9 (292184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70222739	70222739	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70222739delT								SOX9 (100187 upstream) : SLC39A11 (419347 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70236080	70236081	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70236080_70236081delTC								SOX9 (113528 upstream) : SLC39A11 (406005 downstream)																																			---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	70674433	70674433	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70674433delT	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																		---	---	---	---
CDC42EP4	23580	broad.mit.edu	37	17	71285871	71285882	+	Intron	DEL	AGGGAGGGAGGA	-	-	rs112807866		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71285871_71285882delAGGGAGGGAGGA	uc002jjn.2	-						CDC42EP4_uc002jjo.2_Intron|CDC42EP4_uc002jjp.1_Intron	NM_012121	NP_036253			Cdc42 effector protein 4						positive regulation of pseudopodium assembly|regulation of cell shape	actin cytoskeleton|cytoplasm|endomembrane system|membrane|microtubule cytoskeleton	GTP-Rho binding				0			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	71320363	71320364	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71320363_71320364insG								CDC42EP4 (12220 upstream) : SDK2 (10160 downstream)																																			---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71363645	71363645	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71363645delT	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	71411006	71411006	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71411006delC	uc010dfm.2	-						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	71590734	71590735	+	Intron	INS	-	AC	AC	rs138573947	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71590734_71590735insAC	uc010dfm.2	-							NM_001144952	NP_001138424			sidekick 2						cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	71846042	71846042	+	IGR	DEL	A	-	-	rs35961401		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71846042delA								C17orf54 (21366 upstream) : RPL38 (353753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	71966916	71966916	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71966916delT								C17orf54 (142240 upstream) : RPL38 (232879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	72113885	72113887	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72113885_72113887delTTT								C17orf54 (289209 upstream) : RPL38 (85908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	72129485	72129485	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72129485delA								C17orf54 (304809 upstream) : RPL38 (70310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	72457664	72457665	+	IGR	DEL	AA	-	-	rs113706985		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72457664_72457665delAA								GPRC5C (10945 upstream) : CD300A (4857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	72897755	72897756	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72897755_72897756insG								FADS6 (8050 upstream) : USH1G (14420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	73064935	73064936	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73064935_73064936insA								KCTD2 (2956 upstream) : SLC16A5 (18886 downstream)																																			---	---	---	---
ARMC7	79637	broad.mit.edu	37	17	73103114	73103114	+	5'Flank	DEL	A	-	-	rs28485869		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73103114delA	uc002jmw.1	+						ARMC7_uc002jmv.1_5'Flank|ARMC7_uc010wru.1_5'Flank	NM_024585	NP_078861			armadillo repeat containing 7								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)															---	---	---	---
SUMO2	6613	broad.mit.edu	37	17	73167162	73167163	+	Intron	INS	-	T	T	rs139290058	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73167162_73167163insT	uc002jne.2	-						SUMO2_uc002jnf.2_Intron	NM_006937	NP_008868			SMT3 suppressor of mif two 3 homolog 2 isoform a						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation	nucleus	ubiquitin protein ligase binding				0	all_lung(278;0.14)|Lung NSC(278;0.168)																	---	---	---	---
GRB2	2885	broad.mit.edu	37	17	73333465	73333465	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73333465delA	uc002jnx.3	-						GRB2_uc002jny.3_Intron	NM_002086	NP_002077			growth factor receptor-bound protein 2 isoform						axon guidance|blood coagulation|cell junction assembly|cell-cell signaling|cellular response to ionizing radiation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|receptor internalization|signal transduction in response to DNA damage|T cell costimulation	cytosol|Golgi apparatus	epidermal growth factor receptor binding|insulin receptor substrate binding|SH3/SH2 adaptor activity			ovary(3)	3	all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222)		all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185)		Pegademase bovine(DB00061)													---	---	---	---
GRB2	2885	broad.mit.edu	37	17	73335277	73335278	+	Intron	DEL	TT	-	-	rs138039474		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73335277_73335278delTT	uc002jnx.3	-						GRB2_uc002jny.3_Intron	NM_002086	NP_002077			growth factor receptor-bound protein 2 isoform						axon guidance|blood coagulation|cell junction assembly|cell-cell signaling|cellular response to ionizing radiation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|receptor internalization|signal transduction in response to DNA damage|T cell costimulation	cytosol|Golgi apparatus	epidermal growth factor receptor binding|insulin receptor substrate binding|SH3/SH2 adaptor activity			ovary(3)	3	all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222)		all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185)		Pegademase bovine(DB00061)													---	---	---	---
KIAA0195	9772	broad.mit.edu	37	17	73467795	73467796	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73467795_73467796delAA	uc002jnz.3	+							NM_014738	NP_055553			hypothetical protein LOC9772						ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
MYO15B	80022	broad.mit.edu	37	17	73594348	73594348	+	Intron	DEL	A	-	-	rs67823231		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73594348delA	uc002jon.1	+						MYO15B_uc002jom.1_Intron|MYO15B_uc002joo.1_Intron|MYO15B_uc010dgh.2_Intron|MYO15B_uc010wse.1_Intron					RecName: Full=Putative myosin-XVB; AltName: Full=Unconventional myosin-15B; AltName: Full=Myosin XVBP;												0																		---	---	---	---
ACOX1	51	broad.mit.edu	37	17	73963550	73963550	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73963550delA	uc002jqf.2	-						ACOX1_uc010wsq.1_Intron|ACOX1_uc002jqe.2_Intron|ACOX1_uc010wsr.1_Intron	NM_007292	NP_009223			acyl-Coenzyme A oxidase 1 isoform b						fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|prostaglandin metabolic process|very long-chain fatty acid metabolic process	peroxisomal matrix	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity|flavin adenine dinucleotide binding|protein N-terminus binding			ovary(1)	1																		---	---	---	---
ACOX1	51	broad.mit.edu	37	17	73971935	73971936	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73971935_73971936delAG	uc002jqf.2	-						ACOX1_uc010wsq.1_Intron|ACOX1_uc002jqe.2_Intron|ACOX1_uc010wsr.1_Intron	NM_007292	NP_009223			acyl-Coenzyme A oxidase 1 isoform b						fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|prostaglandin metabolic process|very long-chain fatty acid metabolic process	peroxisomal matrix	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity|flavin adenine dinucleotide binding|protein N-terminus binding			ovary(1)	1																		---	---	---	---
RNF157	114804	broad.mit.edu	37	17	74175480	74175480	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74175480delA	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)															---	---	---	---
PRPSAP1	5635	broad.mit.edu	37	17	74308519	74308520	+	Intron	DEL	AA	-	-	rs10709096		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74308519_74308520delAA	uc010wta.1	-						PRPSAP1_uc010wtb.1_Intron	NM_002766	NP_002757			phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|identical protein binding|magnesium ion binding|ribose phosphate diphosphokinase activity			ovary(1)	1																		---	---	---	---
MFSD11	79157	broad.mit.edu	37	17	74740859	74740860	+	Intron	DEL	AT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74740859_74740860delAT	uc002jta.2	+						MFSD11_uc002jtb.2_Intron|MFSD11_uc010dha.2_Intron|MFSD11_uc002jtc.2_Intron|MFSD11_uc002jtd.3_Intron|MFSD11_uc010dhb.2_Intron|MFSD11_uc002jte.2_Intron	NM_024311	NP_077287			major facilitator superfamily domain containing							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	74815776	74815778	+	IGR	DEL	CTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74815776_74815778delCTT								MFSD11 (40440 upstream) : MGAT5B (49020 downstream)																																			---	---	---	---
SEPT9	10801	broad.mit.edu	37	17	75402742	75402743	+	Intron	INS	-	G	G	rs2411112		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75402742_75402743insG	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_Intron|SEPT9_uc002jtx.1_Intron|SEPT9_uc010wtl.1_Intron	NM_001113491	NP_001106963			septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	75497145	75497145	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75497145delC								SEPT9 (469 upstream) : FLJ45079 (377964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	75644725	75644725	+	IGR	DEL	T	-	-	rs113749809		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75644725delT								SEPT9 (148049 upstream) : FLJ45079 (230384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	75913810	75913810	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75913810delA								FLJ45079 (33641 upstream) : TNRC6C (86508 downstream)																																			---	---	---	---
TNRC6C	57690	broad.mit.edu	37	17	76101835	76101835	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76101835delT	uc002jud.2	+	21					TNRC6C_uc002juf.2_3'UTR	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)															---	---	---	---
C17orf99	100141515	broad.mit.edu	37	17	76154382	76154382	+	Intron	DEL	T	-	-	rs6501181	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76154382delT	uc002jus.3	+						C17orf99_uc010wts.1_5'Flank	NM_001163075	NP_001156547			hypothetical protein LOC100141515 precursor							extracellular region					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	76360327	76360327	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76360327delA								SOCS3 (4169 upstream) : PGS1 (14408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	76520699	76520700	+	IGR	INS	-	TGTT	TGTT	rs140963515	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76520699_76520700insTGTT								DNAH17 (51843 upstream) : CYTH1 (149431 downstream)																																			---	---	---	---
DNAH17	8632	broad.mit.edu	37	17	76554439	76554440	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76554439_76554440insG	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)															---	---	---	---
C1QTNF1	114897	broad.mit.edu	37	17	77026398	77026399	+	Intron	INS	-	TT	TT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77026398_77026399insTT	uc002jwp.2	+						uc002jwo.2_5'Flank|C1QTNF1_uc002jwq.2_Intron|C1QTNF1_uc002jwr.3_Intron	NM_030968	NP_112230			C1q and tumor necrosis factor related protein 1							collagen				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(99;0.0294)|OV - Ovarian serous cystadenocarcinoma(97;0.201)															---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77118955	77118955	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77118955delA	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)															---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77284560	77284560	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77284560delC	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	77776072	77776072	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77776072delT								CBX8 (5182 upstream) : CBX4 (30884 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	77790103	77790103	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77790103delG								CBX8 (19213 upstream) : CBX4 (16853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	77836463	77836463	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77836463delG								CBX4 (23250 upstream) : TBC1D16 (77358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	77872360	77872360	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77872360delA								CBX4 (59147 upstream) : TBC1D16 (41461 downstream)																																			---	---	---	---
CCDC40	55036	broad.mit.edu	37	17	78066760	78066760	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78066760delT	uc010dht.2	+						CCDC40_uc002jxm.3_Intron|CCDC40_uc002jxn.3_Intron	NM_017950	NP_060420			coiled-coil domain containing 40						axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium|cytoplasm				ovary(3)	3	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)															---	---	---	---
RNF213	57674	broad.mit.edu	37	17	78367996	78367996	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78367996delA	uc002jyh.1	+	43					uc002jyi.1_Intron|RNF213_uc010dhx.1_3'UTR	NM_020914	NP_065965			ring finger protein 213											ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)															---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78537866	78537867	+	Intron	INS	-	T	T	rs112402667		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78537866_78537867insT	uc002jyt.1	+						RPTOR_uc002jys.2_Intron|RPTOR_uc010wuf.1_Intron|RPTOR_uc010wug.1_Intron|RPTOR_uc002jyr.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																		---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78714523	78714523	+	Intron	DEL	A	-	-	rs113920656		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78714523delA	uc002jyt.1	+						RPTOR_uc002jys.2_Intron|RPTOR_uc010wuf.1_Intron|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																		---	---	---	---
AATK	9625	broad.mit.edu	37	17	79115671	79115674	+	Intron	DEL	TTAC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79115671_79115674delTTAC	uc010dia.2	-							NM_001080395	NP_001073864			apoptosis-associated tyrosine kinase							integral to membrane|mitochondrion|perinuclear region of cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1)	9	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)															---	---	---	---
AZI1	22994	broad.mit.edu	37	17	79186571	79186571	+	Intron	DEL	C	-	-	rs2659003	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79186571delC	uc002jzp.1	-						AZI1_uc002jzn.1_Intron|AZI1_uc002jzo.1_Intron|AZI1_uc010wum.1_Intron	NM_014984	NP_055799			5-azacytidine induced 1 isoform a						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)															---	---	---	---
SLC38A10	124565	broad.mit.edu	37	17	79250189	79250192	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79250189_79250192delTTTT	uc002jzz.1	-						SLC38A10_uc002jzy.1_Intron|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)															---	---	---	---
SLC38A10	124565	broad.mit.edu	37	17	79257418	79257419	+	Intron	DEL	TT	-	-	rs111438281		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79257418_79257419delTT	uc002jzz.1	-						SLC38A10_uc002jzy.1_Intron|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)															---	---	---	---
NPLOC4	55666	broad.mit.edu	37	17	79596219	79596219	+	Intron	DEL	T	-	-	rs141999520		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79596219delT	uc002kat.3	-						NPLOC4_uc002kau.3_Intron|NPLOC4_uc010wur.1_Intron	NM_017921	NP_060391			nuclear protein localization 4						cellular membrane fusion|ER-associated protein catabolic process|Golgi organization	cytosol|endoplasmic reticulum|nuclear outer membrane-endoplasmic reticulum membrane network|nucleus	zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)															---	---	---	---
ANAPC11	51529	broad.mit.edu	37	17	79852592	79852596	+	Intron	DEL	TTTTT	-	-	rs72240917		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79852592_79852596delTTTTT	uc002kbv.1	+						ANAPC11_uc002kbw.1_Intron|ANAPC11_uc002kbx.1_Intron|ANAPC11_uc002kby.1_Intron|ANAPC11_uc002kbz.1_Intron|ANAPC11_uc002kca.1_Intron|ANAPC11_uc002kcb.1_Intron|ANAPC11_uc002kcc.1_Intron|ANAPC11_uc010dih.1_Intron	NM_016476	NP_057560			APC11 anaphase promoting complex subunit 11						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	zinc ion binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)															---	---	---	---
FASN	2194	broad.mit.edu	37	17	80040351	80040351	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80040351delC	uc002kdu.2	-						FASN_uc002kdv.1_5'Flank	NM_004104	NP_004095			fatty acid synthase						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)													---	---	---	---
HEXDC	284004	broad.mit.edu	37	17	80400207	80400208	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80400207_80400208insC	uc002kew.2	+	12	1459_1460	c.1408_1409insC	c.(1408-1410)GCCfs	p.A470fs	HEXDC_uc002kev.3_Frame_Shift_Ins_p.L499fs|HEXDC_uc010diq.2_Frame_Shift_Ins_p.C472fs|HEXDC_uc010wvm.1_RNA			Q8WVB3	HEXDC_HUMAN	SubName: Full=Hexosaminidase (Glycosyl hydrolase family 20, catalytic domain) containing, isoform CRA_c; SubName: Full=Hexosaminidase D;	470					carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)|skin(1)	2	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)															---	---	---	---
NARF	26502	broad.mit.edu	37	17	80431279	80431279	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80431279delT	uc002kfg.3	+						NARF_uc002kff.3_Intron|NARF_uc010wvo.1_Intron|NARF_uc010wvp.1_Intron|NARF_uc010dit.2_Intron|NARF_uc002kfj.3_Intron|NARF_uc002kfi.3_Intron|NARF_uc002kfh.3_Intron|NARF_uc002kfk.2_Intron	NM_012336	NP_036468			nuclear prelamin A recognition factor isoform a							lamin filament	lamin binding			skin(1)	1	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)															---	---	---	---
FOXK2	3607	broad.mit.edu	37	17	80500025	80500025	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80500025delT	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)															---	---	---	---
FOXK2	3607	broad.mit.edu	37	17	80524985	80524985	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80524985delC	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)															---	---	---	---
FOXK2	3607	broad.mit.edu	37	17	80528098	80528098	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80528098delA	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)															---	---	---	---
RAB40B	10966	broad.mit.edu	37	17	80618564	80618565	+	Intron	DEL	AC	-	-	rs66713002		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80618564_80618565delAC	uc002kft.2	-						RAB40B_uc002kfs.2_Intron	NM_006822	NP_006813			RAB40B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			central_nervous_system(1)	1	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)															---	---	---	---
RAB40B	10966	broad.mit.edu	37	17	80629887	80629887	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80629887delA	uc002kft.2	-						RAB40B_uc002kfs.2_Intron	NM_006822	NP_006813			RAB40B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			central_nervous_system(1)	1	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)															---	---	---	---
B3GNTL1	146712	broad.mit.edu	37	17	80917238	80917239	+	Intron	INS	-	GT	GT	rs75562308	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80917238_80917239insGT	uc002kgg.1	-						B3GNTL1_uc002kgf.1_Intron|B3GNTL1_uc002kge.1_Intron	NM_001009905	NP_001009905			UDP-GlcNAc:betaGal								transferase activity, transferring glycosyl groups			ovary(1)|pancreas(1)	2	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	81096445	81096448	+	IGR	DEL	ACAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:81096445_81096448delACAG								METRNL (43856 upstream) : None (None downstream)																																			---	---	---	---
THOC1	9984	broad.mit.edu	37	18	265533	265533	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:265533delA	uc002kkj.3	-						THOC1_uc002kkk.3_Intron|THOC1_uc002kkl.2_Intron	NM_005131	NP_005122			THO complex 1						apoptosis|intronless viral mRNA export from host nucleus|mRNA processing|regulation of transcription elongation, DNA-dependent|RNA splicing|signal transduction|transcription, DNA-dependent	cytoplasm|nuclear matrix|nuclear speck|THO complex part of transcription export complex	DNA binding|protein binding|RNA binding			ovary(1)	1		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	524684	524685	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:524684_524685delTT								COLEC12 (23955 upstream) : CETN1 (55684 downstream)																																			---	---	---	---
YES1	7525	broad.mit.edu	37	18	747470	747470	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:747470delA	uc002kky.2	-						YES1_uc002kkz.2_Intron	NM_005433	NP_005424			viral oncogene yes-1 homolog 1						blood coagulation|leukocyte migration|regulation of vascular permeability|T cell costimulation	cytosol|plasma membrane	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|ovary(1)	3					Dasatinib(DB01254)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	941086	941086	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:941086delT								ADCYAP1 (28915 upstream) : C18orf2 (313304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	966760	966763	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:966760_966763delTTTT								ADCYAP1 (54589 upstream) : C18orf2 (287627 downstream)																																			---	---	---	---
C18orf2	56651	broad.mit.edu	37	18	1375182	1375183	+	Intron	INS	-	AGGAA	AGGAA	rs111313989		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1375182_1375183insAGGAA	uc002kld.1	-											Homo sapiens C18orf2 isoform 1 mRNA, complete sequence, alternatively spliced.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	1959869	1959869	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1959869delT								C18orf2 (552688 upstream) : METTL4 (577656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2173131	2173132	+	IGR	INS	-	TC	TC	rs141313313	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2173131_2173132insTC								C18orf2 (765950 upstream) : METTL4 (364393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2305130	2305130	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2305130delA								C18orf2 (897949 upstream) : METTL4 (232395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2373505	2373509	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2373505_2373509delTTTTT								C18orf2 (966324 upstream) : METTL4 (164016 downstream)																																			---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2705663	2705663	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2705663delT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_5'Flank	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
LPIN2	9663	broad.mit.edu	37	18	2975342	2975342	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2975342delT	uc002klo.2	-							NM_014646	NP_055461			lipin 2						fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity			ovary(1)|skin(1)	2				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)														---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3096451	3096451	+	Intron	DEL	T	-	-	rs112747134		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3096451delT	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																		---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4063037	4063037	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4063037delT	uc010wyz.1	-						uc002kmm.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4317023	4317023	+	Intron	DEL	T	-	-	rs33945197		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4317023delT	uc010wyz.1	-							NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4372928	4372928	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4372928delA	uc010wyz.1	-							NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
ZFP161	7541	broad.mit.edu	37	18	5294509	5294510	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5294509_5294510delCT	uc002kmq.2	-						ZFP161_uc002kmr.2_Intron|ZFP161_uc010dkp.2_Intron	NM_003409	NP_003400			zinc finger protein 161 homolog						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	5366921	5366922	+	IGR	INS	-	AG	AG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5366921_5366922insAG								ZFP161 (70882 upstream) : EPB41L3 (25466 downstream)																																			---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6308030	6308030	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6308030delA	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron	NM_173464	NP_775735			l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	7624492	7624492	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7624492delT	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	7634231	7634231	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7634231delT	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	7663685	7663685	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7663685delA	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	7777972	7777972	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7777972delC	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	8028003	8028003	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8028003delT	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	8217277	8217278	+	Intron	INS	-	T	T	rs140629913	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8217277_8217278insT	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	8518569	8518570	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8518569_8518570insT								PTPRM (111711 upstream) : RAB12 (90865 downstream)																																			---	---	---	---
RAB12	201475	broad.mit.edu	37	18	8636358	8636358	+	Intron	DEL	A	-	-	rs113358113		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8636358delA	uc002knp.2	+							NM_001025300	NP_001020471			RAB12, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding				0																		---	---	---	---
KIAA0802	23255	broad.mit.edu	37	18	8820407	8820407	+	Intron	DEL	A	-	-	rs80015232		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8820407delA	uc002knr.2	+						KIAA0802_uc002knq.2_Intron|KIAA0802_uc002kns.2_Intron	NM_015210	NP_056025			hypothetical protein LOC23255												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	8839261	8839261	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8839261delG								KIAA0802 (6486 upstream) : NDUFV2 (263414 downstream)																																			---	---	---	---
TWSG1	57045	broad.mit.edu	37	18	9396146	9396152	+	Intron	DEL	AAAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9396146_9396152delAAAAAAA	uc002knz.2	+						TWSG1_uc002koa.2_Intron	NM_020648	NP_065699			twisted gastrulation precursor											ovary(1)|pancreas(1)	2																		---	---	---	---
RALBP1	10928	broad.mit.edu	37	18	9478243	9478243	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9478243delT	uc002kob.2	+						RALBP1_uc002koc.2_Intron	NM_006788	NP_006779			ralA binding protein 1						chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	10153305	10153305	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10153305delT								VAPA (193288 upstream) : APCDD1 (301320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	10247880	10247880	+	5'Flank	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10247880delG	uc002kol.1	-											Homo sapiens cDNA FLJ34223 fis, clone FCBBF3023061.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	10434171	10434173	+	IGR	DEL	AAA	-	-	rs33922508		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10434171_10434173delAAA								VAPA (474154 upstream) : APCDD1 (20452 downstream)																																			---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10804668	10804668	+	Intron	DEL	G	-	-	rs74811226	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									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	10820339	10820339	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10820339delT	uc002kow.1	-											RecName: Full=Uncharacterized protein C18orf58;							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
GNAL	2774	broad.mit.edu	37	18	11735832	11735833	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11735832_11735833insA	uc002kqc.2	+							NM_182978	NP_892023			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1																		---	---	---	---
GNAL	2774	broad.mit.edu	37	18	11763412	11763412	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11763412delT	uc010dkz.2	+						GNAL_uc002kqc.2_Intron|GNAL_uc002kqd.2_Intron	NM_001142339	NP_001135811			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1																		---	---	---	---
GNAL	2774	broad.mit.edu	37	18	11857133	11857133	+	Intron	DEL	A	-	-	rs66532953		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11857133delA	uc010dkz.2	+						GNAL_uc002kqc.2_Intron|GNAL_uc002kqd.2_Intron|GNAL_uc010wzt.1_5'Flank	NM_001142339	NP_001135811			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	12303771	12303771	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12303771delA								CIDEA (26179 upstream) : TUBB6 (4469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	12397354	12397356	+	IGR	DEL	GAG	-	-	rs66763402		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12397354_12397356delGAG								AFG3L2 (20160 upstream) : SLMO1 (10539 downstream)																																			---	---	---	---
SLMO1	10650	broad.mit.edu	37	18	12430923	12430924	+	Intron	DEL	AT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12430923_12430924delAT	uc002kra.2	+						SLMO1_uc010wzu.1_Intron|SLMO1_uc010wzv.1_Intron	NM_001142405	NP_001135877			slowmo homolog 1 isoform 1												0																		---	---	---	---
SPIRE1	56907	broad.mit.edu	37	18	12639128	12639129	+	Intron	DEL	AT	-	-	rs143232845	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12639128_12639129delAT	uc002kre.2	-						SPIRE1_uc002krc.2_5'Flank|SPIRE1_uc010wzw.1_Intron|SPIRE1_uc010wzx.1_Intron|SPIRE1_uc010wzy.1_Intron	NM_001128626	NP_001122098			spire homolog 1 isoform a							cytoskeleton|perinuclear region of cytoplasm	actin binding				0																		---	---	---	---
PTPN2	5771	broad.mit.edu	37	18	12850128	12850128	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12850128delT	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	14156368	14156369	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14156368_14156369insA								ZNF519 (23939 upstream) : LOC284233 (181053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14225639	14225639	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14225639delA								ZNF519 (93210 upstream) : LOC284233 (111783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14249682	14249682	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14249682delA								ZNF519 (117253 upstream) : LOC284233 (87740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14360184	14360184	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14360184delT								LOC284233 (17662 upstream) : CXADRP3 (117772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14437113	14437113	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14437113delT								LOC284233 (94591 upstream) : CXADRP3 (40843 downstream)																																			---	---	---	---
ANKRD30B	374860	broad.mit.edu	37	18	14755017	14755017	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14755017delT	uc010dlo.2	+						ANKRD30B_uc010xak.1_Intron	NM_001145029	NP_001138501			ankyrin repeat domain 30B											ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	14874989	14874990	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14874989_14874990delGT								ANKRD30B (22252 upstream) : LOC644669 (438565 downstream)																																			---	---	---	---
ESCO1	114799	broad.mit.edu	37	18	19178663	19178663	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19178663delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	19213503	19213503	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19213503delT								SNRPD1 (3295 upstream) : ABHD3 (17355 downstream)																																			---	---	---	---
ABHD3	171586	broad.mit.edu	37	18	19282251	19282251	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19282251delA	uc002ktl.2	-						ABHD3_uc002ktm.2_Intron|ABHD3_uc010xao.1_Intron|MIB1_uc002ktp.2_5'Flank|ABHD3_uc002kto.2_3'UTR	NM_138340	NP_612213			alpha/beta hydrolase domain containing protein							integral to membrane	carboxylesterase activity			central_nervous_system(1)	1																		---	---	---	---
MIB1	57534	broad.mit.edu	37	18	19378031	19378031	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19378031delT	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	19923035	19923035	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19923035delT								GATA6 (140808 upstream) : CTAGE1 (70529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	20115970	20115973	+	IGR	DEL	TTTT	-	-	rs12962776		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20115970_20115973delTTTT								CTAGE1 (118092 upstream) : RBBP8 (397322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	20649081	20649081	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20649081delG								RBBP8 (42636 upstream) : CABLES1 (65447 downstream)																																			---	---	---	---
C18orf45	85019	broad.mit.edu	37	18	20964320	20964320	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20964320delA	uc002kuf.2	-						C18orf45_uc010xaq.1_Intron|C18orf45_uc010xar.1_Intron|C18orf45_uc002kug.2_Intron|C18orf45_uc002kuh.2_Intron	NM_032933	NP_116322			hypothetical protein LOC85019							integral to membrane					0	all_cancers(21;0.000238)|all_epithelial(16;5.29e-06)|Lung NSC(20;0.00925)|Colorectal(14;0.0202)|all_lung(20;0.0255)|Ovarian(20;0.127)																	---	---	---	---
C18orf8	29919	broad.mit.edu	37	18	21095780	21095780	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21095780delT	uc010xax.1	+						C18orf8_uc010xau.1_Intron|C18orf8_uc010xav.1_Intron|C18orf8_uc010xaw.1_Intron|C18orf8_uc002kul.2_Intron	NM_013326	NP_037458			colon cancer-associated protein Mic1											ovary(1)	1	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)															OREG0024894	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NPC1	4864	broad.mit.edu	37	18	21120909	21120909	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																	---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22642387	22642389	+	3'UTR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22642387_22642389delTTT	uc002kvk.2	-	8					ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_3'UTR|ZNF521_uc002kvl.2_3'UTR	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								---	---	---	---
SS18	6760	broad.mit.edu	37	18	23667438	23667438	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23667438delA	uc002kvm.2	-						SS18_uc002kvn.2_Intron|SS18_uc010xbf.1_Intron|SS18_uc010xbg.1_Intron|SS18_uc010xbh.1_Intron|SS18_uc010xbi.1_Intron|SS18_uc010dlz.1_Intron	NM_001007559	NP_001007560			synovial sarcoma translocation, chromosome 18						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	ligand-dependent nuclear receptor transcription coactivator activity|protein binding		SS18/SSX1(1169)|SS18/SSX2(702)|SS18/SSX4(12)	soft_tissue(1883)|ovary(1)	1884	all_cancers(21;0.000194)|Lung NSC(5;0.000413)|all_lung(6;0.00118)|Ovarian(20;0.124)							T	SSX1| SSX2	synovial sarcoma								---	---	---	---
SS18	6760	broad.mit.edu	37	18	23667733	23667733	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23667733delA	uc002kvm.2	-						SS18_uc002kvn.2_Intron|SS18_uc010xbf.1_Intron|SS18_uc010xbg.1_Intron|SS18_uc010xbh.1_Intron|SS18_uc010xbi.1_Intron|SS18_uc010dlz.1_Intron	NM_001007559	NP_001007560			synovial sarcoma translocation, chromosome 18						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	ligand-dependent nuclear receptor transcription coactivator activity|protein binding		SS18/SSX1(1169)|SS18/SSX2(702)|SS18/SSX4(12)	soft_tissue(1883)|ovary(1)	1884	all_cancers(21;0.000194)|Lung NSC(5;0.000413)|all_lung(6;0.00118)|Ovarian(20;0.124)							T	SSX1| SSX2	synovial sarcoma								---	---	---	---
Unknown	0	broad.mit.edu	37	18	23773776	23773776	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23773776delT								PSMA8 (456 upstream) : TAF4B (32633 downstream)																																			---	---	---	---
CHST9	83539	broad.mit.edu	37	18	24524315	24524316	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24524315_24524316insT	uc002kwd.2	-	4	415_416	c.217_218insA	c.(217-219)ATCfs	p.I73fs	C18orf16_uc010xbm.1_Intron|CHST9_uc002kwc.2_Intron|CHST9_uc002kwe.2_Frame_Shift_Ins_p.I73fs	NM_031422	NP_113610	Q7L1S5	CHST9_HUMAN	GalNAc-4-sulfotransferase 2	73	Lumenal (Potential).				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	25133971	25133972	+	Intron	INS	-	CA	CA	rs146986766	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25133971_25133972insCA	uc002kwf.1	-											Homo sapiens cDNA FLJ45994 fis, clone SKMUS2009557.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	25173087	25173088	+	Intron	INS	-	C	C	rs139734222	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25173087_25173088insC	uc002kwf.1	-											Homo sapiens cDNA FLJ45994 fis, clone SKMUS2009557.																														---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25550957	25550957	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25550957delT	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																		---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25752041	25752042	+	Intron	DEL	GT	-	-	rs72438915		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25752041_25752042delGT	uc002kwg.2	-							NM_001792	NP_001783			cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	26121302	26121303	+	IGR	INS	-	A	A	rs138836013	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26121302_26121303insA								CDH2 (363857 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26483556	26483556	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26483556delG								CDH2 (726111 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26696875	26696875	+	IGR	DEL	A	-	-	rs79131868		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26696875delA								CDH2 (939430 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26782981	26782982	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26782981_26782982delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27386095	27386095	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27386095delA								None (None upstream) : MIR302F (492781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28011148	28011149	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28011148_28011149delTT								MIR302F (132222 upstream) : DSC3 (558904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28241968	28241968	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28241968delA								MIR302F (363042 upstream) : DSC3 (328085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28262001	28262002	+	IGR	INS	-	A	A	rs142745875	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28262001_28262002insA								MIR302F (383075 upstream) : DSC3 (308051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28813088	28813088	+	IGR	DEL	A	-	-	rs113717445		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28813088delA								DSC1 (70269 upstream) : DSG1 (84964 downstream)																																			---	---	---	---
DSG1	1828	broad.mit.edu	37	18	28903604	28903604	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28903604delA	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)															---	---	---	---
DSG4	147409	broad.mit.edu	37	18	28970450	28970450	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28970450delT	uc002kwq.2	+						DSG4_uc002kwr.2_Intron	NM_177986	NP_817123			desmoglein 4 isoform 2 preproprotein						homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8			OV - Ovarian serous cystadenocarcinoma(10;0.00504)															---	---	---	---
DSG2	1829	broad.mit.edu	37	18	29079320	29079321	+	Intron	INS	-	GT	GT	rs140200584	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29079320_29079321insGT	uc002kwu.3	+							NM_001943	NP_001934			desmoglein 2 preproprotein						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)															---	---	---	---
B4GALT6	9331	broad.mit.edu	37	18	29246379	29246379	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29246379delT	uc002kwz.3	-						B4GALT6_uc010dma.2_Intron|B4GALT6_uc010dmb.2_Intron	NM_004775	NP_004766			beta-1,4-galactosyltransferase 6						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	metal ion binding				0			OV - Ovarian serous cystadenocarcinoma(10;0.00791)															---	---	---	---
RNF125	54941	broad.mit.edu	37	18	29612344	29612345	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29612344_29612345delTT	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	29701112	29701112	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29701112delA	uc002kxg.2	+						RNF138_uc002kxh.2_Intron	NM_016271	NP_057355			ring finger protein 138 isoform 1						Wnt receptor signaling pathway	intracellular	ligase activity|protein kinase binding|zinc ion binding				0																		---	---	---	---
MEP1B	4225	broad.mit.edu	37	18	29796832	29796832	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29796832delA	uc002kxj.3	+							NM_005925	NP_005916			meprin A beta precursor						digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	29848873	29848874	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29848873_29848874delTT	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588			family with sequence similarity 59, member A											ovary(1)|skin(1)	2																		---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	29885099	29885100	+	Intron	INS	-	A	A	rs113496311		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29885099_29885100insA	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588			family with sequence similarity 59, member A											ovary(1)|skin(1)	2																		---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	29963784	29963784	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29963784delT	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588			family with sequence similarity 59, member A											ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	30057221	30057224	+	IGR	DEL	TGTG	-	-	rs141706031		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30057221_30057224delTGTG								FAM59A (6774 upstream) : WBP11P1 (34402 downstream)																																			---	---	---	---
KLHL14	57565	broad.mit.edu	37	18	30316769	30316770	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30316769_30316770insT	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	30913143	30913143	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30913143delT	uc002kxn.2	-	9	1016	c.874delA	c.(874-876)ATGfs	p.M292fs	C18orf34_uc010xbr.1_Frame_Shift_Del_p.M292fs|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Frame_Shift_Del_p.M292fs|C18orf34_uc002kxp.2_Frame_Shift_Del_p.M292fs	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	292	Potential.									ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	31121955	31121956	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31121955_31121956delTG								C18orf34 (101270 upstream) : ASXL3 (36585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	31340730	31340733	+	IGR	DEL	TTTA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31340730_31340733delTTTA								ASXL3 (13331 upstream) : NOL4 (90337 downstream)																																			---	---	---	---
NOL4	8715	broad.mit.edu	37	18	31673383	31673383	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31673383delT	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																		---	---	---	---
SLC39A6	25800	broad.mit.edu	37	18	33706994	33706994	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33706994delA	uc010dmy.2	-						SLC39A6_uc002kzj.2_Intron|ELP2_uc002kzk.1_5'Flank|ELP2_uc010xcg.1_5'Flank|ELP2_uc002kzl.1_5'Flank|ELP2_uc002kzm.1_5'Flank|ELP2_uc010xch.1_5'Flank|ELP2_uc002kzn.1_5'Flank|ELP2_uc002kzo.1_5'Flank	NM_012319	NP_036451			solute carrier family 39 (zinc transporter),							integral to membrane|lamellipodium membrane	zinc ion transmembrane transporter activity			ovary(1)|pancreas(1)	2																		---	---	---	---
ELP2	55250	broad.mit.edu	37	18	33738964	33738964	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34465687	34465687	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34465687delT	uc002kzz.2	+							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	34501212	34501212	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34501212delT	uc002kzz.2	+						uc002laa.2_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	34585811	34585812	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34585811_34585812insA	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)														---	---	---	---
CELF4	56853	broad.mit.edu	37	18	35071806	35071806	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35071806delG	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	35158959	35158960	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35158959_35158960delTG								CELF4 (12959 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35357393	35357393	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35357393delT								CELF4 (211393 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36753242	36753242	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36753242delA								None (None upstream) : LOC647946 (33646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	37668042	37668042	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37668042delT	uc002lam.2	+											Homo sapiens cDNA clone IMAGE:4831311.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	38660531	38660532	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38660531_38660532insT								None (None upstream) : KC6 (399706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39230249	39230250	+	IGR	INS	-	GAAA	GAAA	rs140490242	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39230249_39230250insGAAA								KC6 (129688 upstream) : PIK3C3 (304949 downstream)																																			---	---	---	---
PIK3C3	5289	broad.mit.edu	37	18	39556329	39556330	+	Intron	DEL	AA	-	-	rs1944965		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39556329_39556330delAA	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)			---	---	---	---
PIK3C3	5289	broad.mit.edu	37	18	39561948	39561948	+	Intron	DEL	A	-	-	rs75375844		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39561948delA	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	40001157	40001158	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40001157_40001158insT	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.																														---	---	---	---
RIT2	6014	broad.mit.edu	37	18	40390578	40390578	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40390578delG	uc002lav.2	-						RIT2_uc010dnf.2_Intron	NM_002930	NP_002921			Ras-like without CAAX 2						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1																		---	---	---	---
RIT2	6014	broad.mit.edu	37	18	40613838	40613839	+	Intron	INS	-	G	G	rs112790285		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40613838_40613839insG	uc002lav.2	-						RIT2_uc010dnf.2_Intron	NM_002930	NP_002921			Ras-like without CAAX 2						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	41181654	41181657	+	IGR	DEL	GAAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41181654_41181657delGAAG								SYT4 (324039 upstream) : None (None downstream)																																			---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42303473	42303473	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42303473delA	uc010dni.2	+						SETBP1_uc002lay.2_Intron	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	42582052	42582052	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42582052delA	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	42812002	42812002	+	Intron	DEL	A	-	-	rs113423302		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42812002delA	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron	NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43082882	43082883	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43082882_43082883delTT	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron|uc002lbc.1_Intron|uc002lbd.1_Intron	NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43242269	43242270	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43242269_43242270delAA	uc010dnj.2	+						SLC14A2_uc002lbe.2_Intron	NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
RNF165	494470	broad.mit.edu	37	18	43954159	43954159	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43954159delT	uc002lcb.1	+						RNF165_uc002lby.1_Intron|RNF165_uc010dnn.1_Intron	NM_152470	NP_689683			ring finger protein 165								zinc ion binding				0				READ - Rectum adenocarcinoma(1;0.0873)														---	---	---	---
LOXHD1	125336	broad.mit.edu	37	18	44187998	44187999	+	Intron	INS	-	GGAA	GGAA	rs149739560	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44187998_44187999insGGAA	uc010xcw.1	-							NM_144612	NP_653213			lipoxygenase homology domains 1 isoform 1						sensory perception of sound	stereocilium	protein binding				0																		---	---	---	---
ST8SIA5	29906	broad.mit.edu	37	18	44272373	44272373	+	Intron	DEL	T	-	-	rs77603253		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44272373delT	uc002lcj.1	-						ST8SIA5_uc002lci.1_Intron|ST8SIA5_uc010xcy.1_Intron|ST8SIA5_uc010xcz.1_Intron|ST8SIA5_uc010dno.1_Intron	NM_013305	NP_037437			ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3																		---	---	---	---
ST8SIA5	29906	broad.mit.edu	37	18	44335724	44335724	+	Intron	DEL	A	-	-	rs17779820		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44335724delA	uc002lcj.1	-						ST8SIA5_uc010xcy.1_Intron|ST8SIA5_uc010xcz.1_Intron|ST8SIA5_uc010dno.1_Intron	NM_013305	NP_037437			ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3																		---	---	---	---
KATNAL2	83473	broad.mit.edu	37	18	44528390	44528390	+	Intron	DEL	T	-	-	rs150878662		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44528390delT	uc002lco.2	+						KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lcp.3_Intron	NM_031303	NP_112593			katanin p60 subunit A-like 2							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	44712662	44712662	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44712662delT								IER3IP1 (9917 upstream) : SMAD2 (646805 downstream)																																			---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45912522	45912522	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45912522delA	uc010dnw.2	-						ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449			zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46104528	46104528	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46104528delT	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																		---	---	---	---
SMAD7	4092	broad.mit.edu	37	18	46473356	46473356	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46473356delA	uc002ldg.2	-						SMAD7_uc010xde.1_Intron	NM_005904	NP_005895			SMAD family member 7						adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex	activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding				0	Colorectal(1;0.0518)																	---	---	---	---
DYM	54808	broad.mit.edu	37	18	46918156	46918157	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46918156_46918157delAA	uc002ldi.1	-						DYM_uc010xdf.1_Intron	NM_017653	NP_060123			dymeclin							Golgi apparatus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	47054860	47054860	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47054860delT								RPL17 (35954 upstream) : LIPG (33567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	47198739	47198740	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47198739_47198740delAC								LIPG (79463 upstream) : ACAA2 (111135 downstream)																																			---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47670772	47670772	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47670772delT	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	47851239	47851247	+	IGR	DEL	TCCTCCTCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47851239_47851247delTCCTCCTCT								CXXC1 (36547 upstream) : SKA1 (50145 downstream)																																			---	---	---	---
SKA1	220134	broad.mit.edu	37	18	47902928	47902929	+	Intron	INS	-	AGTG	AGTG	rs149131647	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47902928_47902929insAGTG	uc002let.2	+						SKA1_uc002leu.2_Intron|SKA1_uc010xdl.1_Intron	NM_145060	NP_659497			spindle and KT associated 1						cell division|chromosome segregation|mitotic anaphase|mitotic prometaphase|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytosol|spindle microtubule	microtubule binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	47933855	47933856	+	IGR	INS	-	GT	GT	rs150765378	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47933855_47933856insGT								SKA1 (13321 upstream) : MAPK4 (152628 downstream)																																			---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48203938	48203938	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48203938delT	uc002lev.2	+						MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738			mitogen-activated protein kinase 4						cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	48274093	48274093	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48274093delA								MAPK4 (15898 upstream) : MRO (47398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	48290094	48290094	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48290094delA								MAPK4 (31899 upstream) : MRO (31397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	48365292	48365292	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48365292delA								MRO (13538 upstream) : ME2 (40143 downstream)																																			---	---	---	---
ME2	4200	broad.mit.edu	37	18	48446641	48446642	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48446641_48446642insT	uc002ley.2	+						ME2_uc010dpd.2_Intron	NM_002396	NP_002387			malic enzyme 2, NAD(+)-dependent, mitochondrial						malate metabolic process	mitochondrial matrix	electron carrier activity|malate dehydrogenase (decarboxylating) activity|malate dehydrogenase (oxaloacetate-decarboxylating) activity|metal ion binding|NAD binding				0		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)	NADH(DB00157)													---	---	---	---
SMAD4	4089	broad.mit.edu	37	18	48605008	48605008	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48605008delT	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	48729281	48729281	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48729281delA								MEX3C (5591 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	49571490	49571490	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49571490delT								MEX3C (847800 upstream) : DCC (295081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	49706902	49706902	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49706902delA								MEX3C (983212 upstream) : DCC (159669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	51850335	51850336	+	IGR	DEL	TG	-	-	rs146571770		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51850335_51850336delTG								POLI (25733 upstream) : STARD6 (727 downstream)																																			---	---	---	---
TCF4	6925	broad.mit.edu	37	18	52970882	52970882	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52970882delA	uc002lfz.2	-						TCF4_uc002lfw.3_Intron|TCF4_uc010xdu.1_Intron|TCF4_uc010xdv.1_Intron|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_uc002lgb.1_5'Flank|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	52988711	52988711	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52988711delA	uc002lfz.2	-						TCF4_uc002lfw.3_Intron|TCF4_uc010xdu.1_Intron|TCF4_uc010xdv.1_Intron|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	53201932	53201932	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53201932delA	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	54131046	54131046	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54131046delA								TCF4 (827861 upstream) : TXNL1 (139009 downstream)																																			---	---	---	---
TXNL1	9352	broad.mit.edu	37	18	54283634	54283634	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54283634delA	uc002lgg.2	-						TXNL1_uc010xdz.1_Intron|TXNL1_uc002lgh.2_Intron|TXNL1_uc002lgi.2_Intron|TXNL1_uc002lgj.1_Intron	NM_004786	NP_004777			thioredoxin-like 1						cell redox homeostasis|electron transport chain|glycerol ether metabolic process|transport	cytoplasm	electron carrier activity|protein disulfide oxidoreductase activity				0				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)														---	---	---	---
TXNL1	9352	broad.mit.edu	37	18	54297517	54297517	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54297517delG	uc002lgg.2	-						TXNL1_uc010xdz.1_Intron|TXNL1_uc002lgh.2_Intron|TXNL1_uc002lgi.2_Intron|TXNL1_uc002lgj.1_Intron	NM_004786	NP_004777			thioredoxin-like 1						cell redox homeostasis|electron transport chain|glycerol ether metabolic process|transport	cytoplasm	electron carrier activity|protein disulfide oxidoreductase activity				0				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)														---	---	---	---
ST8SIA3	51046	broad.mit.edu	37	18	55019998	55019999	+	5'UTR	INS	-	AT	AT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55019998_55019999insAT	uc002lgn.2	+	1						NM_015879	NP_056963			ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			breast(1)|skin(1)	2				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)														---	---	---	---
ONECUT2	9480	broad.mit.edu	37	18	55104001	55104001	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55104001delC	uc002lgo.2	+	1	1085	c.1053delC	c.(1051-1053)ATCfs	p.I351fs		NM_004852	NP_004843	O95948	ONEC2_HUMAN	one cut domain, family member 2	351	CUT.				organ morphogenesis	nucleus	sequence-specific DNA binding			ovary(2)|central_nervous_system(1)	3		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)														---	---	---	---
ONECUT2	9480	broad.mit.edu	37	18	55138020	55138021	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55138020_55138021delCA	uc002lgo.2	+							NM_004852	NP_004843			one cut domain, family member 2						organ morphogenesis	nucleus	sequence-specific DNA binding			ovary(2)|central_nervous_system(1)	3		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	55183310	55183311	+	IGR	DEL	AT	-	-	rs10585926		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55183310_55183311delAT								ONECUT2 (24781 upstream) : FECH (28763 downstream)																																			---	---	---	---
ATP8B1	5205	broad.mit.edu	37	18	55371796	55371798	+	In_Frame_Del	DEL	AAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55371796_55371798delAAG	uc002lgw.2	-	3	382_384	c.382_384delCTT	c.(382-384)CTTdel	p.L128del	uc002lgv.1_Intron	NM_005603	NP_005594	O43520	AT8B1_HUMAN	ATPase, class I, type 8B, member 1	128	Helical; (Potential).				ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent	apical plasma membrane|integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			breast(5)|ovary(2)|central_nervous_system(2)|lung(1)	10		Colorectal(73;0.229)												Byler_disease				---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55901735	55901735	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55901735delA	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_uc010dpl.1_Intron|NEDD4L_uc002lhg.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	56215560	56215561	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56215560_56215561delTT	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	56246941	56246941	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56246941delA	uc002lhj.3	-	4	1281	c.1067delT	c.(1066-1068)TTAfs	p.L356fs		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	356							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14																OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MALT1	10892	broad.mit.edu	37	18	56390266	56390266	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56390266delT	uc002lhm.1	+						MALT1_uc002lhn.1_Intron	NM_006785	NP_006776			mucosa associated lymphoid tissue lymphoma						activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			ovary(2)|lung(1)|central_nervous_system(1)	4								T	BIRC3	MALT								---	---	---	---
MALT1	10892	broad.mit.edu	37	18	56406021	56406022	+	Intron	INS	-	TG	TG	rs74702254		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56406021_56406022insTG	uc002lhm.1	+						MALT1_uc002lhn.1_Intron	NM_006785	NP_006776			mucosa associated lymphoid tissue lymphoma						activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			ovary(2)|lung(1)|central_nervous_system(1)	4								T	BIRC3	MALT								---	---	---	---
Unknown	0	broad.mit.edu	37	18	56513158	56513158	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56513158delA								MALT1 (95788 upstream) : ZNF532 (16903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	56849539	56849539	+	IGR	DEL	T	-	-	rs113138402		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56849539delT								SEC11C (23478 upstream) : GRP (37861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	56904692	56904699	+	IGR	DEL	AAAAAAAA	-	-	rs142326730		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56904692_56904699delAAAAAAAA								GRP (6692 upstream) : RAX (29570 downstream)																																			---	---	---	---
CPLX4	339302	broad.mit.edu	37	18	56965326	56965327	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56965326_56965327delTT	uc002lhy.2	-							NM_181654	NP_857637			complexin 4 precursor						exocytosis|neurotransmitter transport	cell junction|synapse	syntaxin binding			ovary(1)	1		Colorectal(73;0.175)																---	---	---	---
CPLX4	339302	broad.mit.edu	37	18	56985740	56985740	+	5'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	57577364	57577365	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57577364_57577365insA								PMAIP1 (5826 upstream) : MC4R (461199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58545715	58545716	+	IGR	INS	-	GT	GT	rs113052917		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58545715_58545716insGT								MC4R (505714 upstream) : CDH20 (455272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58608741	58608742	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58608741_58608742insT								MC4R (568740 upstream) : CDH20 (392246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58869497	58869497	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58869497delA								MC4R (829496 upstream) : CDH20 (131491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58985493	58985494	+	IGR	INS	-	AC	AC	rs142002896	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58985493_58985494insAC								MC4R (945492 upstream) : CDH20 (15494 downstream)																																			---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59083828	59083828	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59083828delA	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)																---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59137840	59137840	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59137840delA	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	59224751	59224751	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59224751delA								CDH20 (2386 upstream) : RNF152 (257553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	59233384	59233384	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59233384delA								CDH20 (11019 upstream) : RNF152 (248920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	59618718	59618719	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59618718_59618719insT								RNF152 (58414 upstream) : PIGN (92741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	60274177	60274179	+	IGR	DEL	AAA	-	-	rs34645417		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60274177_60274179delAAA								ZCCHC2 (20215 upstream) : PHLPP1 (108555 downstream)																																			---	---	---	---
BCL2	596	broad.mit.edu	37	18	60943588	60943589	+	Intron	INS	-	T	T	rs145731011	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60943588_60943589insT	uc002lit.1	-						BCL2_uc002liu.1_Intron	NM_000633	NP_000624			B-cell lymphoma protein 2 alpha isoform						activation of pro-apoptotic gene products|anti-apoptosis|apoptosis in response to endoplasmic reticulum stress|B cell proliferation|B cell receptor signaling pathway|defense response to virus|female pregnancy|humoral immune response|induction of apoptosis by intracellular signals|negative regulation of cellular pH reduction|negative regulation of mitochondrial depolarization|negative regulation of neuron apoptosis|neuron apoptosis|positive regulation of B cell proliferation|positive regulation of cell growth|protein polyubiquitination|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|regulation of transmembrane transporter activity|release of cytochrome c from mitochondria|response to cytokine stimulus|response to DNA damage stimulus|response to drug|response to iron ion|response to nicotine|response to toxin	endoplasmic reticulum membrane|mitochondrial outer membrane|nuclear membrane|pore complex	BH3 domain binding|channel activity|protease binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|ubiquitin protein ligase binding			central_nervous_system(1)	1		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Fludarabine(DB01073)|Melatonin(DB01065)|Paclitaxel(DB01229)|Rasagiline(DB01367)			T	IGH@	NHL|CLL								---	---	---	---
BCL2	596	broad.mit.edu	37	18	60968544	60968546	+	Intron	DEL	ATA	-	-	rs10536242		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60968544_60968546delATA	uc002lit.1	-						BCL2_uc002liu.1_Intron	NM_000633	NP_000624			B-cell lymphoma protein 2 alpha isoform						activation of pro-apoptotic gene products|anti-apoptosis|apoptosis in response to endoplasmic reticulum stress|B cell proliferation|B cell receptor signaling pathway|defense response to virus|female pregnancy|humoral immune response|induction of apoptosis by intracellular signals|negative regulation of cellular pH reduction|negative regulation of mitochondrial depolarization|negative regulation of neuron apoptosis|neuron apoptosis|positive regulation of B cell proliferation|positive regulation of cell growth|protein polyubiquitination|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|regulation of transmembrane transporter activity|release of cytochrome c from mitochondria|response to cytokine stimulus|response to DNA damage stimulus|response to drug|response to iron ion|response to nicotine|response to toxin	endoplasmic reticulum membrane|mitochondrial outer membrane|nuclear membrane|pore complex	BH3 domain binding|channel activity|protease binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|ubiquitin protein ligase binding			central_nervous_system(1)	1		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Fludarabine(DB01073)|Melatonin(DB01065)|Paclitaxel(DB01229)|Rasagiline(DB01367)			T	IGH@	NHL|CLL								---	---	---	---
VPS4B	9525	broad.mit.edu	37	18	61082495	61082495	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61082495delT	uc002lix.2	-						VPS4B_uc010dpx.2_Intron|VPS4B_uc010dpy.2_Intron|VPS4B_uc010dpz.1_Intron	NM_004869	NP_004860			vacuolar protein sorting factor 4B						cell cycle|cell division|cellular membrane organization|endosome to lysosome transport via multivesicular body sorting pathway|intracellular cholesterol transport|protein transport|response to lipid	cytosol|early endosome|late endosome membrane|lysosome|nucleus|vacuolar membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding			ovary(1)	1																		---	---	---	---
SERPINB5	5268	broad.mit.edu	37	18	61151975	61151980	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61151975_61151980delTTTTTT	uc002liz.3	+						SERPINB5_uc002liy.2_Intron	NM_002639	NP_002630			serine (or cysteine) proteinase inhibitor, clade						cellular component movement|regulation of proteolysis	cytoplasm|extracellular space	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1																		---	---	---	---
SERPINB5	5268	broad.mit.edu	37	18	61164733	61164735	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61164733_61164735delAAA	uc002liz.3	+							NM_002639	NP_002630			serine (or cysteine) proteinase inhibitor, clade						cellular component movement|regulation of proteolysis	cytoplasm|extracellular space	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1																		---	---	---	---
SERPINB8	5271	broad.mit.edu	37	18	61642347	61642348	+	Intron	DEL	AC	-	-	rs10568370		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61642347_61642348delAC	uc002ljv.2	+						SERPINB8_uc002ljs.1_Intron|SERPINB8_uc002ljt.2_Intron|SERPINB8_uc002lju.2_Intron|SERPINB8_uc010xex.1_Intron	NM_198833	NP_942130			serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	cytosol	protein binding|serine-type endopeptidase inhibitor activity			skin(1)	1		Esophageal squamous(42;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	62986030	62986030	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62986030delA								None (None upstream) : CDH7 (431458 downstream)																																			---	---	---	---
CDH19	28513	broad.mit.edu	37	18	64178925	64178925	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64178925delA	uc002lkc.1	-						CDH19_uc010dql.1_Intron|CDH19_uc010xey.1_Intron	NM_021153	NP_066976			cadherin 19, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2		Esophageal squamous(42;0.0132)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	64490930	64490930	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64490930delT								CDH19 (219714 upstream) : DSEL (682889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	64509853	64509853	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64509853delA								CDH19 (238637 upstream) : DSEL (663966 downstream)																																			---	---	---	---
TMX3	54495	broad.mit.edu	37	18	66381141	66381141	+	Intron	DEL	A	-	-	rs139944394		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66381141delA	uc002lkf.2	-						CCDC102B_uc002lkk.2_5'Flank|TMX3_uc010xez.1_Intron|TMX3_uc010xfa.1_Intron|TMX3_uc002lkg.3_Intron|CCDC102B_uc002lkh.2_5'Flank	NM_019022	NP_061895			thioredoxin domain containing 10 precursor						cell redox homeostasis|glycerol ether metabolic process	endoplasmic reticulum membrane|integral to membrane	electron carrier activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			skin(1)	1																		---	---	---	---
CCDC102B	79839	broad.mit.edu	37	18	66715460	66715460	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66715460delT	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	67042585	67042586	+	IGR	INS	-	AC	AC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67042585_67042586insAC								CCDC102B (320159 upstream) : DOK6 (25705 downstream)																																			---	---	---	---
DOK6	220164	broad.mit.edu	37	18	67279686	67279701	+	Intron	DEL	TGTGCGAGCGTGCATA	-	-	rs79406085	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67279686_67279701delTGTGCGAGCGTGCATA	uc002lkl.2	+							NM_152721	NP_689934			docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)																---	---	---	---
SOCS6	9306	broad.mit.edu	37	18	67985852	67985853	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67985852_67985853delTT	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	68512644	68512644	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68512644delA								SOCS6 (515210 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69456731	69456731	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69456731delT								None (None upstream) : CBLN2 (747184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	70659551	70659551	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70659551delT								NETO1 (124741 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	70919515	70919516	+	Intron	INS	-	AA	AA	rs148319485	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70919515_70919516insAA	uc002lla.1	-						uc002llb.2_Intron					Homo sapiens cDNA clone IMAGE:3842655.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	71145649	71145650	+	IGR	DEL	AC	-	-	rs149651237	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71145649_71145650delAC								NETO1 (610839 upstream) : FBXO15 (594938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71181504	71181505	+	IGR	INS	-	TC	TC	rs140986211	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71181504_71181505insTC								NETO1 (646694 upstream) : FBXO15 (559083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71682693	71682693	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71682693delT								None (None upstream) : FBXO15 (57895 downstream)																																			---	---	---	---
ZNF407	55628	broad.mit.edu	37	18	72335116	72335117	+	Intron	INS	-	GT	GT	rs141207596	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72335116_72335117insGT	uc002llu.2	+							NM_001146190	NP_001139662			zinc finger protein 407 isoform 3						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)														---	---	---	---
ZNF407	55628	broad.mit.edu	37	18	72369858	72369863	+	Intron	DEL	TTCTTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72369858_72369863delTTCTTC	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)												OREG0025055	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ZNF407	55628	broad.mit.edu	37	18	72585669	72585670	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72585669_72585670delAA	uc002llw.2	+						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	73121666	73121666	+	IGR	DEL	T	-	-	rs77088186		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73121666delT								TSHZ1 (119766 upstream) : C18orf62 (161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73200663	73200663	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73200663delT								C18orf62 (61074 upstream) : ZNF516 (870956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73317992	73317993	+	IGR	DEL	AT	-	-	rs34467811		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73317992_73317993delAT								C18orf62 (178403 upstream) : ZNF516 (753626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73971542	73971543	+	IGR	DEL	AG	-	-	rs9945736	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73971542_73971543delAG								C18orf62 (831953 upstream) : ZNF516 (100076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	74351694	74351694	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74351694delG								LOC284276 (79911 upstream) : ZNF236 (184422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	74408415	74408415	+	IGR	DEL	T	-	-	rs79760386		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74408415delT								LOC284276 (136632 upstream) : ZNF236 (127701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75627171	75627172	+	IGR	INS	-	CAC	CAC	rs139159811	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75627171_75627172insCAC								GALR1 (645077 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76636627	76636628	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76636627_76636628delTT								None (None upstream) : SALL3 (103647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76727889	76727889	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76727889delT								None (None upstream) : SALL3 (12386 downstream)																																			---	---	---	---
SALL3	27164	broad.mit.edu	37	18	76737714	76737714	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76737714delA	uc002lmt.2	+							NM_171999	NP_741996			sal-like 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)														---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	76919099	76919099	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76919099delT	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmy.1_Intron|ATP9B_uc002lmz.1_Intron	NM_198531	NP_940933			ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)														---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	76960564	76960564	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76960564delA	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmy.1_Intron|ATP9B_uc002lmz.1_Intron	NM_198531	NP_940933			ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)														---	---	---	---
CTDP1	9150	broad.mit.edu	37	18	77455214	77455214	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77455214delT	uc002lnh.1	+						CTDP1_uc002lni.1_Intron|CTDP1_uc010drd.1_Intron	NM_004715	NP_004706			CTD (carboxy-terminal domain, RNA polymerase II,						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)														---	---	---	---
CTDP1	9150	broad.mit.edu	37	18	77496904	77496905	+	Intron	INS	-	GT	GT	rs34988895		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77496904_77496905insGT	uc002lnh.1	+						CTDP1_uc002lni.1_Intron|CTDP1_uc010drd.1_Intron	NM_004715	NP_004706			CTD (carboxy-terminal domain, RNA polymerase II,						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	481338	481338	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:481338delG								ODF3L2 (6355 upstream) : MADCAM1 (15152 downstream)																																			---	---	---	---
PALM	5064	broad.mit.edu	37	19	712394	712394	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:712394delT	uc002lpm.1	+						PALM_uc010xft.1_Intron|PALM_uc002lpn.1_Intron	NM_002579	NP_002570			paralemmin isoform 1						cellular component movement|negative regulation of adenylate cyclase activity|negative regulation of dopamine receptor signaling pathway|positive regulation of filopodium assembly|regulation of cell shape	cytoplasmic membrane-bounded vesicle|filopodium membrane|integral to plasma membrane					0		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)														---	---	---	---
ARID3A	1820	broad.mit.edu	37	19	954120	954121	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:954120_954121insG	uc002lql.2	+							NM_005224	NP_005215			AT rich interactive domain 3A (BRIGHT- like)							cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
CNN2	1265	broad.mit.edu	37	19	1035393	1035394	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1035393_1035394insC	uc002lqu.2	+						CNN2_uc002lqt.1_Intron|CNN2_uc010drz.1_Intron|CNN2_uc002lqv.2_Intron|CNN2_uc010xgb.1_Intron|CNN2_uc010xgc.1_Intron	NM_004368	NP_004359			calponin 2 isoform a						actomyosin structure organization|cellular response to mechanical stimulus|regulation of actin filament-based process	cell-cell junction|stress fiber	actin binding|calmodulin binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SBNO2	22904	broad.mit.edu	37	19	1145122	1145123	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1145122_1145123delAG	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)														---	---	---	---
SBNO2	22904	broad.mit.edu	37	19	1147432	1147433	+	Intron	DEL	GG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1147432_1147433delGG	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)														---	---	---	---
STK11	6794	broad.mit.edu	37	19	1216579	1216579	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1216579delA	uc002lrl.1	+							NM_000455	NP_000446			serine/threonine protein kinase 11						anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|magnesium ion binding|protein serine/threonine kinase activity	p.0?(19)|p.?(2)		lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1)	266		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)|Renal(1328;0.0183)|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)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)			14	D|Mis|N|F|S		NSCLC|pancreatic	jejunal harmartoma|ovarian|testicular|pancreatic			Peutz-Jeghers_syndrome	TSP Lung(3;<1E-08)			---	---	---	---
STK11	6794	broad.mit.edu	37	19	1218144	1218145	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1218144_1218145delAA	uc002lrl.1	+							NM_000455	NP_000446			serine/threonine protein kinase 11						anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|magnesium ion binding|protein serine/threonine kinase activity	p.0?(19)|p.?(2)		lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1)	266		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)|Renal(1328;0.0183)|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)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)			14	D|Mis|N|F|S		NSCLC|pancreatic	jejunal harmartoma|ovarian|testicular|pancreatic			Peutz-Jeghers_syndrome	TSP Lung(3;<1E-08)			---	---	---	---
NDUFS7	374291	broad.mit.edu	37	19	1381341	1381342	+	5'Flank	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1381341_1381342insA	uc002lse.3	+						NDUFS7_uc002lsf.2_5'Flank|NDUFS7_uc002lsh.2_5'Flank|NDUFS7_uc002lsg.2_5'Flank	NM_024407	NP_077718			NADH-ubiquinone oxidoreductase Fe-S protein 7						mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|transport	mitochondrial respiratory chain complex I	4 iron, 4 sulfur cluster binding|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding|quinone binding				0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)|Breast(49;0.00186)|Lung NSC(49;0.00292)|all_lung(49;0.00419)		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)	NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	1441504	1441505	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1441504_1441505delTT								RPS15 (1012 upstream) : APC2 (8643 downstream)																																			---	---	---	---
REEP6	92840	broad.mit.edu	37	19	1496717	1496718	+	Intron	DEL	GC	-	-	rs34524945	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1496717_1496718delGC	uc002ltc.2	+							NM_138393	NP_612402			receptor accessory protein 6							integral to membrane					0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		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)														---	---	---	---
ADAMTSL5	339366	broad.mit.edu	37	19	1509610	1509611	+	Intron	INS	-	GGAA	GGAA	rs141155053	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1509610_1509611insGGAA	uc002ltd.2	-						ADAMTSL5_uc010dsl.2_Intron|ADAMTSL5_uc010xgq.1_Intron	NM_213604	NP_998769			ADAMTS-like 5 precursor							proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		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	1874492	1874492	+	IGR	DEL	A	-	-	rs78761630	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1874492delA								KLF16 (10928 upstream) : FAM108A1 (2484 downstream)																																			---	---	---	---
DOT1L	84444	broad.mit.edu	37	19	2172193	2172193	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2172193delT	uc002lvb.3	+							NM_032482	NP_115871			DOT1-like, histone H3 methyltransferase							nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
LMNB2	84823	broad.mit.edu	37	19	2428237	2428237	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2428237delA	uc002lvy.2	-	12					TIMM13_uc002lvx.1_5'Flank|LMNB2_uc010dtc.1_RNA	NM_032737	NP_116126			lamin B2							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)														---	---	---	---
LMNB2	84823	broad.mit.edu	37	19	2439736	2439738	+	Intron	DEL	TTT	-	-	rs111663913		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2439736_2439738delTTT	uc002lvy.2	-						LMNB2_uc002lwa.1_Intron	NM_032737	NP_116126			lamin B2							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)														---	---	---	---
GNG7	2788	broad.mit.edu	37	19	2594961	2594962	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2594961_2594962insA	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	2703631	2703631	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2703631delT	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)														---	---	---	---
ZNF556	80032	broad.mit.edu	37	19	2868720	2868721	+	Intron	DEL	TT	-	-	rs72349473		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2868720_2868721delTT	uc002lwp.1	+						ZNF556_uc002lwq.2_Intron	NM_024967	NP_079243			zinc finger protein 556						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)	3				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
TLE6	79816	broad.mit.edu	37	19	2974839	2974839	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2974839delA	uc002lwu.2	+						TLE6_uc002lwt.2_5'Flank|TLE6_uc010dtg.2_5'Flank	NM_024760	NP_079036			transducin-like enhancer of split 6 isoform 2						regulation of transcription, DNA-dependent	nucleus				ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
TLE2	7089	broad.mit.edu	37	19	3013522	3013522	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3013522delA	uc002lww.2	-						TLE2_uc010xhb.1_Intron|TLE2_uc010dth.2_Intron|TLE2_uc010xhc.1_Intron|TLE2_uc010dti.2_Intron|TLE2_uc010xhd.1_Intron	NM_003260	NP_003251			transducin-like enhancer protein 2 isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
TLE2	7089	broad.mit.edu	37	19	3020446	3020446	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3020446delA	uc002lww.2	-						TLE2_uc010xhb.1_Intron|TLE2_uc010dth.2_Intron|TLE2_uc010xhc.1_Intron|TLE2_uc010dti.2_Intron|TLE2_uc010xhd.1_Intron	NM_003260	NP_003251			transducin-like enhancer protein 2 isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	3131446	3131446	+	IGR	DEL	C	-	-	rs66993077		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3131446delC								GNA11 (9994 upstream) : GNA15 (4745 downstream)																																			---	---	---	---
GNA15	2769	broad.mit.edu	37	19	3163193	3163193	+	3'UTR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3163193delC	uc002lxf.2	+	7						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)												OREG0025150	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CELF5	60680	broad.mit.edu	37	19	3292907	3292907	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3292907delA	uc002lxm.2	+						CELF5_uc002lxl.1_Intron|CELF5_uc010dtj.1_Intron|CELF5_uc010xhg.1_Intron|CELF5_uc002lxn.2_Intron	NM_021938	NP_068757			bruno-like 5, RNA binding protein						mRNA processing	cytoplasm|nucleus	nucleotide binding|RNA binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	3332802	3332803	+	IGR	INS	-	CTTA	CTTA	rs138483500	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3332802_3332803insCTTA								CELF5 (35731 upstream) : NFIC (26813 downstream)																																			---	---	---	---
APBA3	9546	broad.mit.edu	37	19	3752611	3752611	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3752611delC	uc002lyp.1	-	8	1467	c.1290delG	c.(1288-1290)GGGfs	p.G430fs	APBA3_uc002lyo.1_Frame_Shift_Del_p.G188fs	NM_004886	NP_004877	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding,	430	PDZ 1.				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)														---	---	---	---
MRPL54	116541	broad.mit.edu	37	19	3765025	3765027	+	Intron	DEL	AAA	-	-	rs79735606		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3765025_3765027delAAA	uc002lyq.3	+							NM_172251	NP_758455			mitochondrial ribosomal protein L54 precursor							mitochondrion|ribosome					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)														---	---	---	---
RAX2	84839	broad.mit.edu	37	19	3775038	3775039	+	5'Flank	INS	-	GG	GG	rs144568953	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3775038_3775039insGG	uc002lys.2	-						RAX2_uc010dtp.1_5'Flank|RAX2_uc002lyr.2_5'Flank	NM_032753	NP_116142			retina and anterior neural fold homeobox 2						response to stimulus|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ZBTB7A	51341	broad.mit.edu	37	19	4047691	4047691	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4047691delT	uc002lzh.2	-	3					ZBTB7A_uc002lzi.2_3'UTR	NM_015898	NP_056982			zinc finger and BTB domain containing 7A						cell differentiation|multicellular organismal development|transcription, DNA-dependent	nucleus	DNA binding|histone acetyltransferase binding|zinc ion binding			pancreas(1)|skin(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.014)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	4148014	4148014	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4148014delA								MAP2K2 (23888 upstream) : CREB3L3 (5615 downstream)																																			---	---	---	---
STAP2	55620	broad.mit.edu	37	19	4338860	4338860	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4338860delC	uc002mab.2	-						STAP2_uc002mac.2_5'Flank|STAP2_uc002mad.2_5'UTR	NM_001013841	NP_001013863			signal transducing adaptor family member 2							cytoplasm|nucleus	protein binding			central_nervous_system(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
KDM4B	23030	broad.mit.edu	37	19	4992462	4992462	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4992462delT	uc002mbq.3	+						KDM4B_uc010xil.1_Intron	NM_015015	NP_055830			jumonji domain containing 2B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1																		---	---	---	---
KDM4B	23030	broad.mit.edu	37	19	4993425	4993426	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4993425_4993426delAA	uc002mbq.3	+						KDM4B_uc010xil.1_Intron	NM_015015	NP_055830			jumonji domain containing 2B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1																		---	---	---	---
KDM4B	23030	broad.mit.edu	37	19	5003820	5003820	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5003820delA	uc002mbq.3	+						KDM4B_uc010xil.1_Intron	NM_015015	NP_055830			jumonji domain containing 2B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1																		---	---	---	---
KDM4B	23030	broad.mit.edu	37	19	5131158	5131158	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5131158delC	uc002mbq.3	+	12	1613	c.1387delC	c.(1387-1389)CCCfs	p.P463fs	KDM4B_uc010xim.1_Frame_Shift_Del_p.P497fs|KDM4B_uc002mbr.3_Frame_Shift_Del_p.P221fs	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B	463	Pro-rich.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1																		---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5296724	5296725	+	Intron	INS	-	GGAGG	GGAGG	rs143777415	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5296724_5296725insGGAGG	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	5525163	5525166	+	IGR	DEL	CTAT	-	-	rs59947674		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5525163_5525166delCTAT								ZNRF4 (68297 upstream) : PLAC2 (33014 downstream)																																			---	---	---	---
SAFB2	9667	broad.mit.edu	37	19	5587282	5587282	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5587282delG	uc002mcd.2	-	21	3046	c.2834delC	c.(2833-2835)CCGfs	p.P945fs		NM_014649	NP_055464	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	945	Interacts with SAFB1.				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)														---	---	---	---
TMEM146	257062	broad.mit.edu	37	19	5737242	5737242	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5737242delT	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																		---	---	---	---
CAPS	828	broad.mit.edu	37	19	5915207	5915207	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5915207delC	uc002mdt.2	+						CAPS_uc002mdu.2_Intron	NM_004058	NP_004049			calcyphosine isoform a						intracellular signal transduction	cytoplasm	calcium ion binding				0																		---	---	---	---
SLC25A23	79085	broad.mit.edu	37	19	6442572	6442572	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6442572delT	uc002mex.1	-						SLC25A23_uc010duu.1_Intron|SLC25A23_uc002meu.2_Intron|SLC25A23_uc002mev.2_Intron|SLC25A23_uc002mew.1_Intron|SLC25A23_uc010xjd.1_Intron	NM_024103	NP_077008			solute carrier family 25, member 23						transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	6485325	6485325	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6485325delA								DENND1C (3527 upstream) : TUBB4 (9005 downstream)																																			---	---	---	---
TUBB4	10382	broad.mit.edu	37	19	6498740	6498740	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6498740delC	uc002mfg.1	-						TUBB4_uc002mff.1_Intron	NM_006087	NP_006078			tubulin, beta 4						'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(2)	2		Hepatocellular(1079;0.00213)|Renal(1328;0.0183)		Lung(535;3.23e-05)|STAD - Stomach adenocarcinoma(1328;8.24e-05)|GBM - Glioblastoma multiforme(1328;0.00839)|READ - Rectum adenocarcinoma(264;0.155)														---	---	---	---
C3	718	broad.mit.edu	37	19	6717048	6717048	+	Intron	DEL	T	-	-	rs113677312		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6717048delT	uc002mfm.2	-							NM_000064	NP_000055			complement component 3 precursor						complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)														---	---	---	---
VAV1	7409	broad.mit.edu	37	19	6843492	6843495	+	Intron	DEL	TTTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6843492_6843495delTTTG	uc002mfu.1	+						VAV1_uc010xjh.1_Intron|VAV1_uc010dva.1_Intron|VAV1_uc002mfv.1_Intron	NM_005428	NP_005419			vav 1 guanine nucleotide exchange factor						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16																		---	---	---	---
EMR4P	326342	broad.mit.edu	37	19	6975193	6975193	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6975193delC	uc010xjk.1	-						EMR4P_uc010dve.1_Intron	NR_024075				RecName: Full=Putative EGF-like module-containing mucin-like hormone receptor-like 4; AltName: Full=G-protein coupled receptor 127; AltName: Full=G-protein coupled receptor PGR16; Flags: Precursor;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	6999561	6999562	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6999561_6999562insA								EMR4P (8704 upstream) : FLJ25758 (5402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	7095675	7095675	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7095675delA								ZNF557 (7699 upstream) : INSR (16591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	7105437	7105438	+	IGR	DEL	AA	-	-	rs71821054		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7105437_7105438delAA								ZNF557 (17461 upstream) : INSR (6828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	7107495	7107497	+	IGR	DEL	TGA	-	-	rs12982611		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7107495_7107497delTGA								ZNF557 (19519 upstream) : INSR (4769 downstream)																																			---	---	---	---
INSR	3643	broad.mit.edu	37	19	7112872	7112872	+	3'UTR	DEL	A	-	-	rs1366601	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7112872delA	uc002mgd.1	-	22					INSR_uc002mge.1_3'UTR	NM_000208	NP_000199			insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
INSR	3643	broad.mit.edu	37	19	7153140	7153141	+	Intron	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7153140_7153141insCA	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199			insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	7637747	7637747	+	IGR	DEL	T	-	-	rs67449995		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7637747delT								PNPLA6 (11095 upstream) : KIAA1543 (23041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	7639290	7639292	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7639290_7639292delAAA								PNPLA6 (12638 upstream) : KIAA1543 (21496 downstream)																																			---	---	---	---
KIAA1543	57662	broad.mit.edu	37	19	7665825	7665828	+	Intron	DEL	CATT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7665825_7665828delCATT	uc002mgv.3	+						KIAA1543_uc002mgu.3_Intron	NM_020902	NP_065953			NEZHA isoform 2						epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	7738413	7738415	+	IGR	DEL	CTC	-	-	rs12977928		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7738413_7738415delCTC								RETN (3073 upstream) : C19orf59 (3528 downstream)																																			---	---	---	---
ELAVL1	1994	broad.mit.edu	37	19	8057473	8057473	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8057473delG	uc002mjb.2	-							NM_001419	NP_001410			ELAV-like 1						3'-UTR-mediated mRNA stabilization|multicellular organismal development	cytoplasm|nucleoplasm	identical protein binding|mRNA binding|nucleotide binding				0																		---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8188250	8188250	+	Intron	DEL	G	-	-	rs10419582	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8188250delG	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	8281265	8281266	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8281265_8281266delAA	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	8498756	8498758	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8498756_8498758delAAA	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																		---	---	---	---
MARCH2	51257	broad.mit.edu	37	19	8503865	8503865	+	3'UTR	DEL	C	-	-	rs35091049		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8503865delC	uc002mjv.2	+	6					MARCH2_uc002mjw.2_3'UTR|MARCH2_uc002mjx.2_3'UTR	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																		---	---	---	---
PRAM1	84106	broad.mit.edu	37	19	8558678	8558678	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8558678delT	uc002mkd.2	-						PRAM1_uc002mkc.2_Intron	NM_032152	NP_115528			PML-RARA regulated adaptor molecule 1								lipid binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	8834333	8834338	+	IGR	DEL	TGTGTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8834333_8834338delTGTGTG								ACTL9 (25161 upstream) : OR2Z1 (7053 downstream)																																			---	---	---	---
ZNF558	148156	broad.mit.edu	37	19	8926473	8926474	+	Intron	INS	-	AG	AG	rs145744383	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8926473_8926474insAG	uc002mkn.1	-						ZNF558_uc010xkh.1_Intron|ZNF558_uc010dwg.1_Intron	NM_144693	NP_653294			zinc finger protein 558						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
OR1M1	125963	broad.mit.edu	37	19	9202341	9202341	+	5'Flank	DEL	A	-	-	rs113355974		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9202341delA	uc010xkj.1	+							NM_001004456	NP_001004456			olfactory receptor, family 1, subfamily M,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	9315424	9315424	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9315424delT								OR7D2 (15931 upstream) : OR7D4 (9151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9342375	9342376	+	IGR	INS	-	T	T	rs78978446		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9342375_9342376insT								OR7D4 (16862 upstream) : OR7E24 (19344 downstream)																																			---	---	---	---
ZNF560	147741	broad.mit.edu	37	19	9591324	9591325	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9591324_9591325delAA	uc002mlp.1	-						ZNF560_uc010dwr.1_Intron	NM_152476	NP_689689			zinc finger protein 560						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																		---	---	---	---
ZNF426	79088	broad.mit.edu	37	19	9639888	9639888	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9639888delT	uc002mlq.2	-	8	1097	c.833delA	c.(832-834)AAGfs	p.K278fs	ZNF426_uc010dws.2_Frame_Shift_Del_p.K240fs	NM_024106	NP_077011	Q9BUY5	ZN426_HUMAN	zinc finger protein 426	278					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	10058673	10058674	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10058673_10058674insA								OLFM2 (11603 upstream) : COL5A3 (11563 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	10190355	10190355	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10190355delA								C3P1 (5544 upstream) : C19orf66 (6451 downstream)																																			---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10260036	10260036	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10260036delA	uc002mng.2	-						DNMT1_uc010xlc.1_Intron|DNMT1_uc002mnh.2_Intron|DNMT1_uc010xld.1_Intron	NM_001379	NP_001370			DNA (cytosine-5-)-methyltransferase 1 isoform b						chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)													---	---	---	---
RAVER1	125950	broad.mit.edu	37	19	10443952	10443952	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10443952delC	uc002moa.2	-							NM_133452	NP_597709			RAVER1							cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)															---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10575900	10575900	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10575900delT	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)													---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10578444	10578444	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10578444delT	uc002moj.2	+	15					PDE4A_uc002mok.2_3'UTR|PDE4A_uc002mol.2_3'UTR|PDE4A_uc002mom.2_3'UTR|PDE4A_uc002mon.2_3'UTR|PDE4A_uc002moo.2_3'UTR	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)													---	---	---	---
DNM2	1785	broad.mit.edu	37	19	10896496	10896496	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10896496delT	uc002mps.1	+						DNM2_uc010dxk.2_Intron|DNM2_uc002mpt.1_Intron|DNM2_uc002mpv.1_Intron|DNM2_uc002mpu.1_Intron|DNM2_uc010dxl.1_Intron|DNM2_uc002mpw.2_Intron	NM_001005361	NP_001005361			dynamin 2 isoform 2						G2/M transition of mitotic cell cycle|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|post-Golgi vesicle-mediated transport|receptor internalization|signal transduction|synaptic vesicle transport|transferrin transport	cell junction|cytosol|Golgi membrane|microtubule|postsynaptic density|postsynaptic membrane	GTP binding|GTPase activity|microtubule binding			central_nervous_system(2)|skin(2)|ovary(1)|breast(1)	6			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)															---	---	---	---
SMARCA4	6597	broad.mit.edu	37	19	11074610	11074610	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11074610delA	uc002mqf.3	+						SMARCA4_uc010dxp.2_Intron|SMARCA4_uc010dxo.2_Intron|SMARCA4_uc002mqe.2_Intron	NM_003072	NP_003063			SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)						F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				---	---	---	---
SMARCA4	6597	broad.mit.edu	37	19	11104328	11104329	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11104328_11104329insT	uc002mqf.3	+						SMARCA4_uc010dxp.2_Intron|SMARCA4_uc010dxo.2_Intron|SMARCA4_uc002mqg.1_Intron|SMARCA4_uc010dxq.2_Intron|SMARCA4_uc010dxr.2_Intron|SMARCA4_uc002mqj.3_Intron|SMARCA4_uc010dxs.2_Intron|SMARCA4_uc002mqe.2_Intron	NM_003072	NP_003063			SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)						F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				---	---	---	---
SMARCA4	6597	broad.mit.edu	37	19	11162088	11162088	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11162088delC	uc002mqf.3	+						SMARCA4_uc010dxp.2_Intron|SMARCA4_uc010dxo.2_Intron|SMARCA4_uc010dxq.2_Intron|SMARCA4_uc010dxr.2_Intron|SMARCA4_uc002mqj.3_Intron|SMARCA4_uc010dxs.2_Intron|SMARCA4_uc002mqh.3_Intron	NM_003072	NP_003063			SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity			lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)						F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				---	---	---	---
LDLR	3949	broad.mit.edu	37	19	11203121	11203122	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11203121_11203122delTT	uc002mqk.3	+						LDLR_uc010xlk.1_Intron|LDLR_uc010xll.1_Intron|LDLR_uc010xlm.1_Intron|LDLR_uc010xln.1_Intron|LDLR_uc010xlo.1_Intron	NM_000527	NP_000518			low density lipoprotein receptor precursor						cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)|skin(2)	4		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)													---	---	---	---
DOCK6	57572	broad.mit.edu	37	19	11348985	11348985	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11348985delG	uc002mqs.3	-						DOCK6_uc010xlq.1_5'Flank|LOC55908_uc010dxw.2_Intron|LOC55908_uc010dxx.2_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																		---	---	---	---
LPPR2	64748	broad.mit.edu	37	19	11472996	11472996	+	Intron	DEL	C	-	-	rs3833252		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11472996delC	uc002mre.1	+						LPPR2_uc002mrf.1_Intron|LPPR2_uc010dxy.1_5'UTR	NM_022737	NP_073574			lipid phosphate phosphatase-related protein type							integral to membrane	phosphatidate phosphatase activity			large_intestine(1)	1																		---	---	---	---
ELAVL3	1995	broad.mit.edu	37	19	11589322	11589322	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11589322delG	uc002mry.1	-						ELAVL3_uc002mrx.1_Intron	NM_001420	NP_001411			ELAV-like protein 3 isoform 1						cell differentiation|nervous system development		AU-rich element binding|nucleotide binding			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
ELOF1	84337	broad.mit.edu	37	19	11665592	11665592	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11665592delA	uc002mse.1	-						ELOF1_uc002msd.1_Intron	NM_032377	NP_115753			elongation factor 1 homolog (ELF1, S.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding				0																		---	---	---	---
ACP5	54	broad.mit.edu	37	19	11690159	11690160	+	5'Flank	INS	-	TTGG	TTGG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11690159_11690160insTTGG	uc002msg.3	-						ACP5_uc002msh.3_5'Flank|ACP5_uc002msi.3_5'Flank|ACP5_uc002msj.3_5'Flank|ACP5_uc010dye.1_5'Flank	NM_001611	NP_001602			acid phosphatase 5, tartrate resistant						water-soluble vitamin metabolic process	cytosol|integral to membrane|lysosome	acid phosphatase activity|ferric iron binding|ferrous iron binding			central_nervous_system(1)	1																		---	---	---	---
ZNF627	199692	broad.mit.edu	37	19	11725762	11725766	+	Intron	DEL	TTTTT	-	-	rs5827132		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11725762_11725766delTTTTT	uc002msk.2	+						ZNF627_uc010dyf.2_Intron	NM_145295	NP_660338			zinc finger protein 627						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
ZNF433	163059	broad.mit.edu	37	19	12128614	12128616	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12128614_12128616delTTT	uc002msy.1	-						uc002msx.1_Intron|ZNF433_uc002msz.1_Intron	NM_001080411	NP_001073880			zinc finger protein 433						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	12153951	12153952	+	IGR	INS	-	AC	AC	rs144240858	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12153951_12153952insAC								ZNF433 (7426 upstream) : ZNF878 (668 downstream)																																			---	---	---	---
ZNF136	7695	broad.mit.edu	37	19	12286012	12286013	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12286012_12286013delTT	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																		---	---	---	---
ZNF791	163049	broad.mit.edu	37	19	12740044	12740044	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12740044delA	uc002mua.2	+	4	1863	c.1701delA	c.(1699-1701)TTAfs	p.L567fs	ZNF791_uc010xml.1_Frame_Shift_Del_p.L535fs|ZNF791_uc010dyu.1_Frame_Shift_Del_p.L458fs|ZNF791_uc010xmm.1_Frame_Shift_Del_p.L458fs	NM_153358	NP_699189	Q3KP31	ZN791_HUMAN	zinc finger protein 791	567	C2H2-type 17.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	12796680	12796680	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12796680delT	uc010xmo.1	+						uc002mul.1_5'Flank					Homo sapiens cDNA clone IMAGE:9057076.																														---	---	---	---
ASNA1	439	broad.mit.edu	37	19	12852573	12852573	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12852573delA	uc002muv.2	+						ASNA1_uc002muw.2_Intron	NM_004317	NP_004308			arsA arsenite transporter, ATP-binding, homolog						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)													---	---	---	---
HOOK2	29911	broad.mit.edu	37	19	12881521	12881521	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12881521delG	uc002muy.2	-						HOOK2_uc002muz.2_Intron	NM_013312	NP_037444			hook homolog 2 isoform 1						early endosome to late endosome transport|endocytosis|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|protein transport	centrosome|FHF complex|microtubule	identical protein binding|microtubule binding			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
FARSA	2193	broad.mit.edu	37	19	13036039	13036040	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13036039_13036040delTT	uc002mvs.2	-						FARSA_uc002mvt.2_Intron|FARSA_uc010xmv.1_Intron|FARSA_uc010dyy.1_Intron	NM_004461	NP_004452			phenylalanyl-tRNA synthetase, alpha subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|phenylalanine-tRNA ligase activity|protein binding|tRNA binding			ovary(1)	1					L-Phenylalanine(DB00120)													---	---	---	---
NFIX	4784	broad.mit.edu	37	19	13184679	13184679	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13184679delC	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	13244169	13244170	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13244169_13244170insA	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																		---	---	---	---
STX10	8677	broad.mit.edu	37	19	13259498	13259498	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13259498delA	uc010xnb.1	-						STX10_uc002mwn.2_Intron|STX10_uc002mwo.2_Intron|STX10_uc010xna.1_Intron|STX10_uc010xnc.1_Intron|IER2_uc002mwr.2_5'Flank	NM_003765	NP_003756			syntaxin 10						Golgi vesicle transport|intracellular protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane	SNAP receptor activity				0			OV - Ovarian serous cystadenocarcinoma(19;3.41e-21)															---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13350601	13350602	+	Intron	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13350601_13350602delGT	uc010dze.2	-						CACNA1A_uc010xnd.1_Intron|CACNA1A_uc002mwx.3_Intron|CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_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	13480914	13480914	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13480914delT	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	13734959	13734959	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13734959delA								CACNA1A (117685 upstream) : CCDC130 (107615 downstream)																																			---	---	---	---
C19orf53	28974	broad.mit.edu	37	19	13888064	13888065	+	Intron	DEL	TT	-	-	rs143465006		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13888064_13888065delTT	uc002mxg.2	+							NM_014047	NP_054766			Leydig cell tumor 10 kDa protein											ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;7.7e-24)|Epithelial(5;2.53e-19)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	13893253	13893253	+	IGR	DEL	T	-	-	rs75676127		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13893253delT								C19orf53 (3669 upstream) : ZSWIM4 (13021 downstream)																																			---	---	---	---
RFX1	5989	broad.mit.edu	37	19	14094503	14094504	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14094503_14094504insC	uc002mxv.2	-						RFX1_uc010dzi.2_Intron	NM_002918	NP_002909			regulatory factor X1						immune response	nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			lung(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)															---	---	---	---
RLN3	117579	broad.mit.edu	37	19	14140168	14140169	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14140168_14140169delTT	uc002mxw.1	+						IL27RA_uc002mxx.2_5'Flank|RLN3_uc010dzj.1_Intron	NM_080864	NP_543140			relaxin 3 preproprotein							extracellular region	hormone activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	14355737	14355737	+	IGR	DEL	T	-	-	rs111469615		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14355737delT								LPHN1 (38740 upstream) : CD97 (136476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	14356573	14356573	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14356573delT								LPHN1 (39576 upstream) : CD97 (135640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	14392464	14392464	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14392464delT								LPHN1 (75467 upstream) : CD97 (99749 downstream)																																			---	---	---	---
GIPC1	10755	broad.mit.edu	37	19	14590165	14590165	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14590165delA	uc002myt.2	-						GIPC1_uc002myu.2_Intron|GIPC1_uc002myv.2_Intron|GIPC1_uc002myw.2_Intron|GIPC1_uc002myx.2_Intron|GIPC1_uc002myy.2_Intron	NM_005716	NP_005707			regulator of G-protein signalling 19 interacting						endothelial cell migration|G-protein coupled receptor protein signaling pathway|glutamate secretion|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|protein targeting|regulation of protein stability|regulation of synaptic plasticity|synaptic transmission	cell cortex|dendritic shaft|dendritic spine|membrane fraction|soluble fraction|synaptic vesicle|vesicle membrane	actin binding|myosin binding|protein homodimerization activity|receptor binding				0																		---	---	---	---
GIPC1	10755	broad.mit.edu	37	19	14607581	14607584	+	5'Flank	DEL	CATT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14607581_14607584delCATT	uc002myt.2	-						GIPC1_uc002myu.2_5'Flank|GIPC1_uc002myv.2_5'Flank|GIPC1_uc002myw.2_5'Flank|GIPC1_uc002myx.2_5'Flank|GIPC1_uc002myy.2_5'Flank	NM_005716	NP_005707			regulator of G-protein signalling 19 interacting						endothelial cell migration|G-protein coupled receptor protein signaling pathway|glutamate secretion|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|protein targeting|regulation of protein stability|regulation of synaptic plasticity|synaptic transmission	cell cortex|dendritic shaft|dendritic spine|membrane fraction|soluble fraction|synaptic vesicle|vesicle membrane	actin binding|myosin binding|protein homodimerization activity|receptor binding				0																		---	---	---	---
TECR	9524	broad.mit.edu	37	19	14643924	14643924	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14643924delA	uc002mza.2	+						TECR_uc002mzb.2_Intron|TECR_uc010xns.1_Intron|TECR_uc002mzc.2_Intron|TECR_uc002mzd.2_Intron	NM_138501	NP_612510			glycoprotein, synaptic 2						fatty acid elongation|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	integral to endoplasmic reticulum membrane	trans-2-enoyl-CoA reductase (NADPH) activity|very long-chain-acyl-CoA dehydrogenase activity				0																		---	---	---	---
EMR3	84658	broad.mit.edu	37	19	14762192	14762193	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14762192_14762193delAA	uc002mzi.3	-						EMR3_uc010dzp.2_Intron|EMR3_uc010xnv.1_Intron	NM_032571	NP_115960			egf-like module-containing mucin-like receptor						neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6																		---	---	---	---
OR7A17	26333	broad.mit.edu	37	19	14992169	14992169	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14992169delT	uc010xob.1	-							NM_030901	NP_112163			olfactory receptor, family 7, subfamily A,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Ovarian(108;0.203)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	14997642	14997644	+	IGR	DEL	AAA	-	-	rs34351275		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14997642_14997644delAAA								OR7A17 (5475 upstream) : OR7C2 (54657 downstream)																																			---	---	---	---
BRD4	23476	broad.mit.edu	37	19	15362869	15362869	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15362869delT	uc002nar.2	-						BRD4_uc002nas.2_Intron	NM_058243	NP_490597			bromodomain-containing protein 4 isoform long						interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle	condensed nuclear chromosome|cytoplasm	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)					T	NUT|C15orf55	lethal midline carcinoma of young people						OREG0025318	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
AKAP8L	26993	broad.mit.edu	37	19	15511206	15511208	+	Intron	DEL	TTT	-	-	rs113004130		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15511206_15511208delTTT	uc002naw.1	-						AKAP8L_uc002nax.1_Intron|AKAP8L_uc010xoh.1_Intron|AKAP8L_uc002nay.1_Intron	NM_014371	NP_055186			A kinase (PRKA) anchor protein 8-like							cytoplasm|nuclear matrix	DEAD/H-box RNA helicase binding|DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
PGLYRP2	114770	broad.mit.edu	37	19	15591561	15591561	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15591561delT	uc002nbf.3	-						PGLYRP2_uc002nbg.3_5'Flank	NM_052890	NP_443122			peptidoglycan recognition protein 2 precursor						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																		---	---	---	---
CYP4F22	126410	broad.mit.edu	37	19	15643068	15643068	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15643068delC	uc002nbh.3	+							NM_173483	NP_775754			cytochrome P450, family 4, subfamily F,							endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen			ovary(1)|pancreas(1)	2																		---	---	---	---
CYP4F22	126410	broad.mit.edu	37	19	15658794	15658807	+	Intron	DEL	GAGAGAGAGAGAGG	-	-	rs113751386	by1000genomes;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15658794_15658807delGAGAGAGAGAGAGG	uc002nbh.3	+							NM_173483	NP_775754			cytochrome P450, family 4, subfamily F,							endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	15692169	15692170	+	IGR	INS	-	TTCC	TTCC	rs147074248	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15692169_15692170insTTCC								CYP4F22 (29042 upstream) : CYP4F8 (33859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	15705681	15705681	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15705681delT								CYP4F22 (42554 upstream) : CYP4F8 (20348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	16111960	16111960	+	IGR	DEL	T	-	-	rs76317518		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16111960delT								OR10H4 (51193 upstream) : LOC126536 (14484 downstream)																																			---	---	---	---
CIB3	117286	broad.mit.edu	37	19	16279646	16279646	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16279646delT	uc002nds.2	-						CIB3_uc010eae.2_Intron|CIB3_uc010eaf.2_Intron|CIB3_uc010eag.2_Intron	NM_054113	NP_473454			DNA-dependent protein kinase catalytic								calcium ion binding			ovary(1)	1																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17124647	17124647	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17124647delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	17144120	17144120	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17144120delT								CPAMD8 (6495 upstream) : HAUS8 (16453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	17159520	17159520	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17159520delA								CPAMD8 (21895 upstream) : HAUS8 (1053 downstream)																																			---	---	---	---
MYO9B	4650	broad.mit.edu	37	19	17276198	17276198	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17276198delT	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-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
USHBP1	83878	broad.mit.edu	37	19	17376949	17376949	+	5'Flank	DEL	T	-	-	rs35256297		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17376949delT	uc002nfs.1	-						USHBP1_uc002nft.1_5'Flank|USHBP1_uc010xpk.1_5'Flank|USHBP1_uc010eam.1_5'Flank|C19orf62_uc010xpl.1_5'Flank|C19orf62_uc002nfu.2_5'Flank|C19orf62_uc002nfv.2_5'Flank|C19orf62_uc010ean.2_5'Flank|C19orf62_uc002nfw.2_5'Flank	NM_031941	NP_114147			Usher syndrome 1C binding protein 1								PDZ domain binding			ovary(1)	1																		---	---	---	---
GLT25D1	79709	broad.mit.edu	37	19	17684624	17684624	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17684624delA	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																		---	---	---	---
GLT25D1	79709	broad.mit.edu	37	19	17686498	17686499	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17686498_17686499insT	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	17750846	17750846	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17750846delT	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																		---	---	---	---
FCHO1	23149	broad.mit.edu	37	19	17881110	17881110	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17881110delA	uc010ebb.2	+						FCHO1_uc002nhg.3_Intron|FCHO1_uc002nhh.2_Intron|FCHO1_uc010xpw.1_Intron|FCHO1_uc010ebc.1_Intron	NM_001161358	NP_001154830			FCH domain only 1 isoform b											breast(1)	1																		---	---	---	---
JAK3	3718	broad.mit.edu	37	19	17958446	17958446	+	Intron	DEL	C	-	-	rs117462032	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17958446delC	uc002nhn.3	-						JAK3_uc010ebh.2_Intron|JAK3_uc002nho.2_Intron|JAK3_uc010xpx.1_Intron|JAK3_uc010xpy.1_Intron	NM_000215	NP_000206			Janus kinase 3						B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	56							2	Mis		acute megakaryocytic leukemia|								---	---	---	---
Unknown	0	broad.mit.edu	37	19	17965977	17965978	+	IGR	INS	-	A	A	rs79472525		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17965977_17965978insA								JAK3 (7136 upstream) : RPL18A (4753 downstream)																																			---	---	---	---
SLC5A5	6528	broad.mit.edu	37	19	17993148	17993151	+	Intron	DEL	TTTT	-	-	rs78838816		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17993148_17993151delTTTT	uc002nhr.3	+							NM_000453	NP_000444			solute carrier family 5 (sodium iodide						cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
PIK3R2	5296	broad.mit.edu	37	19	18273703	18273703	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18273703delA	uc002nia.1	+						PIK3R2_uc002nib.1_Intron|PIK3R2_uc010ebi.1_Intron	NM_005027	NP_005018			phosphoinositide-3-kinase, regulatory subunit 2						fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|negative regulation of anti-apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	GTPase activator activity|phosphatidylinositol 3-kinase regulator activity|protein binding			lung(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
MPV17L2	84769	broad.mit.edu	37	19	18301347	18301347	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18301347delA	uc002nid.2	+						MPV17L2_uc010ebj.2_5'Flank	NM_032683	NP_116072			MPV17 mitochondrial membrane protein-like 2							integral to membrane					0																		---	---	---	---
PDE4C	5143	broad.mit.edu	37	19	18358107	18358107	+	Intron	DEL	T	-	-	rs4808121	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18358107delT	uc002nik.3	-						PDE4C_uc002nil.3_Intron	NM_000923	NP_000914			phosphodiesterase 4C isoform PDE4C-1						signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|skin(2)|central_nervous_system(1)	5					Dyphylline(DB00651)													---	---	---	---
KIAA1683	80726	broad.mit.edu	37	19	18382118	18382118	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18382118delA	uc002nin.2	-						KIAA1683_uc010ebn.2_Intron|KIAA1683_uc010xqe.1_Intron	NM_025249	NP_079525			KIAA1683 isoform b							mitochondrion				ovary(2)	2																		---	---	---	---
ELL	8178	broad.mit.edu	37	19	18629147	18629147	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18629147delA	uc002njh.2	-						ELL_uc010ebq.2_Intron	NM_006532	NP_006523			elongation factor RNA polymerase II						positive regulation of transcription elongation, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	Cajal body|nuclear speck|transcription elongation factor complex	protein binding			lung(1)	1				GBM - Glioblastoma multiforme(1328;7.81e-07)				T	MLL	AL								---	---	---	---
CRTC1	23373	broad.mit.edu	37	19	18810019	18810019	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18810019delC	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	18923052	18923052	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18923052delT								COMP (20938 upstream) : UPF1 (19692 downstream)																																			---	---	---	---
NCAN	1463	broad.mit.edu	37	19	19347411	19347411	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19347411delT	uc002nlz.2	+						NCAN_uc010ecc.1_Intron	NM_004386	NP_004377			chondroitin sulfate proteoglycan 3 precursor						axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)															---	---	---	---
GATAD2A	54815	broad.mit.edu	37	19	19501842	19501843	+	Intron	INS	-	G	G	rs117896238	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19501842_19501843insG	uc010xqt.1	+						GATAD2A_uc010xqu.1_Intron	NM_017660	NP_060130			GATA zinc finger domain containing 2A						DNA methylation|negative regulation of transcription, DNA-dependent	nuclear speck|NuRD complex	protein binding, bridging|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
GMIP	51291	broad.mit.edu	37	19	19753552	19753552	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19753552delG	uc002nnd.2	-						GMIP_uc010xrb.1_Intron|GMIP_uc010xrc.1_Intron	NM_016573	NP_057657			GEM interacting protein						negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1																		---	---	---	---
ZNF101	94039	broad.mit.edu	37	19	19780721	19780721	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19780721delA	uc002nni.1	+						ZNF101_uc010ecg.1_Intron|ZNF101_uc002nnj.1_Intron	NM_033204	NP_149981			zinc finger protein 101						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	19804454	19804455	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19804454_19804455insT								ZNF101 (13091 upstream) : ZNF14 (16826 downstream)																																			---	---	---	---
ZNF506	440515	broad.mit.edu	37	19	19916707	19916707	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19916707delA	uc010eci.2	-						ZNF506_uc002nog.2_Intron|ZNF506_uc002noh.3_Intron|ZNF506_uc010ecj.1_Intron	NM_001099269	NP_001092739			zinc finger protein 506 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF506	440515	broad.mit.edu	37	19	19925514	19925514	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19925514delA	uc010eci.2	-						ZNF506_uc002nog.2_Intron|ZNF506_uc002noh.3_Intron|ZNF506_uc010ecj.1_Intron	NM_001099269	NP_001092739			zinc finger protein 506 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF90	7643	broad.mit.edu	37	19	20236361	20236362	+	RNA	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20236361_20236362delAA	uc002nos.1	+	5		c.1037_1038delAA			ZNF90_uc002not.1_RNA					Synthetic construct DNA, clone: pF1KB9685, Homo sapiens ZNF90 gene for zinc finger protein 90, without stop codon, in Flexi system.							Golgi apparatus|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
ZNF826	664701	broad.mit.edu	37	19	20520770	20520771	+	Intron	INS	-	AC	AC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20520770_20520771insAC	uc002now.1	-						ZNF826_uc010ecl.1_Intron|ZNF826_uc010xrf.1_Intron					Homo sapiens cDNA FLJ44894 fis, clone BRAMY3000692, moderately similar to Zinc finger protein 91.												0																		---	---	---	---
ZNF737	100129842	broad.mit.edu	37	19	20735139	20735139	+	Intron	DEL	A	-	-	rs146002311		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20735139delA	uc002npa.2	-							NM_001159293	NP_001152765			zinc finger protein 737						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZNF626	199777	broad.mit.edu	37	19	20834733	20834733	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20834733delT	uc002npb.1	-						ZNF626_uc002npc.1_Intron|ZNF626_uc002npd.1_Intron	NM_001076675	NP_001070143			zinc finger protein 626 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
ZNF708	7562	broad.mit.edu	37	19	21484117	21484117	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21484117delA	uc002npq.1	-						ZNF708_uc002npr.1_Intron|ZNF708_uc010ecs.1_Intron	NM_021269	NP_067092			zinc finger protein 708						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(4)|skin(2)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	21680866	21680866	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21680866delT	uc002nqa.2	+						uc002nqb.2_Intron|uc002nqc.2_Intron					Homo sapiens cDNA FLJ40062 fis, clone TESOP2000090.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	21747287	21747290	+	IGR	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21747287_21747290delAAAA								ZNF429 (8219 upstream) : ZNF100 (159554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	21817582	21817583	+	IGR	DEL	GC	-	-	rs55707945		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21817582_21817583delGC								ZNF429 (78514 upstream) : ZNF100 (89261 downstream)																																			---	---	---	---
ZNF43	7594	broad.mit.edu	37	19	22000909	22000910	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22000909_22000910delTT	uc002nqj.2	-						ZNF43_uc010ecv.2_Intron|ZNF43_uc002nql.2_Intron|ZNF43_uc002nqm.2_Intron|ZNF43_uc002nqk.2_Intron	NM_003423	NP_003414			zinc finger protein 43						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	23226470	23226470	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23226470delA								ZNF99 (273686 upstream) : ZNF91 (294949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23344835	23344835	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23344835delT								ZNF99 (392051 upstream) : ZNF91 (176584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23423856	23423856	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23423856delA	uc010xri.1	-											SubName: Full=cDNA FLJ56866, moderately similar to Zinc finger protein 43;																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	23515148	23515148	+	IGR	DEL	T	-	-	rs79227082		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23515148delT								ZNF99 (562364 upstream) : ZNF91 (6271 downstream)																																			---	---	---	---
ZNF675	171392	broad.mit.edu	37	19	23867447	23867447	+	Intron	DEL	A	-	-	rs35113707		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23867447delA	uc002nri.2	-							NM_138330	NP_612203			zinc finger protein 675						bone resorption|cytokine-mediated signaling pathway|hemopoiesis|I-kappaB kinase/NF-kappaB cascade|negative regulation of JNK cascade|negative regulation of osteoclast differentiation|negative regulation of protein kinase activity|negative regulation of transcription, DNA-dependent|regulation of ossification|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|kidney(1)	2		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	24065805	24065805	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24065805delT								RPSAP58 (54888 upstream) : ZNF254 (150442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27845351	27845352	+	IGR	DEL	AA	-	-	rs71221284		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27845351_27845352delAA								None (None upstream) : LOC148189 (436050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28322738	28322739	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28322738_28322739delTT								LOC148189 (37890 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28881307	28881308	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28881307_28881308insA								LOC148189 (596459 upstream) : LOC148145 (574732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29095387	29095388	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29095387_29095388delAA	uc002nsa.1	-											Homo sapiens cDNA clone IMAGE:5297319, with apparent retained intron.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	29144995	29144996	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29144995_29144996delAA	uc002nsa.1	-											Homo sapiens cDNA clone IMAGE:5297319, with apparent retained intron.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	29506422	29506423	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29506422_29506423delTC								LOC148145 (46367 upstream) : UQCRFS1 (191744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29897354	29897355	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29897354_29897355delAA	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	30113656	30113656	+	IGR	DEL	A	-	-	rs77365344		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30113656delA								POP4 (5494 upstream) : PLEKHF1 (42671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30379206	30379208	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30379206_30379208delAAA								CCNE1 (63988 upstream) : C19orf2 (35343 downstream)																																			---	---	---	---
C19orf2	8725	broad.mit.edu	37	19	30496536	30496536	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30496536delT	uc002nsr.2	+						C19orf2_uc002nsq.2_Intron|C19orf2_uc002nss.2_Intron|C19orf2_uc002nst.2_Intron	NM_003796	NP_003787			RPB5-mediating protein isoform a						protein folding|regulation of transcription from RNA polymerase II promoter|response to virus	DNA-directed RNA polymerase II, core complex|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)|kidney(1)	2	Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)	Hepatocellular(1079;0.137)|Renal(1328;0.228)	STAD - Stomach adenocarcinoma(5;5.36e-06)|Lung(7;0.0144)|LUAD - Lung adenocarcinoma(5;0.115)	STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	30667129	30667129	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30667129delT								C19orf2 (160518 upstream) : ZNF536 (196199 downstream)																																			---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	30957129	30957129	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30957129delA	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	31358146	31358146	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31358146delA								ZNF536 (309181 upstream) : DKFZp566F0947 (282637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31420873	31420874	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31420873_31420874insA								ZNF536 (371908 upstream) : DKFZp566F0947 (219909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31495795	31495796	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31495795_31495796insT								ZNF536 (446830 upstream) : DKFZp566F0947 (144987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32305938	32305938	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32305938delC								TSHZ3 (465748 upstream) : ZNF507 (530576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32475516	32475518	+	IGR	DEL	CTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32475516_32475518delCTT								TSHZ3 (635326 upstream) : ZNF507 (360996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32618736	32618736	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32618736delA								TSHZ3 (778546 upstream) : ZNF507 (217778 downstream)																																			---	---	---	---
ANKRD27	84079	broad.mit.edu	37	19	33113679	33113679	+	Intron	DEL	T	-	-	rs77974943		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33113679delT	uc002ntn.1	-							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)																	---	---	---	---
TDRD12	91646	broad.mit.edu	37	19	33237843	33237844	+	Intron	INS	-	GA	GA	rs139242818	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33237843_33237844insGA	uc002ntq.2	+						TDRD12_uc002ntr.3_Intron					RecName: Full=Tudor domain-containing protein 12; AltName: Full=ES cell-associated transcript 8 protein;								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	Esophageal squamous(110;0.137)																	---	---	---	---
CCDC123	84902	broad.mit.edu	37	19	33406825	33406826	+	Intron	DEL	AA	-	-	rs72330999		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33406825_33406826delAA	uc002nty.2	-						CCDC123_uc002ntx.2_Intron|CCDC123_uc010edg.2_Intron|CCDC123_uc002ntz.1_Intron	NM_032816	NP_116205			coiled-coil domain containing 123							centrosome|spindle pole					0	Esophageal squamous(110;0.137)																	---	---	---	---
CCDC123	84902	broad.mit.edu	37	19	33439158	33439158	+	Intron	DEL	T	-	-	rs12710001	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33439158delT	uc002nty.2	-						CCDC123_uc002ntx.2_Intron|CCDC123_uc010edg.2_Intron|CCDC123_uc002ntz.1_Intron|CCDC123_uc002nua.2_Intron|CCDC123_uc002nub.1_Intron	NM_032816	NP_116205			coiled-coil domain containing 123							centrosome|spindle pole					0	Esophageal squamous(110;0.137)																	---	---	---	---
CCDC123	84902	broad.mit.edu	37	19	33439642	33439642	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33439642delT	uc002nty.2	-						CCDC123_uc002ntx.2_Intron|CCDC123_uc010edg.2_Intron|CCDC123_uc002ntz.1_Intron|CCDC123_uc002nua.2_Intron|CCDC123_uc002nub.1_Intron	NM_032816	NP_116205			coiled-coil domain containing 123							centrosome|spindle pole					0	Esophageal squamous(110;0.137)																	---	---	---	---
RHPN2	85415	broad.mit.edu	37	19	33536715	33536715	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33536715delA	uc002nuf.2	-						RHPN2_uc010xro.1_Intron	NM_033103	NP_149094			rhophilin, Rho GTPase binding protein 2						signal transduction	perinuclear region of cytoplasm	protein binding			central_nervous_system(5)|ovary(1)	6	Esophageal squamous(110;0.137)																	---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33618047	33618047	+	Intron	DEL	A	-	-	rs113508660		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33618047delA	uc002nug.1	+						GPATCH1_uc002nuh.1_Intron	NM_018025	NP_060495			G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)																	---	---	---	---
WDR88	126248	broad.mit.edu	37	19	33640564	33640564	+	Intron	DEL	T	-	-	rs113775920		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33640564delT	uc002nui.2	+							NM_173479	NP_775750			PQQ repeat and WD repeat domain containing											ovary(1)|breast(1)|central_nervous_system(1)	3	Esophageal squamous(110;0.137)																	---	---	---	---
PEPD	5184	broad.mit.edu	37	19	33888526	33888527	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33888526_33888527insG	uc002nur.3	-						PEPD_uc010xrr.1_Intron|PEPD_uc010xrs.1_Intron	NM_000285	NP_000276			prolidase isoform 1						cellular amino acid metabolic process|collagen catabolic process|proteolysis		aminopeptidase activity|dipeptidase activity|manganese ion binding|metallocarboxypeptidase activity			ovary(2)	2	Esophageal squamous(110;0.137)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	34600385	34600386	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34600385_34600386insA								KCTD15 (293720 upstream) : LSM14A (62966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34730255	34730255	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34730255delT								LSM14A (9836 upstream) : KIAA0355 (15201 downstream)																																			---	---	---	---
KIAA0355	9710	broad.mit.edu	37	19	34781261	34781261	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34781261delA	uc002nvd.3	+						KIAA0355_uc010edk.1_Intron	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-4292-01	TCGA-BR-4292-01									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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	35128511	35128512	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35128511_35128512insA	uc002nvo.1	-											Homo sapiens cDNA FLJ36176 fis, clone TESTI2026491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	35872479	35872480	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35872479_35872480insT								FFAR3 (21092 upstream) : FFAR2 (66723 downstream)																																			---	---	---	---
COX6B1	1340	broad.mit.edu	37	19	36144037	36144037	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36144037delT	uc002oav.2	+							NM_001863	NP_001854			cytochrome c oxidase subunit VIb polypeptide 1						respiratory electron transport chain	mitochondrial inner membrane|mitochondrial intermembrane space	cytochrome-c oxidase activity				0	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
TMEM149	79713	broad.mit.edu	37	19	36233251	36233251	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36233251delA	uc002obc.2	-						TMEM149_uc002obb.2_5'Flank|TMEM149_uc002obd.3_Intron|TMEM149_uc010xsy.1_Intron|TMEM149_uc010eej.2_Intron	NM_024660	NP_078936			transmembrane protein 149 precursor							integral to membrane|plasma membrane	protein binding|receptor activity				0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	36488257	36488257	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36488257delA								SDHAF1 (1044 upstream) : C19orf46 (5745 downstream)																																			---	---	---	---
CLIP3	25999	broad.mit.edu	37	19	36508304	36508304	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36508304delT	uc010eeq.1	-	11	1782	c.1500delA	c.(1498-1500)AAAfs	p.K500fs	uc002ocy.2_Intron|CLIP3_uc002ocz.1_Frame_Shift_Del_p.K500fs	NM_015526	NP_056341	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	500	GoLD.				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)															---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36563013	36563013	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36563013delC	uc002odc.2	+						WDR62_uc002odd.2_Intron|WDR62_uc002odb.2_Intron	NM_173636	NP_775907			WD repeat domain 62 isoform 2						cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36564439	36564439	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36564439delC	uc002odc.2	+						WDR62_uc002odd.2_Intron|WDR62_uc002odb.2_Intron	NM_173636	NP_775907			WD repeat domain 62 isoform 2						cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
ZFP14	57677	broad.mit.edu	37	19	36860704	36860704	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36860704delA	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)																	---	---	---	---
ZFP82	284406	broad.mit.edu	37	19	36885147	36885147	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36885147delA	uc002ody.1	-							NM_133466	NP_597723			zinc finger protein 82 homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
ZNF529	57711	broad.mit.edu	37	19	37053120	37053121	+	Intron	DEL	AA	-	-	rs77728894	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37053120_37053121delAA	uc002oeh.3	-						ZNF529_uc010xth.1_Intron|ZNF529_uc010xti.1_Intron|ZNF529_uc002oeg.3_Intron	NM_020951	NP_066002			zinc finger protein 529 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	Esophageal squamous(110;0.198)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	37268040	37268042	+	IGR	DEL	TTT	-	-	rs77700185		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37268040_37268042delTTT								ZNF567 (53792 upstream) : ZNF790 (40291 downstream)																																			---	---	---	---
ZNF793	390927	broad.mit.edu	37	19	38028415	38028415	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38028415delT	uc010efm.2	+	8	1297	c.855delT	c.(853-855)TGTfs	p.C285fs	ZNF793_uc010xts.1_Frame_Shift_Del_p.C285fs|ZNF793_uc010efo.2_Intron	NM_001013659	NP_001013681	Q6ZN11	ZN793_HUMAN	zinc finger protein 793	285	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF540	163255	broad.mit.edu	37	19	38102620	38102620	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38102620delA	uc002ogq.2	+	5	771	c.439delA	c.(439-441)AAAfs	p.K147fs	ZNF540_uc002ogu.2_Frame_Shift_Del_p.K147fs|ZNF540_uc010efq.2_Frame_Shift_Del_p.K115fs	NM_152606	NP_689819	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	147					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)															---	---	---	---
ZNF781	163115	broad.mit.edu	37	19	38162209	38162210	+	Intron	INS	-	GC	GC	rs146261664		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38162209_38162210insGC	uc002ogy.2	-						ZNF781_uc002ogz.2_Intron	NM_152605	NP_689818			zinc finger protein 781						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF607	84775	broad.mit.edu	37	19	38206505	38206508	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38206505_38206508delAAAA	uc002ohc.1	-						ZNF607_uc002ohb.1_Intron	NM_032689	NP_116078			zinc finger protein 607						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)															---	---	---	---
SPINT2	10653	broad.mit.edu	37	19	38764866	38764867	+	Intron	DEL	AA	-	-	rs72005477		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38764866_38764867delAA	uc002ohr.1	+						SPINT2_uc002ohs.1_Intron	NM_021102	NP_066925			serine protease inhibitor, Kunitz type, 2						cellular component movement	cytoplasm|extracellular region|integral to membrane|soluble fraction	serine-type endopeptidase inhibitor activity				0	all_cancers(60;6.83e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
SPRED3	399473	broad.mit.edu	37	19	38881699	38881699	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38881699delT	uc002oim.2	+						SPRED3_uc002oil.1_Intron	NM_001042522	NP_001035987			sprouty-related, EVH1 domain containing 3						multicellular organismal development					central_nervous_system(2)|lung(1)|skin(1)	4	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38988611	38988611	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38988611delA	uc002oit.2	+						RYR1_uc002oiu.2_Intron|RYR1_uc002oiv.1_Intron	NM_000540	NP_000531			skeletal muscle ryanodine receptor isoform 1						muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39009568	39009569	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39009568_39009569delAA	uc002oit.2	+						RYR1_uc002oiu.2_Intron|RYR1_uc002oiv.1_Intron|RYR1_uc010xuf.1_Intron	NM_000540	NP_000531			skeletal muscle ryanodine receptor isoform 1						muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	39507423	39507423	+	IGR	DEL	A	-	-	rs75068247		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39507423delA								FBXO17 (41043 upstream) : FBXO27 (7241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	39535888	39535890	+	IGR	DEL	AAA	-	-	rs34400871		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39535888_39535890delAAA								FBXO27 (12690 upstream) : PAPL (39055 downstream)																																			---	---	---	---
PAK4	10298	broad.mit.edu	37	19	39665496	39665496	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39665496delG	uc002okj.1	+						PAK4_uc002okl.1_Intron|PAK4_uc002okn.1_Intron|PAK4_uc002okm.1_Intron|PAK4_uc002oko.1_Intron|PAK4_uc002okp.1_Intron	NM_001014831	NP_001014831			p21-activated kinase 4 isoform 1						cellular component movement|signal transduction	Golgi apparatus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	39700027	39700028	+	IGR	INS	-	CA	CA	rs146852966	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39700027_39700028insCA								SYCN (5121 upstream) : IL28B (34245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	39715673	39715673	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39715673delA								SYCN (20767 upstream) : IL28B (18600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	39721964	39721964	+	IGR	DEL	T	-	-	rs112728861		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39721964delT								SYCN (27058 upstream) : IL28B (12309 downstream)																																			---	---	---	---
PAF1	54623	broad.mit.edu	37	19	39878781	39878781	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39878781delA	uc002old.2	-						PAF1_uc002ole.1_Intron|PAF1_uc010xuv.1_Intron	NM_019088	NP_061961			Paf1, RNA polymerase II associated factor,						histone H2B ubiquitination|histone monoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			pancreas(1)	1	all_cancers(60;9.14e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.88e-06)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)															---	---	---	---
SUPT5H	6829	broad.mit.edu	37	19	39934207	39934207	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39934207delT	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)															---	---	---	---
CLC	1178	broad.mit.edu	37	19	40226833	40226833	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40226833delA	uc002omh.2	-							NM_001828	NP_001819			Charcot-Leyden crystal protein						lipid catabolic process|multicellular organismal development		carboxylesterase activity|lysophospholipase activity|sugar binding				0	all_cancers(60;2.99e-06)|all_lung(34;4.7e-08)|Lung NSC(34;5.46e-08)|Ovarian(47;0.06)	Renal(1328;0.000147)|Hepatocellular(1079;0.0202)|Myeloproliferative disorder(2;0.0255)	Epithelial(26;6.43e-25)|OV - Ovarian serous cystadenocarcinoma(5;1.07e-24)|all cancers(26;8.38e-23)	GBM - Glioblastoma multiforme(1328;4.97e-06)|STAD - Stomach adenocarcinoma(1328;0.00655)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	40257020	40257020	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40257020delA								CLC (28352 upstream) : LEUTX (10214 downstream)																																	OREG0025465	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	19	40258736	40258737	+	IGR	DEL	AA	-	-	rs78992382		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40258736_40258737delAA								CLC (30068 upstream) : LEUTX (8497 downstream)																																			---	---	---	---
PSMC4	5704	broad.mit.edu	37	19	40480653	40480654	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40480653_40480654insC	uc002omq.2	+	6	628_629	c.591_592insC	c.(589-594)GATCCCfs	p.D197fs	PSMC4_uc002omr.2_Frame_Shift_Ins_p.D166fs	NM_006503	NP_006494	P43686	PRS6B_HUMAN	proteasome 26S ATPase subunit 4 isoform 1	197_198					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	mitochondrion|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding			ovary(1)	1	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)																	---	---	---	---
HIPK4	147746	broad.mit.edu	37	19	40889492	40889492	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)															---	---	---	---
LTBP4	8425	broad.mit.edu	37	19	41132910	41132911	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41132910_41132911insC	uc002ooh.1	+	32	4217_4218	c.4217_4218insC	c.(4216-4218)CGCfs	p.R1406fs	LTBP4_uc002oog.1_Frame_Shift_Ins_p.R1369fs|LTBP4_uc002ooi.1_Frame_Shift_Ins_p.R1339fs|LTBP4_uc002ooj.1_Frame_Shift_Ins_p.R279fs|LTBP4_uc002ook.1_Frame_Shift_Ins_p.R540fs|LTBP4_uc002ool.1_Frame_Shift_Ins_p.R418fs|LTBP4_uc010xvp.1_Frame_Shift_Ins_p.R166fs	NM_001042544	NP_001036009	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding	1406					growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
EGLN2	112398	broad.mit.edu	37	19	41289585	41289585	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41289585delG	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)													---	---	---	---
EGLN2	112398	broad.mit.edu	37	19	41306222	41306222	+	Intron	DEL	T	-	-	rs35057638		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41306222delT	uc010ehd.2	+						EGLN2_uc002opg.3_Intron|EGLN2_uc002oph.2_Intron|EGLN2_uc002opi.2_5'UTR	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)													---	---	---	---
CYP2A7	1549	broad.mit.edu	37	19	41520702	41520703	+	Intron	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41520702_41520703delAG	uc002opo.2	-						CYP2B6_uc002opr.1_Intron|CYP2B6_uc010xvu.1_Intron	NM_000764	NP_000755			cytochrome P450, family 2, subfamily A,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	41616962	41616962	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41616962delT								CYP2A13 (14864 upstream) : CYP2F1 (3391 downstream)																																			---	---	---	---
AXL	558	broad.mit.edu	37	19	41726502	41726502	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41726502delG	uc010ehj.2	+						CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Intron|AXL_uc010ehk.2_Intron	NM_021913	NP_068713			AXL receptor tyrosine kinase isoform 1							integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13																		---	---	---	---
AXL	558	broad.mit.edu	37	19	41738902	41738903	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41738902_41738903insT	uc010ehj.2	+						CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Intron|AXL_uc010ehk.2_Intron	NM_021913	NP_068713			AXL receptor tyrosine kinase isoform 1							integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13																		---	---	---	---
AXL	558	broad.mit.edu	37	19	41749512	41749512	+	Intron	DEL	C	-	-	rs139678321	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41749512delC	uc010ehj.2	+						CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Intron|AXL_uc010ehk.2_Intron	NM_021913	NP_068713			AXL receptor tyrosine kinase isoform 1							integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13																		---	---	---	---
HNRNPUL1	11100	broad.mit.edu	37	19	41790917	41790919	+	Intron	DEL	AAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41790917_41790919delAAG	uc002oqb.3	+						CYP2F1_uc010xvw.1_Intron|HNRNPUL1_uc002opz.3_Intron|HNRNPUL1_uc002oqa.3_Intron|HNRNPUL1_uc010ehm.2_Intron|HNRNPUL1_uc002oqc.3_Intron|HNRNPUL1_uc002oqe.3_Intron|HNRNPUL1_uc002oqd.3_Intron|HNRNPUL1_uc010ehn.2_Intron|HNRNPUL1_uc010eho.2_Intron|HNRNPUL1_uc010xvy.1_Intron|HNRNPUL1_uc010ehp.2_Intron|HNRNPUL1_uc010ehl.1_Intron	NM_007040	NP_008971			heterogeneous nuclear ribonucleoprotein U-like 1						nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	enzyme binding|RNA binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
HNRNPUL1	11100	broad.mit.edu	37	19	41797899	41797899	+	Intron	DEL	C	-	-	rs66916970		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41797899delC	uc002oqb.3	+						CYP2F1_uc010xvw.1_Intron|HNRNPUL1_uc002opz.3_Intron|HNRNPUL1_uc002oqa.3_Intron|HNRNPUL1_uc010ehm.2_Intron|HNRNPUL1_uc002oqc.3_Intron|HNRNPUL1_uc002oqe.3_Intron|HNRNPUL1_uc002oqd.3_Intron|HNRNPUL1_uc010ehn.2_Intron|HNRNPUL1_uc010eho.2_Intron|HNRNPUL1_uc010xvy.1_Intron|HNRNPUL1_uc010ehp.2_Intron|HNRNPUL1_uc010ehl.1_Intron	NM_007040	NP_008971			heterogeneous nuclear ribonucleoprotein U-like 1						nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	enzyme binding|RNA binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
CCDC97	90324	broad.mit.edu	37	19	41828552	41828554	+	In_Frame_Del	DEL	GAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41828552_41828554delGAG	uc002oqg.2	+	5	1086_1088	c.964_966delGAG	c.(964-966)GAGdel	p.E324del	CYP2F1_uc010xvw.1_Intron	NM_052848	NP_443080	Q96F63	CCD97_HUMAN	coiled-coil domain containing 97	324											0																		---	---	---	---
CYP2F1	1572	broad.mit.edu	37	19	41836152	41836152	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41836152delA	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	41884727	41884730	+	Intron	DEL	GTGA	-	-	rs71731386		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41884727_41884730delGTGA	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																		---	---	---	---
CYP2F1	1572	broad.mit.edu	37	19	41935532	41935532	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41935532delA	uc010xvw.1	+						B3GNT8_uc002oqs.2_5'Flank|B3GNT8_uc002oqt.1_5'Flank					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																		---	---	---	---
CYP2F1	1572	broad.mit.edu	37	19	42053123	42053126	+	Intron	DEL	ACAC	-	-	rs112343451		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42053123_42053126delACAC	uc010xvw.1	+						CEACAM21_uc002orc.1_5'Flank					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																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	42102319	42102319	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42102319delA								CEACAM21 (9123 upstream) : CEACAM4 (23025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	42328534	42328537	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42328534_42328537delTTTT								CEACAM3 (12943 upstream) : LYPD4 (12613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	42466793	42466793	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42466793delA								RABAC1 (3265 upstream) : ATP1A3 (3943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	42680234	42680237	+	IGR	DEL	AAAA	-	-	rs79917901		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42680234_42680237delAAAA								POU2F2 (43604 upstream) : DEDD2 (22515 downstream)																																			---	---	---	---
PSG5	5673	broad.mit.edu	37	19	43674451	43674451	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43674451delT	uc002ovu.2	-						PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_Intron|PSG5_uc002ovx.2_Intron|PSG5_uc002ovv.2_Intron|PSG5_uc002ovw.2_Intron	NM_002781	NP_002772			pregnancy specific beta-1-glycoprotein 5						female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)																---	---	---	---
PSG9	5678	broad.mit.edu	37	19	43773926	43773938	+	5'Flank	DEL	ACACACAGAAGAG	-	-	rs138857035		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43773926_43773938delACACACAGAAGAG	uc002owd.3	-						PSG9_uc002owe.3_5'Flank|PSG9_uc010xwm.1_5'Flank|PSG9_uc002owf.3_5'Flank|PSG9_uc002owg.2_5'Flank|PSG9_uc002owh.2_5'Flank	NM_002784	NP_002775			pregnancy specific beta-1-glycoprotein 9						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)																---	---	---	---
CADM4	199731	broad.mit.edu	37	19	44127619	44127619	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44127619delG	uc002oxc.1	-							NM_145296	NP_660339			cell adhesion molecule 4 precursor						cell adhesion	integral to membrane					0		Prostate(69;0.0199)																---	---	---	---
KCNN4	3783	broad.mit.edu	37	19	44281477	44281478	+	Intron	DEL	GG	-	-	rs72282703		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44281477_44281478delGG	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)													---	---	---	---
ZNF221	7638	broad.mit.edu	37	19	44458941	44458941	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44458941delA	uc002oxx.2	+						ZNF221_uc010ejb.1_Intron	NM_013359	NP_037491			zinc finger protein 221						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1		Prostate(69;0.0352)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	44686849	44686849	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44686849delA								ZNF226 (5013 upstream) : ZNF227 (29842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	44695919	44695920	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44695919_44695920delAA								ZNF226 (14083 upstream) : ZNF227 (20771 downstream)																																			---	---	---	---
ZNF235	9310	broad.mit.edu	37	19	44803174	44803174	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44803174delT	uc002oza.3	-						ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_Intron|ZNF235_uc002ozb.3_Intron|ZNF235_uc010xwx.1_Intron	NM_004234	NP_004225			zinc finger protein 93 homolog						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	45244520	45244523	+	IGR	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45244520_45244523delAAAA								CEACAM16 (30536 upstream) : BCL3 (7455 downstream)																																			---	---	---	---
BCL3	602	broad.mit.edu	37	19	45255336	45255337	+	Intron	DEL	CA	-	-	rs66870773		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45255336_45255337delCA	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 								---	---	---	---
Unknown	0	broad.mit.edu	37	19	45270072	45270073	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45270072_45270073insA								BCL3 (6772 upstream) : CBLC (11053 downstream)																																			---	---	---	---
RELB	5971	broad.mit.edu	37	19	45532108	45532108	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45532108delT	uc002paj.1	+							NM_006509	NP_006500			reticuloendotheliosis viral oncogene homolog B							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00986)														---	---	---	---
GEMIN7	79760	broad.mit.edu	37	19	45588595	45588595	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45588595delA	uc002pap.1	+						GEMIN7_uc002paq.1_Intron|GEMIN7_uc002par.1_Intron	NM_001007270	NP_001007271			gemin 7						ncRNA metabolic process|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding			ovary(1)	1		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0131)														---	---	---	---
TRAPPC6A	79090	broad.mit.edu	37	19	45669172	45669173	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45669172_45669173delTT	uc002paw.2	-						TRAPPC6A_uc002pav.2_Intron					SubName: Full=TRAPPC6Adelta29-42; SubName: Full=Trafficking protein particle complex 6A, isoform CRA_a;						vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00872)|GBM - Glioblastoma multiforme(486;0.233)														---	---	---	---
ERCC1	2067	broad.mit.edu	37	19	45969530	45969530	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45969530delA	uc002pbu.1	-						FOSB_uc002pbw.2_5'Flank|FOSB_uc002pbx.3_5'Flank|FOSB_uc010eke.2_5'Flank|FOSB_uc002pby.3_5'Flank|FOSB_uc010eka.1_5'Flank|FOSB_uc010ekb.1_5'Flank|FOSB_uc010ekc.1_5'Flank|FOSB_uc010ekf.2_5'Flank|FOSB_uc010ekd.1_5'Flank|FOSB_uc010ekg.2_5'Flank					SubName: Full=cDNA FLJ34720 fis, clone MESAN2005724, highly similar to DNA EXCISION REPAIR PROTEIN ERCC-1;						mitotic recombination|negative regulation of telomere maintenance|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|nucleotide-excision repair, DNA incision, 5'-to lesion|response to oxidative stress|transcription-coupled nucleotide-excision repair	cytoplasm|nuclear chromosome, telomeric region|nucleoplasm|nucleotide-excision repair complex	damaged DNA binding|endonuclease activity|protein C-terminus binding|protein domain specific binding|single-stranded DNA binding			ovary(2)	2		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)									NER					---	---	---	---
EML2	24139	broad.mit.edu	37	19	46113146	46113148	+	Intron	DEL	TTT	-	-	rs73050333	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46113146_46113148delTTT	uc002pcn.2	-						EML2_uc002pco.2_Intron|EML2_uc002pcp.2_Intron|EML2_uc010xxl.1_Intron|EML2_uc010xxm.1_Intron	NM_012155	NP_036287			echinoderm microtubule associated protein like						sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)														---	---	---	---
GIPR	2696	broad.mit.edu	37	19	46177864	46177865	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46177864_46177865delAA	uc002pcu.1	+						GIPR_uc002pct.1_Intron|GIPR_uc010xxp.1_Intron|GIPR_uc010xxq.1_Intron|MIR642_hsa-mir-642|MI0003657_5'Flank	NM_000164	NP_000155			gastric inhibitory polypeptide receptor						generation of precursor metabolites and energy|response to nutrient	integral to membrane|plasma membrane				skin(1)	1		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)														---	---	---	---
QPCTL	54814	broad.mit.edu	37	19	46206596	46206596	+	3'UTR	DEL	T	-	-	rs111583500		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46206596delT	uc010xxr.1	+	7					QPCTL_uc010ekn.2_3'UTR	NM_017659	NP_060129			glutaminyl-peptide cyclotransferase-like isoform						peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase|proteolysis	Golgi membrane|integral to membrane	acyltransferase activity|glutaminyl-peptide cyclotransferase activity|peptidase activity|protein binding|zinc ion binding			skin(1)	1		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0059)|GBM - Glioblastoma multiforme(486;0.0882)|Epithelial(262;0.208)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	46377670	46377671	+	IGR	INS	-	T	T	rs35586577		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46377670_46377671insT								FOXA3 (616 upstream) : IRF2BP1 (9195 downstream)																																			---	---	---	---
MYPOP	339344	broad.mit.edu	37	19	46398513	46398514	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46398513_46398514insT	uc002pdt.2	-							NM_001012643	NP_001012661			Myb protein P42POP							nucleus	DNA binding				0																		---	---	---	---
CCDC61	729440	broad.mit.edu	37	19	46509050	46509050	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46509050delT	uc002pdw.2	+							NM_001080402	NP_001073871			coiled-coil domain containing 61											ovary(1)	1		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)														---	---	---	---
HIF3A	64344	broad.mit.edu	37	19	46811005	46811005	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46811005delA	uc002peh.2	+						HIF3A_uc002pef.1_Intron|HIF3A_uc002peg.3_Intron|HIF3A_uc010xxx.1_Intron|HIF3A_uc002pei.3_Intron|HIF3A_uc002pej.1_Intron|HIF3A_uc002pek.2_Intron|HIF3A_uc010xxy.1_Intron|HIF3A_uc002pel.2_Intron|HIF3A_uc010xxz.1_Intron	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)														---	---	---	---
PPP5C	5536	broad.mit.edu	37	19	46852548	46852548	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46852548delA	uc002pem.2	+						PPP5C_uc010xya.1_Intron|PPP5C_uc002pen.2_Intron	NM_006247	NP_006238			protein phosphatase 5, catalytic subunit						mitosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein dephosphorylation|transcription, DNA-dependent	Golgi apparatus|nucleus	metal ion binding|protein binding|protein serine/threonine phosphatase activity|signal transducer activity			lung(1)|pancreas(1)	2		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)														---	---	---	---
FKRP	79147	broad.mit.edu	37	19	47252496	47252496	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47252496delG	uc002pfn.2	+						STRN4_uc002pfm.2_5'Flank|STRN4_uc002pfl.2_5'Flank|STRN4_uc010xyf.1_5'Flank|STRN4_uc010xyg.1_5'Flank|FKRP_uc002pfp.2_Intron	NM_024301	NP_077277			fukutin-related protein							extracellular space|Golgi apparatus|rough endoplasmic reticulum|sarcolemma	transferase activity			pancreas(1)	1		all_epithelial(76;5.08e-05)|Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000541)|all cancers(93;0.00128)|Epithelial(262;0.0207)|GBM - Glioblastoma multiforme(486;0.0336)														---	---	---	---
ZC3H4	23211	broad.mit.edu	37	19	47584202	47584202	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47584202delT	uc002pga.3	-						ZC3H4_uc002pgb.1_Intron	NM_015168	NP_055983			zinc finger CCCH-type containing 4								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)														---	---	---	---
ZC3H4	23211	broad.mit.edu	37	19	47616963	47616963	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47616963delA	uc002pga.3	-						ZC3H4_uc002pgb.1_5'Flank	NM_015168	NP_055983			zinc finger CCCH-type containing 4								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)														---	---	---	---
ZC3H4	23211	broad.mit.edu	37	19	47617336	47617336	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47617336delT	uc002pga.3	-						ZC3H4_uc002pgb.1_5'Flank	NM_015168	NP_055983			zinc finger CCCH-type containing 4								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)														---	---	---	---
C5AR1	728	broad.mit.edu	37	19	47814422	47814422	+	Intron	DEL	T	-	-	rs75798874		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47814422delT	uc002pgj.1	+							NM_001736	NP_001727			complement component 5 receptor 1						activation of MAPK activity|activation of phospholipase C activity|cellular defense response|elevation of cytosolic calcium ion concentration|immune response|sensory perception of chemical stimulus	integral to plasma membrane	C5a anaphylatoxin receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_cancers(25;2e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000267)|OV - Ovarian serous cystadenocarcinoma(262;0.000618)|Epithelial(262;0.0142)|GBM - Glioblastoma multiforme(486;0.0242)														---	---	---	---
DHX34	9704	broad.mit.edu	37	19	47864714	47864714	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47864714delA	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)														---	---	---	---
DHX34	9704	broad.mit.edu	37	19	47868036	47868036	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47868036delT	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	47962985	47962986	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47962985_47962986delTG	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	48008832	48008832	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48008832delG	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)														---	---	---	---
ZNF541	84215	broad.mit.edu	37	19	48042555	48042556	+	Intron	DEL	TT	-	-	rs74458720		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48042555_48042556delTT	uc010xyt.1	-						ZNF541_uc002phg.3_Intron|ZNF541_uc010elh.2_Intron|ZNF541_uc010eli.2_Intron	NM_001101419	NP_001094889			zinc finger protein 541						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1																		---	---	---	---
GLTSCR1	29998	broad.mit.edu	37	19	48170280	48170280	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48170280delT	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)														---	---	---	---
GLTSCR2	29997	broad.mit.edu	37	19	48257535	48257535	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48257535delA	uc002phm.2	+						GLTSCR2_uc002phk.2_Intron|GLTSCR2_uc002phl.2_Intron|GLTSCR2_uc010elj.2_Intron|GLTSCR2_uc010elk.1_Intron|SNORD23_uc010ell.2_5'Flank	NM_015710	NP_056525			glioma tumor suppressor candidate region gene 2							nucleolus				central_nervous_system(1)	1		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	48293378	48293378	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48293378delT								SEPW1 (5439 upstream) : TPRX1 (11122 downstream)																																	OREG0025596	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	19	48319069	48319069	+	IGR	DEL	A	-	-	rs74627348		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48319069delA								TPRX1 (12208 upstream) : CRX (6030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	48792358	48792358	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48792358delT								ZNF114 (1495 upstream) : CCDC114 (7351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	48884667	48884668	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48884667_48884668delAC								SYNGR4 (5040 upstream) : KDELR1 (1159 downstream)																																			---	---	---	---
GRIN2D	2906	broad.mit.edu	37	19	48900030	48900030	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48900030delC	uc002pjc.3	+							NM_000836	NP_000827			N-methyl-D-aspartate receptor subunit 2D							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	48922310	48922310	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48922310delT	uc002pjc.3	+						GRIN2D_uc010elx.2_5'Flank	NM_000836	NP_000827			N-methyl-D-aspartate receptor subunit 2D							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)													---	---	---	---
SULT2B1	6820	broad.mit.edu	37	19	49068645	49068646	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49068645_49068646delGA	uc002pjl.2	+							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)														---	---	---	---
FAM83E	54854	broad.mit.edu	37	19	49107038	49107038	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49107038delG	uc002pjn.2	-	4	954	c.889delC	c.(889-891)CAGfs	p.Q297fs	SPACA4_uc002pjo.2_5'Flank	NM_017708	NP_060178	Q2M2I3	FA83E_HUMAN	hypothetical protein LOC54854	297										ovary(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;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)														---	---	---	---
CGB	1082	broad.mit.edu	37	19	49550508	49550510	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49550508_49550510delTTT	uc010yad.1	-							NM_033183	NP_149439			chorionic gonadotropin, beta polypeptide 8						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)													---	---	---	---
SNRNP70	6625	broad.mit.edu	37	19	49592736	49592736	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49592736delA	uc002pmk.2	+						SNRNP70_uc002pmh.1_Intron|SNRNP70_uc002pmi.1_Intron|SNRNP70_uc002pml.2_Intron|SNRNP70_uc002pmm.2_Intron	NM_003089	NP_003080			U1 small nuclear ribonucleoprotein 70 kDa						nuclear mRNA splicing, via spliceosome|regulation of RNA splicing	nucleoplasm|spliceosomal complex	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
SNRNP70	6625	broad.mit.edu	37	19	49604874	49604875	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49604874_49604875delTT	uc002pmk.2	+						SNRNP70_uc002pmh.1_Intron|SNRNP70_uc002pmi.1_Intron|SNRNP70_uc002pml.2_Intron|SNRNP70_uc002pmm.2_Intron	NM_003089	NP_003080			U1 small nuclear ribonucleoprotein 70 kDa						nuclear mRNA splicing, via spliceosome|regulation of RNA splicing	nucleoplasm|spliceosomal complex	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	49724554	49724555	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49724554_49724555delTT								TRPM4 (9463 upstream) : SLC6A16 (68339 downstream)																																			---	---	---	---
TEAD2	8463	broad.mit.edu	37	19	49851747	49851755	+	Intron	DEL	CAGCTGCAT	-	-	rs33974425		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49851747_49851755delCAGCTGCAT	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)														---	---	---	---
TEAD2	8463	broad.mit.edu	37	19	49855239	49855239	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49855239delA	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)														---	---	---	---
FCGRT	2217	broad.mit.edu	37	19	50021618	50021621	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50021618_50021621delTTTT	uc002poe.2	+						FCGRT_uc002pod.2_Intron|FCGRT_uc002pog.2_Intron|FCGRT_uc002pof.1_Intron|FCGRT_uc010yax.1_Intron|FCGRT_uc002poh.1_Intron	NM_001136019	NP_001129491			Fc fragment of IgG, receptor, transporter, alpha						antigen processing and presentation|female pregnancy|immune response	integral to membrane|MHC class I protein complex	IgG binding|receptor activity			ovary(1)	1		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)														---	---	---	---
AP2A1	160	broad.mit.edu	37	19	50269339	50269341	+	5'Flank	DEL	AAA	-	-	rs112855705	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50269339_50269341delAAA	uc002ppn.2	+						TSKS_uc002ppm.2_5'Flank|AP2A1_uc010enj.1_5'Flank|AP2A1_uc002ppo.2_5'Flank	NM_014203	NP_055018			adaptor-related protein complex 2, alpha 1						axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|Golgi to endosome transport|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|clathrin coat of trans-Golgi network vesicle|cytosol	protein binding|protein transporter activity			ovary(2)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)														---	---	---	---
AP2A1	160	broad.mit.edu	37	19	50289487	50289487	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50289487delA	uc002ppn.2	+						AP2A1_uc010enj.1_Intron|AP2A1_uc002ppo.2_Intron	NM_014203	NP_055018			adaptor-related protein complex 2, alpha 1						axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|Golgi to endosome transport|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|clathrin coat of trans-Golgi network vesicle|cytosol	protein binding|protein transporter activity			ovary(2)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)														---	---	---	---
PTOV1	53635	broad.mit.edu	37	19	50363639	50363639	+	3'UTR	DEL	G	-	-	rs139090214	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50363639delG	uc002pqf.1	+	12					PTOV1_uc002ppz.3_Intron|PTOV1_uc002pqb.3_Intron|PTOV1_uc002pqa.2_Intron|PTOV1_uc002pqc.1_Intron|PTOV1_uc002pqd.2_Intron|PTOV1_uc002pqe.1_Intron	NM_017432	NP_059128			prostate tumor overexpressed 1						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)														---	---	---	---
IL4I1	259307	broad.mit.edu	37	19	50432447	50432447	+	Intron	DEL	C	-	-	rs5828422		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50432447delC	uc002pqu.1	-						IL4I1_uc002pqv.1_Intron|IL4I1_uc010eno.1_Intron|IL4I1_uc002pqw.1_Intron|NUP62_uc002pqx.2_Intron|NUP62_uc002pqy.2_Intron|NUP62_uc002pqz.2_Intron|NUP62_uc002pra.2_Intron|NUP62_uc002prb.2_Intron|NUP62_uc002prc.2_Intron|ATF5_uc010enq.1_Intron|ATF5_uc002prd.2_5'Flank	NM_172374	NP_758962			interleukin 4 induced 1 isoform 2							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)														---	---	---	---
NAPSB	256236	broad.mit.edu	37	19	50846226	50846226	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50846226delT	uc002prw.2	-						NR1H2_uc002prv.3_Intron	NR_002798				Homo sapiens napsin B pseudogene, mRNA sequence.											central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	51003173	51003174	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51003173_51003174delGA								C19orf63 (16566 upstream) : JOSD2 (6085 downstream)																																			---	---	---	---
LRRC4B	94030	broad.mit.edu	37	19	51071756	51071756	+	5'Flank	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51071756delG	uc002pss.2	-							NM_001080457	NP_001073926			leucine rich repeat containing 4B precursor							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	51138153	51138153	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51138153delT	uc002pst.2	-						SYT3_uc002psv.2_Intron|SYT3_uc010ycd.1_Intron	NM_032298	NP_115674			synaptotagmin III							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	51346849	51346849	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51346849delT								KLK15 (12070 upstream) : KLK3 (11322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	51367113	51367113	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51367113delT								KLK3 (3093 upstream) : KLK2 (9576 downstream)																																			---	---	---	---
KLK5	25818	broad.mit.edu	37	19	51457044	51457044	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51457044delT	uc002pue.2	-						KLK5_uc002puf.2_5'Flank|KLK5_uc002pug.2_5'Flank	NM_001077491	NP_001070959			kallikrein-related peptidase 5 preproprotein						epidermis development|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis	extracellular space	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00379)|GBM - Glioblastoma multiforme(134;0.00888)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	51972345	51972345	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51972345delA								SIGLEC8 (10637 upstream) : CEACAM18 (7493 downstream)																																			---	---	---	---
CEACAM18	729767	broad.mit.edu	37	19	51979530	51979530	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51979530delA	uc002pwv.1	+							NM_001080405	NP_001073874			carcinoembryonic antigen-related cell adhesion							integral to membrane				skin(1)	1		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	52232727	52232727	+	IGR	DEL	A	-	-	rs113030482		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52232727delA								HAS1 (5506 upstream) : FPR1 (16300 downstream)																																			---	---	---	---
ZNF613	79898	broad.mit.edu	37	19	52444715	52444715	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52444715delT	uc002pxz.1	+						ZNF613_uc002pya.1_Intron	NM_001031721	NP_001026891			zinc finger protein 613 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	52607149	52607149	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52607149delT								ZNF841 (8131 upstream) : ZNF616 (10505 downstream)																																			---	---	---	---
ZNF83	55769	broad.mit.edu	37	19	53183860	53183874	+	Intron	DEL	TTTTTTTTTTTTTTT	-	-	rs72414217		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53183860_53183874delTTTTTTTTTTTTTTT	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)														---	---	---	---
ZNF816A	125893	broad.mit.edu	37	19	53455153	53455153	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53455153delA	uc002qal.1	-						ZNF321_uc010eqj.2_Intron|ZNF321_uc002qak.1_Intron|ZNF816A_uc002qam.1_Intron	NM_001031665	NP_001026835			zinc finger protein 816A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0313)														---	---	---	---
ZNF702P	79986	broad.mit.edu	37	19	53499536	53499537	+	5'Flank	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53499536_53499537delAA	uc002qan.3	-							NR_003578				Synthetic construct DNA, clone: pF1KB9679, Homo sapiens ZNF702 gene for zinc finger protein 702, without stop codon, in Flexi system.												0																		---	---	---	---
ZNF347	84671	broad.mit.edu	37	19	53652158	53652158	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53652158delA	uc002qbb.1	-						ZNF347_uc010eql.1_Intron|ZNF347_uc002qbc.1_Intron	NM_032584	NP_115973			zinc finger protein 347						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0179)														---	---	---	---
ZNF665	79788	broad.mit.edu	37	19	53695099	53695099	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53695099delA	uc010eqm.1	-							NM_024733	NP_079009			zinc finger protein 665						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.0196)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	53728831	53728831	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53728831delG								ZNF665 (32212 upstream) : ZNF677 (9807 downstream)																																			---	---	---	---
ZNF765	91661	broad.mit.edu	37	19	53870388	53870388	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53870388delT	uc010ydx.1	+						ZNF525_uc010eqn.2_Intron|ZNF525_uc002qbl.2_Intron	NM_001040185	NP_001035275			zinc finger protein 765						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00379)														---	---	---	---
ZNF813	126017	broad.mit.edu	37	19	53983619	53983623	+	Intron	DEL	AAAAA	-	-	rs35502614		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53983619_53983623delAAAAA	uc002qbu.2	+							NM_001004301	NP_001004301			zinc finger protein 813						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)														---	---	---	---
ZNF331	55422	broad.mit.edu	37	19	54077453	54077453	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54077453delT	uc002qbx.1	+						ZNF331_uc002qby.1_Intron|ZNF331_uc002qbz.1_Intron|ZNF331_uc002qca.1_Intron|ZNF331_uc010eqr.1_Intron|ZNF331_uc002qcb.1_Intron|ZNF331_uc002qcc.1_Intron|ZNF331_uc002qcd.1_Intron	NM_018555	NP_061025			zinc finger protein 331						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								---	---	---	---
MIR520C	574476	broad.mit.edu	37	19	54209670	54209670	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54209670delT	hsa-mir-520c|MI0003158	+						MIR518C_hsa-mir-518c|MI0003159_5'Flank																	0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	54284437	54284437	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54284437delT								MIR519A2 (18753 upstream) : MIR371 (6492 downstream)																																			---	---	---	---
PRKCG	5582	broad.mit.edu	37	19	54400980	54400981	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54400980_54400981delAA	uc002qcq.1	+						PRKCG_uc010yef.1_Intron|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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	54450148	54450148	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54450148delT								CACNG7 (3880 upstream) : CACNG8 (16146 downstream)																																			---	---	---	---
TFPT	29844	broad.mit.edu	37	19	54611261	54611261	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54611261delC	uc010yej.1	-							NM_013342	NP_037474			TCF3 (E2A) fusion partner						apoptosis|DNA recombination|DNA repair|induction of apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex	DNA binding|protein binding				0	all_cancers(19;0.004)|all_epithelial(19;0.00195)|all_lung(19;0.0193)|Lung NSC(19;0.0358)|Breast(117;0.137)|Ovarian(34;0.19)							T	TCF3	pre-B ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	19	54637993	54637996	+	IGR	DEL	CTCC	-	-	rs112566549		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54637993_54637996delCTCC								PRPF31 (2843 upstream) : CNOT3 (3453 downstream)																																			---	---	---	---
MBOAT7	79143	broad.mit.edu	37	19	54692246	54692246	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54692246delC	uc002qdq.2	-						MBOAT7_uc010erg.2_5'Flank|MBOAT7_uc010yem.1_5'Flank|MBOAT7_uc002qdr.2_Intron|MBOAT7_uc002qds.2_Intron|MBOAT7_uc010yen.1_Intron|MBOAT7_uc002qdt.3_Intron|TSEN34_uc010yeo.1_5'Flank|TSEN34_uc002qdu.2_5'Flank|TSEN34_uc002qdv.2_5'Flank|TSEN34_uc002qdw.2_5'Flank	NM_024298	NP_077274			membrane bound O-acyltransferase domain						phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)																	---	---	---	---
LILRA5	353514	broad.mit.edu	37	19	54822823	54822823	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54822823delG	uc002qfe.2	-	5	693	c.573delC	c.(571-573)CCCfs	p.P191fs	LILRA5_uc002qff.2_Frame_Shift_Del_p.P179fs|LILRA5_uc010yev.1_Frame_Shift_Del_p.P191fs|LILRA5_uc010yew.1_Frame_Shift_Del_p.P179fs|LILRA5_uc002qfh.1_Frame_Shift_Del_p.P179fs|LILRA5_uc002qfg.1_Frame_Shift_Del_p.P191fs	NM_021250	NP_067073	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor subfamily	191	Extracellular (Potential).|Ig-like C2-type 2.				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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	54898057	54898057	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54898057delT								LAIR1 (15893 upstream) : TTYH1 (28578 downstream)																																			---	---	---	---
TTYH1	57348	broad.mit.edu	37	19	54925442	54925443	+	5'Flank	INS	-	CAT	CAT	rs146951043		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54925442_54925443insCAT	uc002qfq.2	+						TTYH1_uc010yey.1_5'Flank|TTYH1_uc002qfr.2_5'Flank|TTYH1_uc002qft.2_5'Flank	NM_020659	NP_065710			tweety 1 isoform 1						cell adhesion	chloride channel complex|plasma membrane	chloride channel activity|iron ion transmembrane transporter activity				0	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)														---	---	---	---
LILRB4	11006	broad.mit.edu	37	19	55175135	55175135	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55175135delG	uc002qgp.2	+						LILRB4_uc002qgo.1_Intron|LILRB4_uc002qgq.2_Intron|LILRB4_uc010ers.1_Intron|LILRB4_uc002qgr.2_Intron|LILRB4_uc010ert.2_Intron|LILRB4_uc010eru.2_Intron	NM_006847	NP_006838			leukocyte immunoglobulin-like receptor,							integral to membrane|plasma membrane	antigen binding|receptor activity			ovary(3)	3				GBM - Glioblastoma multiforme(193;0.035)														---	---	---	---
KIR2DL3	3804	broad.mit.edu	37	19	55271765	55271766	+	Intron	DEL	GA	-	-	rs112795662		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55271765_55271766delGA	uc010erw.1	+						KIR2DS4_uc010yfj.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL3_uc002qha.1_Intron|KIR3DP1_uc010yfi.1_Intron	NM_015868	NP_056952			killer cell immunoglobulin-like receptor, two						immune response|regulation of immune response	integral to plasma membrane	antigen binding|protein binding|receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(193;0.0192)														---	---	---	---
NLRP7	199713	broad.mit.edu	37	19	55460614	55460614	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55460614delC	uc002qih.3	-						NLRP7_uc002qig.3_5'Flank|NLRP7_uc002qii.3_5'Flank|NLRP7_uc010esk.2_5'Flank|NLRP7_uc010esl.2_Intron	NM_206828	NP_996611			NACHT, leucine rich repeat and PYD containing 7								ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)														---	---	---	---
EPS8L1	54869	broad.mit.edu	37	19	55587649	55587649	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55587649delG	uc002qis.3	+						EPS8L1_uc010ess.1_Intron|EPS8L1_uc010est.1_Intron|EPS8L1_uc010yfr.1_Intron|EPS8L1_uc010esu.1_5'Flank	NM_133180	NP_573441			epidermal growth factor receptor pathway							cytoplasm					0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	55640005	55640005	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55640005delA								PPP1R12C (11078 upstream) : TNNT1 (4157 downstream)																																			---	---	---	---
BRSK1	84446	broad.mit.edu	37	19	55815036	55815036	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55815036delC	uc002qkg.2	+	12	1405	c.1128delC	c.(1126-1128)GACfs	p.D376fs	BRSK1_uc002qkf.2_Frame_Shift_Del_p.D392fs|BRSK1_uc002qkh.2_Frame_Shift_Del_p.D71fs	NM_032430	NP_115806	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	376					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)														---	---	---	---
TMEM150B	284417	broad.mit.edu	37	19	55826054	55826055	+	Intron	INS	-	G	G	rs143404219	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55826054_55826055insG	uc010esw.1	-						TMEM150B_uc010yfu.1_Intron|TMEM150B_uc010yfv.1_Intron|TMEM150B_uc010yfw.1_Intron	NM_001085488	NP_001078957			transmembrane protein 150B precursor							integral to membrane					0																		---	---	---	---
U2AF2	11338	broad.mit.edu	37	19	56171468	56171469	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56171468_56171469insG	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	56210117	56210117	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56210117delT								EPN1 (2985 upstream) : NLRP9 (9682 downstream)																																			---	---	---	---
NLRP9	338321	broad.mit.edu	37	19	56220431	56220431	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56220431delT	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)														---	---	---	---
NLRP9	338321	broad.mit.edu	37	19	56226376	56226376	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56226376delA	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)														---	---	---	---
ZSCAN5A	79149	broad.mit.edu	37	19	56807791	56807792	+	Intron	INS	-	T	T	rs144650157	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56807791_56807792insT	uc002qmr.2	-						ZSCAN5A_uc010ygi.1_Intron	NM_024303	NP_077279			zinc finger and SCAN domain containing 5A						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
ZSCAN5A	79149	broad.mit.edu	37	19	56813950	56813964	+	Intron	DEL	CCCTTTTCTTCCTCT	-	-	rs55713318	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56813950_56813964delCCCTTTTCTTCCTCT	uc002qmr.2	-						ZSCAN5A_uc010ygi.1_Intron	NM_024303	NP_077279			zinc finger and SCAN domain containing 5A						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
ZNF583	147949	broad.mit.edu	37	19	56922494	56922497	+	Intron	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56922494_56922497delAAAA	uc010ygl.1	+						ZNF583_uc002qnc.2_Intron|ZNF583_uc010ygm.1_Intron	NM_001159860	NP_001153332			zinc finger protein 583						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)														---	---	---	---
ZNF71	58491	broad.mit.edu	37	19	57104276	57104276	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57104276delA	uc002qnm.3	+							NM_021216	NP_067039			zinc finger protein 71							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)														---	---	---	---
ZNF71	58491	broad.mit.edu	37	19	57119815	57119815	+	Intron	DEL	T	-	-	rs35502249		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57119815delT	uc002qnm.3	+							NM_021216	NP_067039			zinc finger protein 71							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)														---	---	---	---
ZIM2	23619	broad.mit.edu	37	19	57287026	57287026	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57287026delA	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)														---	---	---	---
ZIM2	23619	broad.mit.edu	37	19	57320531	57320531	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57320531delA	uc002qnr.2	-						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57487026	57487026	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57487026delA								MIMT1 (127104 upstream) : USP29 (144483 downstream)																																			---	---	---	---
ZNF543	125919	broad.mit.edu	37	19	57833263	57833263	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57833263delA	uc002qoi.1	+							NM_213598	NP_998763			zinc finger protein 543						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)|pancreas(1)	2		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;0.0257)														---	---	---	---
ZNF772	400720	broad.mit.edu	37	19	57986969	57986969	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57986969delA	uc002qot.2	-						ZNF547_uc002qpm.3_Intron|ZNF772_uc010ygy.1_Intron|ZNF772_uc010ygz.1_Intron|ZNF772_uc010yha.1_Intron|ZNF772_uc002qou.2_Intron	NM_001024596	NP_001019767			zinc finger protein 772 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)														---	---	---	---
ZNF547	284306	broad.mit.edu	37	19	57998322	57998323	+	Intron	INS	-	CA	CA	rs10649348		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57998322_57998323insCA	uc002qpm.3	+						ZNF419_uc010ety.1_5'Flank|ZNF419_uc002qov.2_5'Flank|ZNF419_uc010etz.1_5'Flank|ZNF419_uc010eua.1_5'Flank|ZNF419_uc002qow.2_5'Flank|ZNF419_uc010eub.1_5'Flank|ZNF419_uc010euc.1_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	58322530	58322531	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58322530_58322531delTT	uc002qqb.2	+						ZNF552_uc002qqg.2_Intron|ZNF552_uc010yhg.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	58530089	58530089	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58530089delA								ZNF606 (15375 upstream) : ZSCAN1 (15345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	58566219	58566219	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58566219delT								ZSCAN1 (220 upstream) : ZNF135 (4393 downstream)																																			---	---	---	---
ZSCAN18	65982	broad.mit.edu	37	19	58613828	58613829	+	Intron	INS	-	AAAC	AAAC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58613828_58613829insAAAC	uc010yht.1	-							NM_001145542	NP_001139014			zinc finger and SCAN domain containing 18						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.114)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	58727943	58727943	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58727943delA								ZNF274 (3016 upstream) : ZNF544 (12127 downstream)																																			---	---	---	---
ZNF544	27300	broad.mit.edu	37	19	58748111	58748112	+	Intron	DEL	TT	-	-	rs112780440		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58748111_58748112delTT	uc010euo.2	+						ZNF544_uc010eun.1_Intron|ZNF544_uc010yhw.1_Intron|ZNF544_uc010yhx.1_Intron|ZNF544_uc010yhy.1_Intron|ZNF544_uc002qrt.3_Intron|ZNF544_uc002qru.3_Intron|ZNF544_uc002qrv.2_Intron	NM_014480	NP_055295			zinc finger protein 544						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)														---	---	---	---
ZNF324	25799	broad.mit.edu	37	19	58976800	58976800	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58976800delT	uc002qsw.1	+							NM_014347	NP_055162			zinc finger protein 324						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	59049589	59049589	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59049589delT								ZBTB45 (18401 upstream) : TRIM28 (6247 downstream)																																			---	---	---	---
MZF1	7593	broad.mit.edu	37	19	59079185	59079185	+	Intron	DEL	T	-	-	rs71709970		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59079185delT	uc002qto.2	-						LOC100131691_uc002qtm.2_Intron|MZF1_uc002qtn.2_Intron	NM_198055	NP_932172			zinc finger protein 42 isoform 2						viral reproduction	nucleus	protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)	1		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)														---	---	---	---
RBCK1	10616	broad.mit.edu	37	20	409650	409652	+	In_Frame_Del	DEL	AGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:409650_409652delAGA	uc002wdp.3	+	11	2057_2059	c.1364_1366delAGA	c.(1363-1368)CAGAAG>CAG	p.K457del	RBCK1_uc002wdq.3_In_Frame_Del_p.K415del|RBCK1_uc010fzy.2_RNA|RBCK1_uc002wdr.3_In_Frame_Del_p.K287del	NM_031229	NP_112506	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing	457	IBR-type 2.				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)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	453148	453149	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:453148_453149delGA								TBC1D20 (9961 upstream) : CSNK2A1 (10189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	700868	700868	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:700868delG								SRXN1 (44045 upstream) : C20orf54 (39857 downstream)																																			---	---	---	---
FKBP1A	2280	broad.mit.edu	37	20	1316198	1316198	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1316198delT	uc010gac.2	-						uc002wew.2_Intron|uc002wex.2_Intron					Homo sapiens FKBP12-Exip2 mRNA for FK506 binding protein12, complete cds.						'de novo' protein folding|beta-amyloid formation|fibril organization|heart trabecula formation|negative regulation of protein phosphatase type 2B activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of protein binding|positive regulation of protein ubiquitination|protein maturation by protein folding|protein refolding|regulation of activin receptor signaling pathway|regulation of immune response|regulation of ryanodine-sensitive calcium-release channel activity|SMAD protein complex assembly|T cell activation|ventricular cardiac muscle tissue morphogenesis	axon|cytosol|sarcoplasmic reticulum membrane|terminal cisterna	activin binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity|signal transducer activity|SMAD binding|type I transforming growth factor beta receptor binding				0					Pimecrolimus(DB00337)|Sirolimus(DB00877)|Tacrolimus(DB00864)													---	---	---	---
FKBP1A	2280	broad.mit.edu	37	20	1350035	1350036	+	3'UTR	INS	-	AT	AT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1350035_1350036insAT	uc002wey.2	-	5					FKBP1A_uc010gac.2_Intron|uc002wew.2_Intron|uc002wex.2_Intron|FKBP1A_uc002wez.2_3'UTR|FKBP1A_uc010gad.2_RNA	NM_000801	NP_000792			FK506 binding protein 1A, 12kDa						'de novo' protein folding|beta-amyloid formation|fibril organization|heart trabecula formation|negative regulation of protein phosphatase type 2B activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of protein binding|positive regulation of protein ubiquitination|protein maturation by protein folding|protein refolding|regulation of activin receptor signaling pathway|regulation of immune response|regulation of ryanodine-sensitive calcium-release channel activity|SMAD protein complex assembly|T cell activation|ventricular cardiac muscle tissue morphogenesis	axon|cytosol|sarcoplasmic reticulum membrane|terminal cisterna	activin binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity|signal transducer activity|SMAD binding|type I transforming growth factor beta receptor binding				0					Pimecrolimus(DB00337)|Sirolimus(DB00877)|Tacrolimus(DB00864)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	1778926	1778927	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1778926_1778927delAA								SIRPG (140501 upstream) : SIRPA (95886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	1940245	1940245	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1940245delA	uc002wfu.1	+											Homo sapiens cDNA FLJ33362 fis, clone BRACE2005337.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	1949784	1949784	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1949784delT	uc002wfu.1	+											Homo sapiens cDNA FLJ33362 fis, clone BRACE2005337.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	2056532	2056532	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2056532delA								PDYN (81829 upstream) : STK35 (25996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	2511715	2511715	+	IGR	DEL	A	-	-	rs112874764		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2511715delA								ZNF343 (6550 upstream) : TMC2 (5538 downstream)																																			---	---	---	---
CPXM1	56265	broad.mit.edu	37	20	2777466	2777466	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2777466delG	uc002wgu.2	-						CPXM1_uc010gas.2_Intron	NM_019609	NP_062555			carboxypeptidase X, member 1 precursor						cell adhesion|proteolysis		metallocarboxypeptidase activity|zinc ion binding			ovary(2)|skin(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	2811308	2811308	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2811308delT								C20orf141 (12596 upstream) : FAM113A (4663 downstream)																																			---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	2870871	2870871	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2870871delT	uc010zqb.1	+						VPS16_uc002whh.2_Intron|PTPRA_uc002whj.2_Intron|PTPRA_uc010zqc.1_Intron|PTPRA_uc002whk.2_Intron|PTPRA_uc010zqd.1_Intron|PTPRA_uc002whl.2_Intron|PTPRA_uc002whm.2_Intron					SubName: Full=cDNA FLJ60525, highly similar to Receptor-type tyrosine-protein phosphatase alpha (EC 3.1.3.48);						axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
ProSAPiP1	9762	broad.mit.edu	37	20	3146039	3146039	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3146039delC	uc002wia.1	-						ProSAPiP1_uc002wib.1_Intron	NM_014731	NP_055546			ProSAPiP1 protein							cell junction|cytoplasm|postsynaptic density|postsynaptic membrane				pancreas(1)	1																		---	---	---	---
SLC4A11	83959	broad.mit.edu	37	20	3210469	3210469	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3210469delG	uc002wig.2	-						SLC4A11_uc010zqe.1_Intron|SLC4A11_uc002wih.2_Intron|SLC4A11_uc010zqf.1_Intron	NM_032034	NP_114423			solute carrier family 4 member 11						cellular cation homeostasis|fluid transport|phosphoenolpyruvate-dependent sugar phosphotransferase system	basolateral plasma membrane|integral to membrane	bicarbonate transmembrane transporter activity|borate transmembrane transporter activity|hydrogen ion channel activity|inorganic anion exchanger activity|sodium channel activity|sugar:hydrogen symporter activity			ovary(1)	1																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3565224	3565224	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3565224delA	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																		---	---	---	---
SIGLEC1	6614	broad.mit.edu	37	20	3668115	3668115	+	3'UTR	DEL	G	-	-	rs71809129		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3668115delG	uc002wja.2	-	21					SIGLEC1_uc002wjb.1_3'UTR|SIGLEC1_uc002wiz.3_3'UTR	NM_023068	NP_075556			sialoadhesin precursor						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	3770636	3770637	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3770636_3770637delAA	uc010zqk.1	+						CDC25B_uc010zql.1_Intron|CDC25B_uc010zqm.1_Intron	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																		---	---	---	---
CDC25B	994	broad.mit.edu	37	20	3778963	3778973	+	Intron	DEL	TTTTTTTTTTT	-	-	rs72385170		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3778963_3778973delTTTTTTTTTTT	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_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	4001608	4001608	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4001608delT								RNF24 (5392 upstream) : SMOX (127842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	4008764	4008783	+	IGR	DEL	CTTCCTTCTTTCCTTCCTTC	-	-	rs71195879		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4008764_4008783delCTTCCTTCTTTCCTTCCTTC								RNF24 (12548 upstream) : SMOX (120667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	4587934	4587934	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4587934delT								ADRA1D (358275 upstream) : PRNP (78863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	4635667	4635668	+	IGR	INS	-	GA	GA	rs144731571	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4635667_4635668insGA								ADRA1D (406008 upstream) : PRNP (31129 downstream)																																			---	---	---	---
RASSF2	9770	broad.mit.edu	37	20	4767704	4767706	+	Intron	DEL	AAA	-	-	rs112411943		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4767704_4767706delAAA	uc002wld.2	-						RASSF2_uc002wlc.2_Intron|RASSF2_uc002wle.2_Intron|RASSF2_uc002wlf.2_Intron|RASSF2_uc010gbh.2_RNA	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	4843454	4843454	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4843454delC	uc002wlg.1	-	14	1831	c.1456delG	c.(1456-1458)GTGfs	p.V486fs	SLC23A2_uc010zqr.1_Frame_Shift_Del_p.V371fs|SLC23A2_uc002wlh.1_Frame_Shift_Del_p.V486fs	NM_005116	NP_005107	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (nucleobase	486	Helical; (Potential).				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																		---	---	---	---
SLC23A2	9962	broad.mit.edu	37	20	4956807	4956808	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4956807_4956808insT	uc002wlg.1	-						SLC23A2_uc010zqr.1_Intron|SLC23A2_uc002wlh.1_Intron|SLC23A2_uc002wli.2_Intron|SLC23A2_uc002wlj.1_Intron	NM_005116	NP_005107			solute carrier family 23 (nucleobase						L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	5000316	5000316	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5000316delG								SLC23A2 (9377 upstream) : C20orf30 (48814 downstream)																																			---	---	---	---
PCNA	5111	broad.mit.edu	37	20	5105274	5105275	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5105274_5105275delAA	uc002wlq.2	-						CDS2_uc002wlr.1_5'Flank|CDS2_uc002wls.2_5'Flank|CDS2_uc010zqt.1_5'Flank|CDS2_uc002wlu.2_5'Flank|CDS2_uc010zqu.1_5'Flank|PCNA_uc010zqs.1_Intron	NM_002592	NP_002583			proliferating cell nuclear antigen						cell proliferation|DNA strand elongation involved in DNA replication|mismatch repair|nucleotide-excision repair, DNA gap filling|phosphatidylinositol-mediated signaling|positive regulation of deoxyribonuclease activity|regulation of DNA replication|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair|translesion synthesis	cytoplasm|DNA replication factor C complex|microtubule cytoskeleton|nuclear replication fork|nucleoplasm|PCNA complex|PCNA-p21 complex	dinucleotide insertion or deletion binding|DNA polymerase processivity factor activity|MutLalpha complex binding|purine-specific mismatch base pair DNA N-glycosylase activity			lung(1)	1													DNA_polymerases_(catalytic_subunits)					---	---	---	---
C20orf196	149840	broad.mit.edu	37	20	5779851	5779851	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5779851delA	uc002wmf.2	+							NM_152504	NP_689717			hypothetical protein LOC149840												0																		---	---	---	---
MCM8	84515	broad.mit.edu	37	20	5934425	5934426	+	Intron	DEL	TT	-	-	rs112487054		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5934425_5934426delTT	uc002wmi.2	+						MCM8_uc002wmj.2_Intron|MCM8_uc002wmk.2_Intron|MCM8_uc002wml.2_Intron|MCM8_uc010gbp.2_Intron	NM_032485	NP_115874			minichromosome maintenance complex component 8						cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1																		---	---	---	---
MCM8	84515	broad.mit.edu	37	20	5965737	5965737	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5965737delT	uc002wmi.2	+						MCM8_uc002wmj.2_Intron|MCM8_uc002wmk.2_Intron|MCM8_uc002wml.2_Intron|MCM8_uc010gbp.2_Intron|MCM8_uc002wmm.2_Intron	NM_032485	NP_115874			minichromosome maintenance complex component 8						cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1																		---	---	---	---
CRLS1	54675	broad.mit.edu	37	20	5991665	5991665	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5991665delA	uc002wmn.3	+						CRLS1_uc010gbq.2_Intron|CRLS1_uc010gbr.2_Intron|CRLS1_uc010gbs.1_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	6116546	6116547	+	IGR	INS	-	GT	GT	rs139978385	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6116546_6116547insGT								FERMT1 (12355 upstream) : BMP2 (632198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	6151757	6151757	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6151757delC								FERMT1 (47566 upstream) : BMP2 (596988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	6665523	6665523	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6665523delA								FERMT1 (561332 upstream) : BMP2 (83222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	6973987	6973988	+	IGR	INS	-	A	A	rs6054652		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6973987_6973988insA								BMP2 (213077 upstream) : HAO1 (889643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7576883	7576884	+	IGR	DEL	TT	-	-	rs71329662		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7576883_7576884delTT								BMP2 (815973 upstream) : HAO1 (286747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7734199	7734199	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7734199delT								BMP2 (973289 upstream) : HAO1 (129432 downstream)																																			---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8300174	8300174	+	Intron	DEL	A	-	-	rs111997224		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8300174delA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8560520	8560520	+	Intron	DEL	A	-	-	rs11087810		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8560520delA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8624211	8624211	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8624211delA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	9006377	9006377	+	IGR	DEL	A	-	-	rs71331353		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9006377delA								PLCB1 (140832 upstream) : PLCB4 (43324 downstream)																																			---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9238670	9238670	+	Intron	DEL	A	-	-	rs112712204		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9238670delA	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	9465702	9465703	+	IGR	DEL	TT	-	-	rs66551043		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9465702_9465703delTT								PLCB4 (4242 upstream) : C20orf103 (29568 downstream)																																			---	---	---	---
PAK7	57144	broad.mit.edu	37	20	9804538	9804538	+	Intron	DEL	T	-	-	rs34836860		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9804538delT	uc002wnl.2	-						PAK7_uc002wnk.2_Intron|PAK7_uc002wnj.2_Intron|PAK7_uc010gby.1_Intron	NM_020341	NP_065074			p21-activated kinase 7								ATP binding|protein binding|protein serine/threonine kinase activity			lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1)	23			COAD - Colon adenocarcinoma(9;0.194)															---	---	---	---
MKKS	8195	broad.mit.edu	37	20	10397127	10397127	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10397127delA	uc002wnt.1	-						MKKS_uc002wnu.1_Intron|MKKS_uc010zrd.1_Intron	NM_018848	NP_061336			McKusick-Kaufman syndrome protein						brain morphogenesis|cerebral cortex development|convergent extension involved in gastrulation|detection of mechanical stimulus involved in sensory perception of sound|fat cell differentiation|flagellum assembly|gonad development|heart looping|hippocampus development|intracellular transport|melanosome transport|photoreceptor cell maintenance|pigment granule aggregation in cell center|protein folding|regulation of cilium beat frequency involved in ciliary motility|sensory perception of smell|social behavior|spermatid development|striatum development	cytosol|microtubule organizing center|motile cilium	ATP binding|unfolded protein binding				0														Bardet-Biedl_syndrome				---	---	---	---
C20orf94	128710	broad.mit.edu	37	20	10471720	10471720	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10471720delA	uc010zre.1	+							NM_001009608	NP_001009608			hypothetical protein LOC128710								protein binding				0																		---	---	---	---
C20orf94	128710	broad.mit.edu	37	20	10527937	10527938	+	Intron	INS	-	TTACTC	TTACTC	rs137949817	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10527937_10527938insTTACTC	uc010zre.1	+							NM_001009608	NP_001009608			hypothetical protein LOC128710								protein binding				0																		---	---	---	---
JAG1	182	broad.mit.edu	37	20	10630345	10630345	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10630345delA	uc002wnw.2	-						JAG1_uc010gcd.1_Intron	NM_000214	NP_000205			jagged 1 precursor						angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1)	9														Alagille_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	20	10764377	10764377	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10764377delA								JAG1 (109683 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11192288	11192291	+	IGR	DEL	TGTA	-	-	rs60865372		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11192288_11192291delTGTA								JAG1 (537594 upstream) : BTBD3 (679186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11325581	11325581	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11325581delA								JAG1 (670887 upstream) : BTBD3 (545896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11772406	11772406	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11772406delT								None (None upstream) : BTBD3 (99071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12080901	12080902	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12080901_12080902delTT								BTBD3 (173659 upstream) : SPTLC3 (908725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12244453	12244453	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12244453delT								BTBD3 (337211 upstream) : SPTLC3 (745174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12482977	12482978	+	IGR	INS	-	TGG	TGG	rs142376534	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12482977_12482978insTGG								BTBD3 (575735 upstream) : SPTLC3 (506649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12867609	12867609	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12867609delC								BTBD3 (960367 upstream) : SPTLC3 (122018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12915209	12915210	+	IGR	DEL	AA	-	-	rs74181384		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12915209_12915210delAA								None (None upstream) : SPTLC3 (74417 downstream)																																			---	---	---	---
ISM1	140862	broad.mit.edu	37	20	13260483	13260483	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13260483delG	uc010gce.1	+	3	587	c.581delG	c.(580-582)AGGfs	p.R194fs	TASP1_uc010zri.1_Intron	NM_080826	NP_543016	B1AKI9	ISM1_HUMAN	isthmin 1 homolog precursor	194						extracellular region					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	13674352	13674353	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13674352_13674353insC								TASP1 (54769 upstream) : ESF1 (20617 downstream)																																			---	---	---	---
FLRT3	23767	broad.mit.edu	37	20	14305761	14305761	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14305761delT	uc002wov.1	-	3					MACROD2_uc002wot.2_Intron|MACROD2_uc002wou.2_Intron|FLRT3_uc002wow.1_3'UTR	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	14749272	14749272	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14749272delT	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	14846040	14846040	+	Intron	DEL	T	-	-	rs387073	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14846040delT	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	14889312	14889312	+	Intron	DEL	A	-	-	rs112862531		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14889312delA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|uc002woy.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	14921304	14921304	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14921304delT	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	14926846	14926847	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14926846_14926847delAA	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	15725339	15725348	+	Intron	DEL	ACACACACAC	-	-	rs11470799		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15725339_15725348delACACACACAC	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.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	15948034	15948034	+	Intron	DEL	A	-	-	rs6080063	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15948034delA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	16152010	16152011	+	IGR	INS	-	GGAGGAAAGGGAG	GGAGGAAAGGGAG	rs150320684	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16152010_16152011insGGAGGAAAGGGAG								MACROD2 (118171 upstream) : KIF16B (100738 downstream)																																			---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16470342	16470343	+	Intron	DEL	AA	-	-	rs74175696		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16470342_16470343delAA	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	16569902	16569902	+	IGR	DEL	A	-	-	rs79551688		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16569902delA								KIF16B (15824 upstream) : SNRPB2 (140727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	16667248	16667249	+	IGR	INS	-	TC	TC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16667248_16667249insTC								KIF16B (113170 upstream) : SNRPB2 (43380 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17473441	17473442	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17473441_17473442insT								PCSK2 (8221 upstream) : BFSP1 (1109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17839484	17839485	+	IGR	DEL	GT	-	-	rs72267956		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17839484_17839485delGT								BANF2 (122967 upstream) : SNX5 (82761 downstream)																																			---	---	---	---
OVOL2	58495	broad.mit.edu	37	20	18031264	18031264	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18031264delC	uc002wqi.1	-							NM_021220	NP_067043			zinc finger protein 339						negative regulation of keratinocyte differentiation|negative regulation of Notch signaling pathway|negative regulation of transcription by competitive promoter binding|regulation of cell cycle|regulation of keratinocyte proliferation|transcription, DNA-dependent	nucleus	DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	19113955	19113955	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19113955delA								C20orf79 (318922 upstream) : SLC24A3 (79335 downstream)																																			---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19250847	19250847	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19250847delA	uc002wrl.2	+						LOC100130264_uc010zsd.1_Intron	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	19415393	19415395	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19415393_19415395delTTT	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	19690268	19690268	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19690268delA	uc002wrl.2	+							NM_020689	NP_065740			solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	19759943	19759943	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19759943delA								SLC24A3 (56403 upstream) : RIN2 (110267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	19988687	19988688	+	IGR	DEL	GT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19988687_19988688delGT								RIN2 (5587 upstream) : NAA20 (9249 downstream)																																			---	---	---	---
CRNKL1	51340	broad.mit.edu	37	20	20031422	20031422	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20031422delA	uc002wrs.2	-						C20orf26_uc010gcw.1_5'Flank|C20orf26_uc010zse.1_5'Flank|C20orf26_uc002wru.2_5'Flank|CRNKL1_uc002wrt.1_Intron	NM_016652	NP_057736			crooked neck-like 1 protein						spliceosome assembly	catalytic step 2 spliceosome|cytoplasm|nuclear speck	RNA binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20317987	20317990	+	Intron	DEL	TGGG	-	-	rs138008701	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20317987_20317990delTGGG	uc002wru.2	+						C20orf26_uc002wrw.2_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	20	20730984	20730984	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20730984delA								RALGAPA2 (37718 upstream) : PLK1S1 (375640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	20816415	20816416	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20816415_20816416delTT								RALGAPA2 (123149 upstream) : PLK1S1 (290208 downstream)																																			---	---	---	---
PLK1S1	55857	broad.mit.edu	37	20	21110746	21110746	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21110746delT	uc002wsb.2	+						PLK1S1_uc010zsh.1_Intron|PLK1S1_uc010zsi.1_Intron|PLK1S1_uc010zsj.1_Intron	NM_018474	NP_060944			polo-like kinase 1 substrate 1 isoform 1						spindle organization	centrosome	protein kinase binding				0																		---	---	---	---
PLK1S1	55857	broad.mit.edu	37	20	21196192	21196192	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21196192delT	uc002wsb.2	+						PLK1S1_uc010zsh.1_Intron|PLK1S1_uc010zsi.1_Intron|PLK1S1_uc010zsj.1_Intron|uc002wsc.2_Intron|PLK1S1_uc002wsd.2_Intron|uc002wse.2_Intron	NM_018474	NP_060944			polo-like kinase 1 substrate 1 isoform 1						spindle organization	centrosome	protein kinase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	21785807	21785807	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21785807delT								PAX1 (89187 upstream) : LOC284788 (595164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22078303	22078303	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22078303delT								PAX1 (381683 upstream) : LOC284788 (302668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22483733	22483733	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22483733delT								LOC284788 (82452 upstream) : C20orf56 (57461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22597326	22597327	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22597326_22597327delCT								FOXA2 (31225 upstream) : SSTR4 (418730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	23069783	23069784	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23069783_23069784insG								CD93 (2806 upstream) : NXT1 (261589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	23630114	23630114	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23630114delT								CST3 (11540 upstream) : CST4 (36163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24272817	24272817	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24272817delT								GGTLC1 (303401 upstream) : TMEM90B (177018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24364184	24364186	+	IGR	DEL	TTT	-	-	rs139185267		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24364184_24364186delTTT								GGTLC1 (394768 upstream) : TMEM90B (85649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24784458	24784461	+	IGR	DEL	TTTG	-	-	rs11469145		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24784458_24784461delTTTG								TMEM90B (137291 upstream) : CST7 (145405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25736314	25736314	+	IGR	DEL	T	-	-	rs79313128		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25736314delT								ZNF337 (58845 upstream) : FAM182B (7788 downstream)																																			---	---	---	---
FAM182B	728882	broad.mit.edu	37	20	25831101	25831102	+	Intron	INS	-	C	C	rs147373877	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25831101_25831102insC	uc002wvd.1	-						FAM182B_uc002wve.2_Intron					Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25910266	25910267	+	IGR	INS	-	T	T	rs149342775		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25910266_25910267insT								FAM182B (61480 upstream) : LOC100134868 (80168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25912775	25912775	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25912775delT								FAM182B (63989 upstream) : LOC100134868 (77660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26107789	26107790	+	IGR	INS	-	T	T	rs138056023	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26107789_26107790insT								C20orf191 (13112 upstream) : MIR663 (81032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26252699	26252700	+	IGR	INS	-	T	T	rs143639929		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26252699_26252700insT								MIR663 (63785 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29477118	29477118	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29477118delA								None (None upstream) : FRG1B (134761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29480977	29480978	+	IGR	INS	-	G	G	rs148111006	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29480977_29480978insG								None (None upstream) : FRG1B (130901 downstream)																																			---	---	---	---
HM13	81502	broad.mit.edu	37	20	30120314	30120315	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30120314_30120315delTT	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)															---	---	---	---
BCL2L1	598	broad.mit.edu	37	20	30280714	30280715	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30280714_30280715delAA	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)															---	---	---	---
BCL2L1	598	broad.mit.edu	37	20	30286731	30286732	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30286731_30286732delTT	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	30462213	30462217	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30462213_30462217delTTTTT	uc010gdx.1	+						TTLL9_uc002wwy.1_Intron|TTLL9_uc002wwz.1_Intron|TTLL9_uc002wxa.1_Intron|TTLL9_uc002wxb.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)															---	---	---	---
TM9SF4	9777	broad.mit.edu	37	20	30719285	30719286	+	Intron	DEL	GT	-	-	rs33957493		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30719285_30719286delGT	uc002wxj.2	+						TM9SF4_uc010ztr.1_Intron|TM9SF4_uc010zts.1_Intron|TM9SF4_uc002wxk.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)															---	---	---	---
TM9SF4	9777	broad.mit.edu	37	20	30729932	30729933	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30729932_30729933delAA	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)															---	---	---	---
C20orf112	140688	broad.mit.edu	37	20	31041556	31041556	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31041556delG	uc002wxu.3	-	4	553	c.396delC	c.(394-396)CCCfs	p.P132fs	C20orf112_uc010gec.2_5'UTR	NM_080616	NP_542183	Q96MY1	CT112_HUMAN	hypothetical protein LOC140688	132											0																		---	---	---	---
C20orf112	140688	broad.mit.edu	37	20	31074444	31074444	+	Intron	DEL	A	-	-	rs111823457		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31074444delA	uc002wxw.1	-											Homo sapiens cDNA FLJ31724 fis, clone NT2RI2006703, moderately similar to Homo sapiens nolp mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	31397439	31397439	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31397439delA								DNMT3B (278 upstream) : MAPRE1 (10260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	31402695	31402695	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31402695delA								DNMT3B (5534 upstream) : MAPRE1 (5004 downstream)																																			---	---	---	---
MAPRE1	22919	broad.mit.edu	37	20	31404914	31404914	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31404914delT	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																		---	---	---	---
MAPRE1	22919	broad.mit.edu	37	20	31409325	31409325	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31409325delT	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																		---	---	---	---
SUN5	140732	broad.mit.edu	37	20	31578843	31578844	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31578843_31578844insA	uc002wyi.2	-							NM_080675	NP_542406			sperm associated antigen 4-like						spermatogenesis					skin(1)	1																		---	---	---	---
SNTA1	6640	broad.mit.edu	37	20	32022241	32022241	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32022241delA	uc002wzd.1	-						SNTA1_uc010zuf.1_Intron	NM_003098	NP_003089			acidic alpha 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|sarcolemma	actin binding|calmodulin binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	32782937	32782939	+	IGR	DEL	AAA	-	-	rs35765277		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32782937_32782939delAAA								EIF2S2 (82852 upstream) : ASIP (65232 downstream)																																			---	---	---	---
ITCH	83737	broad.mit.edu	37	20	33001768	33001769	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33001768_33001769insT	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	33065566	33065566	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33065566delT	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																		---	---	---	---
TP53INP2	58476	broad.mit.edu	37	20	33296578	33296578	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33296578delC	uc002xau.1	+	3	370	c.35delC	c.(34-36)ACCfs	p.T12fs		NM_021202	NP_067025	Q8IXH6	T53I2_HUMAN	tumor protein p53 inducible nuclear protein 2	12						nucleus					0																		---	---	---	---
NCOA6	23054	broad.mit.edu	37	20	33338326	33338326	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33338326delA	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																		---	---	---	---
NCOA6	23054	broad.mit.edu	37	20	33356693	33356694	+	Intron	INS	-	TG	TG	rs145646339	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33356693_33356694insTG	uc002xav.2	-						NCOA6_uc002xaw.2_Intron|NCOA6_uc010gew.1_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																		---	---	---	---
GSS	2937	broad.mit.edu	37	20	33537227	33537231	+	Intron	DEL	TTTTT	-	-	rs72033361		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33537227_33537231delTTTTT	uc002xbg.2	-						GSS_uc010zun.1_5'Flank|GSS_uc010zuo.1_Intron|GSS_uc010zup.1_Intron|GSS_uc002xbh.2_Intron|GSS_uc010gez.1_Intron	NM_000178	NP_000169			glutathione synthetase						nervous system development|response to oxidative stress|xenobiotic metabolic process	cytosol	ATP binding|glutathione binding|glutathione synthase activity|magnesium ion binding|protein homodimerization activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(18;0.035)		Glutathione(DB00143)|Glycine(DB00145)|L-Cysteine(DB00151)													---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33905727	33905728	+	Intron	INS	-	GGGCT	GGGCT	rs148034541	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33905727_33905728insGGGCT	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	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	33971657	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33971656_33971657delAA	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	34009803	34009803	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34009803delT	uc010gfc.1	-							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)															---	---	---	---
C20orf173	140873	broad.mit.edu	37	20	34109438	34109441	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34109438_34109441delTTTT	uc010gff.2	-							NM_001145350				hypothetical protein LOC140873												0																		---	---	---	---
C20orf173	140873	broad.mit.edu	37	20	34115454	34115454	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34115454delT	uc002xcp.2	-						C20orf173_uc010gff.2_Intron|C20orf173_uc010zvf.1_Intron					RecName: Full=Uncharacterized protein C20orf173;												0																		---	---	---	---
FER1L4	80307	broad.mit.edu	37	20	34174449	34174449	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34174449delT	uc010gfg.1	-						FER1L4_uc002xcy.3_Intron					RecName: Full=Fer-1-like protein 4;												0																		---	---	---	---
RBM39	9584	broad.mit.edu	37	20	34305786	34305788	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34305786_34305788delTTT	uc002xeb.2	-						RBM39_uc002xdz.2_Intron|RBM39_uc002xea.2_Intron|RBM39_uc010gfn.2_Intron|RBM39_uc010zvm.1_Intron|RBM39_uc002xeg.2_Intron|RBM39_uc002xec.2_Intron|RBM39_uc002xed.2_Intron|RBM39_uc002xee.2_Intron|RBM39_uc002xef.2_Intron|RBM39_uc010zvn.1_Intron	NM_184234	NP_909122			RNA binding motif protein 39 isoform a						mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)																	---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34387590	34387590	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34387590delT	uc002xek.1	+						PHF20_uc002xei.1_Intron|PHF20_uc010gfo.1_Intron|PHF20_uc002xej.1_Intron|PHF20_uc002xeh.2_Intron	NM_016436	NP_057520			PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34511881	34511881	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34511881delT	uc002xek.1	+							NM_016436	NP_057520			PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	34643225	34643225	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34643225delT								LOC647979 (4343 upstream) : EPB41L1 (36201 downstream)																																			---	---	---	---
EPB41L1	2036	broad.mit.edu	37	20	34698456	34698457	+	Intron	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34698456_34698457insCA	uc002xev.2	+						EPB41L1_uc002xeu.2_Intron|EPB41L1_uc010zvo.1_Intron|EPB41L1_uc002xew.2_Intron|EPB41L1_uc002xex.2_Intron|EPB41L1_uc002xey.2_5'Flank|EPB41L1_uc002xez.2_5'Flank	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)																	---	---	---	---
DLGAP4	22839	broad.mit.edu	37	20	35156622	35156623	+	3'UTR	INS	-	T	T	rs141906314	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35156622_35156623insT	uc002xff.2	+	13					DLGAP4_uc010zvp.1_3'UTR|DLGAP4_uc002xfg.2_3'UTR|DLGAP4_uc002xfh.2_3'UTR|DLGAP4_uc002xfi.2_3'UTR|DLGAP4_uc002xfj.2_3'UTR|uc002xfk.3_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)																---	---	---	---
C20orf117	140710	broad.mit.edu	37	20	35407840	35407841	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35407840_35407841insC	uc002xgd.1	-							NM_199181	NP_954650			hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	35618249	35618250	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35618249_35618250delAA								SAMHD1 (38073 upstream) : RBL1 (6822 downstream)																																			---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35696592	35696592	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																---	---	---	---
SRC	6714	broad.mit.edu	37	20	36023318	36023319	+	Intron	INS	-	GT	GT	rs139551868	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36023318_36023319insGT	uc002xgx.2	+						SRC_uc002xgy.2_Intron	NM_005417	NP_005408			proto-oncogene tyrosine-protein kinase SRC						axon guidance|bone resorption|cell junction assembly|cellular membrane organization|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular protein kinase cascade|leukocyte migration|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of integrin activation|Ras protein signal transduction|regulation of bone resorption|regulation of vascular permeability|response to interleukin-1|signal complex assembly|T cell costimulation	caveola|cytosol|mitochondrial inner membrane	ATP binding|heme binding|integrin binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|SH3/SH2 adaptor activity			large_intestine(10)|lung(1)|central_nervous_system(1)|endometrium(1)	13		Myeloproliferative disorder(115;0.00878)			Dasatinib(DB01254)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	36038007	36038008	+	IGR	DEL	TT	-	-	rs11478595		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36038007_36038008delTT								SRC (4188 upstream) : BLCAP (107812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	36318863	36318865	+	IGR	DEL	TTT	-	-	rs140957337		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36318863_36318865delTTT								BLCAP (162560 upstream) : CTNNBL1 (3569 downstream)																																			---	---	---	---
CTNNBL1	56259	broad.mit.edu	37	20	36336331	36336332	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36336331_36336332delGA	uc010zvw.1	+						CTNNBL1_uc010zvv.1_Intron	NM_030877	NP_110517			beta catenin-like 1						apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
VSTM2L	128434	broad.mit.edu	37	20	36565327	36565328	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36565327_36565328delAA	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	36572379	36572380	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36572379_36572380insA	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)																---	---	---	---
KIAA0406	9675	broad.mit.edu	37	20	36625457	36625458	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36625457_36625458delGA	uc002xhl.2	-						KIAA0406_uc002xhm.2_Intron	NM_014657	NP_055472			hypothetical protein LOC9675								binding				0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37154179	37154179	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37154179delT	uc002xiw.2	+						RALGAPB_uc002xix.2_Intron|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.2_Intron|RALGAPB_uc002xja.1_Intron	NM_020336	NP_065069			Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	37220779	37220780	+	IGR	DEL	GA	-	-	rs67856662		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37220779_37220780delGA								ADIG (3675 upstream) : SLC32A1 (132325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37277257	37277257	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37277257delT								ADIG (60153 upstream) : SLC32A1 (75848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37281792	37281794	+	IGR	DEL	ATA	-	-	rs76366444		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37281792_37281794delATA								ADIG (64688 upstream) : SLC32A1 (71311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37322881	37322881	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37322881delT								ADIG (105777 upstream) : SLC32A1 (30224 downstream)																																			---	---	---	---
PPP1R16B	26051	broad.mit.edu	37	20	37544713	37544714	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37544713_37544714delAA	uc002xje.2	+						PPP1R16B_uc010ggc.2_Intron	NM_015568	NP_056383			protein phosphatase 1 regulatory inhibitor						regulation of filopodium assembly|signal transduction	nucleus|plasma membrane	protein phosphatase binding			upper_aerodigestive_tract(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	37692036	37692039	+	IGR	DEL	TCTT	-	-	rs149057252		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37692036_37692039delTCTT								DHX35 (23673 upstream) : LOC339568 (150385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39450928	39450929	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39450928_39450929insT								MAFB (133052 upstream) : TOP1 (206533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39479967	39479968	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39479967_39479968insT								MAFB (162091 upstream) : TOP1 (177494 downstream)																																			---	---	---	---
ZHX3	23051	broad.mit.edu	37	20	39898525	39898526	+	Intron	DEL	AA	-	-	rs77687785		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39898525_39898526delAA	uc002xjs.1	-						ZHX3_uc002xjq.1_5'Flank|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)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	40874514	40874514	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40874514delC	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	41130506	41130506	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41130506delT	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)																---	---	---	---
TOX2	84969	broad.mit.edu	37	20	42563439	42563440	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42563439_42563440delTG	uc010ggo.2	+						TOX2_uc002xle.3_Intron|TOX2_uc010ggp.2_Intron	NM_001098797	NP_001092267			TOX high mobility group box family member 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	43090929	43090930	+	Intron	INS	-	A	A	rs147265115	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43090929_43090930insA	uc002xmb.3	-											RecName: Full=Uncharacterized protein C20orf62;																														---	---	---	---
SERINC3	10955	broad.mit.edu	37	20	43132817	43132818	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43132817_43132818insA	uc002xme.2	-						SERINC3_uc002xmf.1_Intron|SERINC3_uc010ggs.1_Intron|SERINC3_uc010zwp.1_Intron	NM_198941	NP_945179			tumor differentially expressed protein 1							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)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	43155752	43155752	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43155752delT								SERINC3 (5026 upstream) : PKIG (4684 downstream)																																			---	---	---	---
PKIG	11142	broad.mit.edu	37	20	43197114	43197115	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43197114_43197115delTT	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)															---	---	---	---
WFDC8	90199	broad.mit.edu	37	20	44184633	44184633	+	Intron	DEL	A	-	-	rs78363134		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44184633delA	uc002xow.2	-						WFDC8_uc002xox.2_Intron	NM_181510	NP_852611			WAP four-disulfide core domain 8 precursor							extracellular region	serine-type endopeptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
WFDC8	90199	broad.mit.edu	37	20	44206044	44206044	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44206044delT	uc002xow.2	-						WFDC8_uc002xox.2_Intron	NM_181510	NP_852611			WAP four-disulfide core domain 8 precursor							extracellular region	serine-type endopeptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
DNTTIP1	116092	broad.mit.edu	37	20	44427124	44427124	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44427124delA	uc002xpk.2	+							NM_052951	NP_443183			terminal deoxynucleotidyltransferase interacting							nucleus				ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
UBE2C	11065	broad.mit.edu	37	20	44442159	44442159	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44442159delT	uc002xpm.2	+						UBE2C_uc002xpl.2_Intron|UBE2C_uc002xpn.2_Intron|UBE2C_uc002xpo.2_Intron|UBE2C_uc002xpp.2_Intron|UBE2C_uc002xpq.2_Intron	NM_007019	NP_008950			ubiquitin-conjugating enzyme E2C isoform 1						activation of anaphase-promoting complex activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cyclin catabolic process|exit from mitosis|free ubiquitin chain polymerization|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|positive regulation of exit from mitosis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination|protein K48-linked ubiquitination|spindle organization	anaphase-promoting complex|cytosol|nucleoplasm	ATP binding|protein binding|ubiquitin-protein ligase activity				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	44514855	44514856	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44514855_44514856delAA								ZSWIM1 (951 upstream) : C20orf165 (275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	44728843	44728843	+	IGR	DEL	A	-	-	rs112043390		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44728843delA								NCOA5 (10263 upstream) : CD40 (18063 downstream)																																			---	---	---	---
CD40	958	broad.mit.edu	37	20	44746847	44746847	+	5'Flank	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44746847delC	uc002xrg.1	+						CD40_uc002xrf.1_5'Flank|CD40_uc002xrh.1_5'Flank|CD40_uc002xri.1_5'Flank|CD40_uc002xrj.1_5'Flank|CD40_uc002xrk.1_5'Flank	NM_001250	NP_001241			CD40 antigen isoform 1 precursor						B cell proliferation|cellular response to mechanical stimulus|inflammatory response|platelet activation|positive regulation of endothelial cell apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein complex assembly	CD40 receptor complex|extracellular region	enzyme binding|receptor activity			lung(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)			Simvastatin(DB00641)									Immune_Deficiency_with_Hyper-IgM				---	---	---	---
CDH22	64405	broad.mit.edu	37	20	44894585	44894588	+	Intron	DEL	ACAC	-	-	rs10536307		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44894585_44894588delACAC	uc010ghk.1	-							NM_021248	NP_067071			cadherin 22 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)																---	---	---	---
CDH22	64405	broad.mit.edu	37	20	44911749	44911749	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44911749delC	uc010ghk.1	-							NM_021248	NP_067071			cadherin 22 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	45116880	45116880	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45116880delT								LOC100240726 (22949 upstream) : ZNF334 (12829 downstream)																																			---	---	---	---
SLC13A3	64849	broad.mit.edu	37	20	45211240	45211240	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45211240delA	uc002xsf.1	-						SLC13A3_uc010ghn.1_Intron|SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron|SLC13A3_uc010zxv.1_Intron	NM_022829	NP_073740			solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)													---	---	---	---
SLC13A3	64849	broad.mit.edu	37	20	45228423	45228423	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45228423delT	uc002xsf.1	-						SLC13A3_uc010ghn.1_Intron|SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron	NM_022829	NP_073740			solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)													---	---	---	---
TP53RK	112858	broad.mit.edu	37	20	45316155	45316156	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45316155_45316156insA	uc002xsk.2	-						TP53RK_uc002xsj.2_Intron	NM_033550	NP_291028			p53-related protein kinase						lipopolysaccharide biosynthetic process	membrane|nucleus	ATP binding|p53 binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45689040	45689041	+	Intron	INS	-	AG	AG	rs150164068	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45689040_45689041insAG	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	45938054	45938054	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45938054delT	uc002xta.1	-						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|ZMYND8_uc002xth.2_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)															---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46256271	46256271	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46256271delT	uc002xtk.2	+						NCOA3_uc010ght.1_Intron|NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron|NCOA3_uc010zyc.1_Intron	NM_181659	NP_858045			nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5																		---	---	---	---
SULF2	55959	broad.mit.edu	37	20	46292944	46292944	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46292944delC	uc002xto.2	-						SULF2_uc002xtr.2_Intron|SULF2_uc002xtq.2_Intron|SULF2_uc010zyd.1_Intron	NM_018837	NP_061325			sulfatase 2 isoform a precursor						bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	20	47235888	47235888	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47235888delC								LOC284749 (236507 upstream) : PREX1 (4905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	47238926	47238926	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47238926delA								LOC284749 (239545 upstream) : PREX1 (1867 downstream)																																			---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47252755	47252756	+	Intron	INS	-	TC	TC	rs138856412	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47252755_47252756insTC	uc002xtw.1	-						PREX1_uc002xtv.1_Intron	NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47258162	47258162	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47258162delA	uc002xtw.1	-						PREX1_uc002xtv.1_Intron	NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	47458549	47458550	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47458549_47458550insT								PREX1 (14129 upstream) : ARFGEF2 (79725 downstream)																																			---	---	---	---
ARFGEF2	10564	broad.mit.edu	37	20	47536642	47536643	+	5'Flank	INS	-	T	T	rs140621774	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47536642_47536643insT	uc002xtx.3	+							NM_006420	NP_006411			ADP-ribosylation factor guanine						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	48236206	48236207	+	IGR	INS	-	GGAT	GGAT	rs141199932	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48236206_48236207insGGAT								PTGIS (51499 upstream) : B4GALT5 (13278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	48911702	48911702	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48911702delT	uc002xvk.2	+											Homo sapiens cDNA FLJ33286 fis, clone ASTRO2014174.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	49061025	49061028	+	IGR	DEL	GTGT	-	-	rs11467769		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49061025_49061028delGTGT								CEBPB (251813 upstream) : PTPN1 (65863 downstream)																																			---	---	---	---
PTPN1	5770	broad.mit.edu	37	20	49143885	49143887	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49143885_49143887delTTT	uc002xvl.2	+						PTPN1_uc010zys.1_Intron	NM_002827	NP_002818			protein tyrosine phosphatase, non-receptor type						blood coagulation|interferon-gamma-mediated signaling pathway|negative regulation of insulin receptor signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytosol|endoplasmic reticulum membrane	protein tyrosine phosphatase activity|zinc ion binding				0		Lung NSC(126;0.163)			Clodronate(DB00720)|Tiludronate(DB01133)													---	---	---	---
BCAS4	55653	broad.mit.edu	37	20	49430375	49430376	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49430375_49430376delAA	uc002xvq.2	+						BCAS4_uc002xvp.1_Intron|BCAS4_uc002xvr.2_Intron|BCAS4_uc002xvs.2_Intron	NM_017843	NP_060313			breast carcinoma amplified sequence 4 isoform a							cytoplasm					0																		---	---	---	---
DPM1	8813	broad.mit.edu	37	20	49565355	49565355	+	Intron	DEL	A	-	-	rs76899294		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49565355delA	uc002xvw.1	-						DPM1_uc002xvv.1_5'Flank|DPM1_uc002xvx.1_Intron	NM_003859	NP_003850			dolichyl-phosphate mannosyltransferase 1						C-terminal protein lipidation|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|protein N-linked glycosylation via asparagine|protein O-linked mannosylation	dolichol-phosphate-mannose synthase complex|endoplasmic reticulum membrane|membrane fraction	dolichyl-phosphate beta-D-mannosyltransferase activity|dolichyl-phosphate-mannose-protein mannosyltransferase activity|protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	49717469	49717469	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49717469delT								KCNG1 (77794 upstream) : NFATC2 (290297 downstream)																																			---	---	---	---
NFATC2	4773	broad.mit.edu	37	20	50084095	50084095	+	Intron	DEL	A	-	-	rs73625463		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50084095delA	uc002xwd.2	-						NFATC2_uc002xwc.2_Intron|NFATC2_uc010zyv.1_Intron|NFATC2_uc010zyw.1_Intron|NFATC2_uc010zyx.1_Intron|NFATC2_uc010zyy.1_Intron|NFATC2_uc010zyz.1_Intron|NFATC2_uc002xwe.2_Intron	NM_173091	NP_775114			nuclear factor of activated T-cells,						B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)																	---	---	---	---
NFATC2	4773	broad.mit.edu	37	20	50107823	50107823	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50107823delA	uc002xwd.2	-						NFATC2_uc002xwc.2_Intron|NFATC2_uc010zyv.1_Intron|NFATC2_uc010zyw.1_Intron|NFATC2_uc010zyx.1_Intron|NFATC2_uc010zyy.1_Intron|NFATC2_uc010zyz.1_Intron|NFATC2_uc002xwe.2_Intron	NM_173091	NP_775114			nuclear factor of activated T-cells,						B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)																	---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50345166	50345166	+	Intron	DEL	A	-	-	rs66963134		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50345166delA	uc002xwg.1	-						ATP9A_uc010gih.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	50398713	50398717	+	IGR	DEL	AAAAA	-	-	rs75216887		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50398713_50398717delAAAAA								ATP9A (13805 upstream) : SALL4 (1868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50447957	50447957	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50447957delT								SALL4 (28909 upstream) : ZFP64 (252594 downstream)																																			---	---	---	---
ZFP64	55734	broad.mit.edu	37	20	50750736	50750737	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50750736_50750737insT	uc002xwk.2	-							NM_199427	NP_955459			zinc finger protein 64 isoform d						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	50872211	50872212	+	IGR	DEL	TT	-	-	rs72283118		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50872211_50872212delTT								ZFP64 (63687 upstream) : TSHZ2 (716665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51001637	51001638	+	IGR	INS	-	AC	AC	rs148985060	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51001637_51001638insAC								ZFP64 (193113 upstream) : TSHZ2 (587239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51071799	51071799	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51071799delT								ZFP64 (263275 upstream) : TSHZ2 (517078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51153359	51153360	+	IGR	INS	-	T	T	rs148268599	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51153359_51153360insT								ZFP64 (344835 upstream) : TSHZ2 (435517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51268163	51268163	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51268163delT								ZFP64 (459639 upstream) : TSHZ2 (320714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51306539	51306540	+	IGR	INS	-	TCC	TCC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51306539_51306540insTCC								ZFP64 (498015 upstream) : TSHZ2 (282337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51513388	51513388	+	IGR	DEL	G	-	-	rs4809922		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51513388delG								ZFP64 (704864 upstream) : TSHZ2 (75489 downstream)																																			---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51629200	51629201	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51629200_51629201delCA	uc002xwo.2	+							NM_173485	NP_775756			teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51957464	51957464	+	Intron	DEL	A	-	-	rs76890157		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51957464delA	uc002xwo.2	+							NM_173485	NP_775756			teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	52403838	52403838	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52403838delT								ZNF217 (193037 upstream) : SUMO1P1 (87204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52451589	52451589	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52451589delT								ZNF217 (240788 upstream) : SUMO1P1 (39453 downstream)																																			---	---	---	---
DOK5	55816	broad.mit.edu	37	20	53151833	53151833	+	Intron	DEL	T	-	-	rs112169921		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53151833delT	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	53864871	53864871	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53864871delA								DOK5 (597162 upstream) : CBLN4 (707626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54521226	54521226	+	IGR	DEL	A	-	-	rs111748908		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54521226delA								None (None upstream) : CBLN4 (51271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54649036	54649037	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54649036_54649037insA								CBLN4 (69024 upstream) : MC3R (174751 downstream)																																			---	---	---	---
AURKA	6790	broad.mit.edu	37	20	54959235	54959235	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54959235delT	uc002xxd.1	-						AURKA_uc002xxe.1_Intron|AURKA_uc002xxf.1_Intron|AURKA_uc002xxg.1_Intron|AURKA_uc002xxh.1_Intron|AURKA_uc002xxi.1_Intron|AURKA_uc002xxj.1_Intron|AURKA_uc002xxk.1_Intron|AURKA_uc010zzd.1_Intron	NM_198433	NP_940835			serine/threonine protein kinase 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|phosphatidylinositol-mediated signaling|regulation of protein stability|spindle organization	cytosol|nucleus|perinuclear region of cytoplasm|spindle microtubule|spindle pole centrosome	ATP binding|protein kinase binding|protein serine/threonine kinase activity			lung(3)|ovary(2)|breast(1)|large_intestine(1)|skin(1)	8			Colorectal(105;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	55376273	55376273	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55376273delA								TFAP2C (161937 upstream) : BMP7 (367536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55579331	55579332	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55579331_55579332delAA								TFAP2C (364995 upstream) : BMP7 (164477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55679141	55679141	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55679141delA								TFAP2C (464805 upstream) : BMP7 (64668 downstream)																																			---	---	---	---
BMP7	655	broad.mit.edu	37	20	55807472	55807473	+	Intron	INS	-	A	A	rs75492781		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55807472_55807473insA	uc010gip.1	-						BMP7_uc010giq.1_Intron|BMP7_uc002xyc.2_Intron	NM_001719	NP_001710			bone morphogenetic protein 7 precursor						BMP signaling pathway|cartilage development|cellular response to hypoxia|epithelial to mesenchymal transition|growth|mesonephros development|negative regulation of glomerular mesangial cell proliferation|negative regulation of MAP kinase activity|negative regulation of mitosis|negative regulation of neuron differentiation|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of phosphorylation|negative regulation of striated muscle cell apoptosis|negative regulation of transcription, DNA-dependent|ossification|pathway-restricted SMAD protein phosphorylation|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|protein localization to nucleus|regulation of removal of superoxide radicals|SMAD protein signal transduction|steroid hormone mediated signaling pathway|ureteric bud development	extracellular space	cytokine activity|growth factor activity			skin(1)	1	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)															---	---	---	---
SPO11	23626	broad.mit.edu	37	20	55911150	55911150	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55911150delT	uc002xye.2	+						SPO11_uc002xyf.2_Intron	NM_012444	NP_036576			meiotic recombination protein SPO11 isoform a						female gamete generation|reciprocal meiotic recombination	chromosome|nucleus	ATP binding|DNA binding|hydrolase activity			breast(2)|skin(1)	3	Lung NSC(12;0.0066)|all_lung(29;0.0188)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.73e-14)|Epithelial(14;9.02e-10)|all cancers(14;9.31e-09)										Editing_and_processing_nucleases					---	---	---	---
PMEPA1	56937	broad.mit.edu	37	20	56288102	56288102	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56288102delA	uc002xys.2	-						PMEPA1_uc002xyr.2_5'Flank|PMEPA1_uc002xyt.2_5'Flank	NM_199169	NP_954638			transmembrane prostate androgen-induced protein						androgen receptor signaling pathway	integral to membrane|plasma membrane	WW domain binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	56329969	56329970	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56329969_56329970delTT								PMEPA1 (43428 upstream) : C20orf85 (396013 downstream)																																			---	---	---	---
PPP4R1L	55370	broad.mit.edu	37	20	56809499	56809499	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56809499delT	uc002xyw.2	-						PPP4R1L_uc010gjn.1_Intron					Homo sapiens PRO1085 mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	57120448	57120448	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57120448delA	uc002xzg.1	+											Homo sapiens cDNA FLJ30075 fis, clone BGGI11000285.																														---	---	---	---
TH1L	51497	broad.mit.edu	37	20	57566552	57566553	+	Intron	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57566552_57566553delCT	uc002yag.2	+						TH1L_uc002yaf.1_Intron|TH1L_uc002yah.2_Intron	NM_198976	NP_945327			TH1-like protein						negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	all_lung(29;0.00711)		Colorectal(105;0.109)															---	---	---	---
ATP5E	514	broad.mit.edu	37	20	57606612	57606612	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57606612delA	uc002yal.2	-							NM_001001977	NP_001001977			ATP synthase, H+ transporting, mitochondrial F1						respiratory electron transport chain	mitochondrial matrix|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)	hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism				0	all_lung(29;0.00711)		Colorectal(105;0.109)															---	---	---	---
SLMO2	51012	broad.mit.edu	37	20	57611829	57611829	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57611829delA	uc002yam.2	-						SLMO2_uc010zzv.1_Intron	NM_016045	NP_057129			slowmo homolog 2											skin(1)	1	all_lung(29;0.00711)		Colorectal(105;0.109)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	57959496	57959496	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57959496delG								EDN3 (58450 upstream) : PHACTR3 (193068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59585302	59585303	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59585302_59585303insT								MIR646 (701677 upstream) : CDH4 (242256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59739515	59739515	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59739515delA								MIR646 (855890 upstream) : CDH4 (88044 downstream)																																			---	---	---	---
CDH4	1002	broad.mit.edu	37	20	59849589	59849589	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59849589delG	uc002ybn.1	+							NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	59915646	59915647	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59915646_59915647delTT	uc002ybn.1	+							NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
TAF4	6874	broad.mit.edu	37	20	60609099	60609101	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60609099_60609101delAAA	uc002ybs.2	-							NM_003185	NP_003176			TBP-associated factor 4						interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|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 TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)															---	---	---	---
NTSR1	4923	broad.mit.edu	37	20	61341143	61341143	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61341143delC	uc002ydf.2	+	1	955	c.584delC	c.(583-585)GCCfs	p.A195fs		NM_002531	NP_002522	P30989	NTR1_HUMAN	neurotensin receptor 1	195	Helical; Name=4; (Potential).					endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	neurotensin receptor activity, G-protein coupled			skin(2)|lung(1)|central_nervous_system(1)	4	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)															---	---	---	---
SLC17A9	63910	broad.mit.edu	37	20	61589140	61589141	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61589140_61589141delTG	uc002yea.3	+						SLC17A9_uc002ydz.3_Intron|SLC17A9_uc011aap.1_Intron	NM_022082	NP_071365			vesicular nucleotide transporter SLC17A9						exocytosis|transmembrane transport	integral to membrane	transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	61967844	61967845	+	IGR	INS	-	GT	GT	rs146818481	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61967844_61967845insGT								COL20A1 (5560 upstream) : CHRNA4 (6820 downstream)																																			---	---	---	---
ZBTB46	140685	broad.mit.edu	37	20	62382255	62382255	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62382255delA	uc002ygv.1	-						ZBTB46_uc002ygu.2_Intron	NM_025224	NP_079500			zinc finger and BTB domain containing 46						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)																	---	---	---	---
UCKL1	54963	broad.mit.edu	37	20	62577788	62577788	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62577788delC	uc010gkn.2	-						UCKL1_uc011abm.1_Intron|UCKL1_uc011abn.1_Intron|UCKL1_uc011abo.1_Intron	NM_017859	NP_060329			uridine-cytidine kinase 1-like 1						interspecies interaction between organisms	endoplasmic reticulum|nucleus	ATP binding|phosphotransferase activity, alcohol group as acceptor|protein binding|uridine kinase activity				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)																	---	---	---	---
UCKL1	54963	broad.mit.edu	37	20	62578434	62578436	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62578434_62578436delAAA	uc010gkn.2	-						UCKL1_uc011abm.1_Intron|UCKL1_uc011abn.1_Intron|UCKL1_uc011abo.1_Intron	NM_017859	NP_060329			uridine-cytidine kinase 1-like 1						interspecies interaction between organisms	endoplasmic reticulum|nucleus	ATP binding|phosphotransferase activity, alcohol group as acceptor|protein binding|uridine kinase activity				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)																	---	---	---	---
PRPF6	24148	broad.mit.edu	37	20	62647477	62647479	+	Intron	DEL	TTT	-	-	rs78547320		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62647477_62647479delTTT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	62746495	62746495	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62746495delT								NPBWR2 (8311 upstream) : MYT1 (36649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9414350	9414351	+	IGR	DEL	AT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9414350_9414351delAT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9415562	9415562	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9415562delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9483288	9483288	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9483288delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9662822	9662823	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9662822_9662823insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9668163	9668163	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9668163delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9753235	9753235	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9753235delA	uc011abu.1	+											Homo sapiens, clone IMAGE:4720764, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10407524	10407525	+	IGR	INS	-	T	T	rs71273047		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10407524_10407525insT								None (None upstream) : TPTE (499218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10535407	10535407	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10535407delT	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10588349	10588350	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10588349_10588350delTT	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10647425	10647425	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10647425delT								None (None upstream) : TPTE (259318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10734173	10734174	+	IGR	INS	-	TGA	TGA	rs138115959		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10734173_10734174insTGA								None (None upstream) : TPTE (172569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10816153	10816172	+	IGR	DEL	AATGGAATGGAATGGAAAGG	-	-	rs149316420		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10816153_10816172delAATGGAATGGAATGGAAAGG								None (None upstream) : TPTE (90571 downstream)																																			---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10907706	10907706	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10907706delA	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	10950850	10950850	+	Intron	DEL	G	-	-	rs212128		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10950850delG	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	11083997	11083998	+	Intron	DEL	TT	-	-	rs60923226		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11083997_11083998delTT	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	14360253	14360254	+	IGR	INS	-	A	A	rs151198233		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14360253_14360254insA								None (None upstream) : C21orf99 (50233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14360853	14360853	+	IGR	DEL	A	-	-	rs113034034		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14360853delA								None (None upstream) : C21orf99 (49634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14377702	14377703	+	IGR	INS	-	GT	GT	rs146274523	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14377702_14377703insGT								None (None upstream) : C21orf99 (32784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14398961	14398962	+	IGR	DEL	AA	-	-	rs76194953		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14398961_14398962delAA								None (None upstream) : C21orf99 (11525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	15202489	15202490	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15202489_15202490delAC								POTED (188583 upstream) : C21orf15 (12965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	15275937	15275938	+	5'Flank	INS	-	A	A	rs147035684	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15275937_15275938insA	uc002yjg.2	+											DQ579288																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	15289076	15289076	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15289076delT								C21orf15 (68391 upstream) : C21orf81 (27020 downstream)																																			---	---	---	---
LIPI	149998	broad.mit.edu	37	21	15498046	15498046	+	Intron	DEL	T	-	-	rs78197103		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15498046delT	uc002yjm.2	-						uc002yjk.2_Intron|uc002yjl.2_Intron	NM_198996	NP_945347			lipase, member I						lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)														---	---	---	---
LIPI	149998	broad.mit.edu	37	21	15513960	15513962	+	Intron	DEL	TTG	-	-	rs10543778		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15513960_15513962delTTG	uc002yjm.2	-						uc002yjk.2_Intron|uc002yjl.2_Intron	NM_198996	NP_945347			lipase, member I						lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	16065430	16065430	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16065430delT								SAMSN1 (109707 upstream) : NRIP1 (268126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16212154	16212154	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16212154delA	uc002yjw.1	-											full-length cDNA clone CS0DI053YO09 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	16654362	16654362	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16654362delT								NRIP1 (217236 upstream) : USP25 (448134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	17377029	17377030	+	IGR	DEL	AC	-	-	rs72424300		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17377029_17377030delAC								USP25 (124652 upstream) : C21orf34 (65812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	18218981	18218982	+	IGR	DEL	AC	-	-	rs60639586		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18218981_18218982delAC								C21orf34 (236887 upstream) : CXADR (666348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	18769985	18769985	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18769985delA								C21orf34 (787891 upstream) : CXADR (115345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	18785219	18785219	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18785219delA								C21orf34 (803125 upstream) : CXADR (100111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	18791024	18791025	+	IGR	INS	-	A	A	rs143669082	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18791024_18791025insA								C21orf34 (808930 upstream) : CXADR (94305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20079224	20079225	+	Intron	INS	-	C	C	rs112250921		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20079224_20079225insC	uc010glf.1	-						uc002ykx.2_Intron					Homo sapiens, clone IMAGE:5392784, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	20126398	20126398	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20126398delC	uc002ykx.2	-											Homo sapiens, clone IMAGE:5392784, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	21112407	21112408	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21112407_21112408delGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21130778	21130779	+	IGR	INS	-	A	A	rs138002134	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21130778_21130779insA								None (None upstream) : C21orf131 (984135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	22260628	22260628	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22260628delA								C21orf131 (85202 upstream) : NCAM2 (110005 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23367122	23367125	+	IGR	DEL	TGTA	-	-	rs141037701	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23367122_23367125delTGTA								NCAM2 (455908 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23794219	23794219	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23794219delA								NCAM2 (883005 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	24194562	24194563	+	IGR	INS	-	CT	CT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24194562_24194563insCT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	25345616	25345616	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25345616delT								None (None upstream) : None (None downstream)																																			---	---	---	---
MRPL39	54148	broad.mit.edu	37	21	26962138	26962139	+	Intron	INS	-	G	G	rs138959025	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26962138_26962139insG	uc002ylo.2	-						MRPL39_uc002yln.2_Intron	NM_017446	NP_059142			mitochondrial ribosomal protein L39 isoform a							mitochondrial ribosome	nucleotide binding				0																		---	---	---	---
JAM2	58494	broad.mit.edu	37	21	27013127	27013128	+	Intron	INS	-	TCTC	TCTC	rs147248766	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27013127_27013128insTCTC	uc002ylp.1	+						JAM2_uc011ace.1_Intron|JAM2_uc002ylq.1_Intron|JAM2_uc011acf.1_Intron|JAM2_uc010glh.1_Intron|JAM2_uc002ylr.1_Intron|JAM2_uc010gli.1_Intron	NM_021219	NP_067042			junctional adhesion molecule 2 precursor						blood coagulation|cell-cell adhesion|leukocyte migration	integral to plasma membrane|tight junction					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	27183756	27183756	+	IGR	DEL	C	-	-	rs28393898	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27183756delC								GABPA (38986 upstream) : APP (69106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28658130	28658130	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28658130delT								ADAMTS5 (318691 upstream) : NCRNA00113 (436568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	29183360	29183361	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29183360_29183361delAA								NCRNA00113 (59808 upstream) : C21orf94 (202321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	29382318	29382318	+	IGR	DEL	T	-	-	rs71185467		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29382318delT								NCRNA00113 (258766 upstream) : C21orf94 (3364 downstream)																																			---	---	---	---
USP16	10600	broad.mit.edu	37	21	30415681	30415681	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30415681delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	30561978	30561978	+	IGR	DEL	T	-	-	rs67750455		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30561978delT								C21orf7 (13778 upstream) : NCRNA00189 (3823 downstream)																																			---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	31226827	31226827	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31226827delA	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)													---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32681489	32681489	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32681489delT	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	32875560	32875560	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32875560delT	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	33058909	33058909	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33058909delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	33146338	33146340	+	IGR	DEL	AAA	-	-	rs67874783		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33146338_33146340delAAA								SFRS15 (41907 upstream) : HUNK (99288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	33183163	33183166	+	IGR	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33183163_33183166delTTTT								SFRS15 (78732 upstream) : HUNK (62462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	33659555	33659556	+	IGR	DEL	CA	-	-	rs73901378	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33659555_33659556delCA								C21orf45 (8179 upstream) : MRAP (4568 downstream)																																			---	---	---	---
C21orf63	59271	broad.mit.edu	37	21	33857255	33857255	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33857255delT	uc002ypr.1	+						C21orf63_uc002yps.1_Intron|C21orf63_uc010glw.1_Intron|C21orf63_uc002ypt.1_Intron|C21orf63_uc002ypu.1_Intron	NM_058187	NP_478067			hypothetical protein LOC59271 precursor							integral to membrane	sugar binding			ovary(2)|pancreas(1)	3																		---	---	---	---
GCFC1	94104	broad.mit.edu	37	21	34107532	34107532	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34107532delA	uc002yqn.2	-						uc002yqk.2_Intron|GCFC1_uc002yql.2_Intron|GCFC1_uc002yqm.2_Intron|GCFC1_uc002yqo.2_Intron	NM_016631	NP_057715			GC-rich sequence DNA-binding factor candidate							cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	34550554	34550556	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34550554_34550556delAAA								C21orf54 (8013 upstream) : IFNAR2 (51675 downstream)																																			---	---	---	---
IFNAR1	3454	broad.mit.edu	37	21	34696189	34696201	+	5'Flank	DEL	ATATAGAGATGGG	-	-	rs71194835		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34696189_34696201delATATAGAGATGGG	uc002yrn.2	+						IFNAR1_uc011adv.1_5'Flank	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-4292-01	TCGA-BR-4292-01									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	34724909	34724909	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34724909delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	34758091	34758091	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34758091delA								IFNAR1 (25965 upstream) : IFNGR2 (17111 downstream)																																			---	---	---	---
CRYZL1	9946	broad.mit.edu	37	21	34989331	34989331	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34989331delT	uc011adw.1	-						DONSON_uc002ysn.1_Intron|CRYZL1_uc002ysr.1_Intron|CRYZL1_uc002yss.1_Intron|CRYZL1_uc002yst.1_Intron|CRYZL1_uc002ysu.2_Intron	NM_145858	NP_665857			crystallin, zeta-like 1						quinone cofactor metabolic process	cytosol	NADP binding|NADPH:quinone reductase activity|zinc ion binding				0																		---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35184456	35184456	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35184456delA	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Intron|ITSN1_uc002ysz.2_Intron|ITSN1_uc010gmg.2_Intron|ITSN1_uc010gmh.2_Intron|ITSN1_uc002ysw.2_Intron|ITSN1_uc010gmi.2_Intron|ITSN1_uc010gmj.2_Intron|ITSN1_uc002ysy.2_Intron|ITSN1_uc002ysx.2_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytc.1_Intron|ITSN1_uc002ytd.2_Intron|ITSN1_uc010gmk.2_Intron|ITSN1_uc010gml.2_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron|ITSN1_uc002yte.2_Intron|ITSN1_uc002ytf.1_Intron	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35231209	35231209	+	Intron	DEL	T	-	-	rs5843624		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35231209delT	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	35352235	35352235	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35352235delT								ATP5O (64077 upstream) : MRPS6 (93588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	35386729	35386731	+	IGR	DEL	AAA	-	-	rs79809635		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35386729_35386731delAAA								ATP5O (98571 upstream) : MRPS6 (59092 downstream)																																			---	---	---	---
RCAN1	1827	broad.mit.edu	37	21	35962801	35962801	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35962801delA	uc002yue.2	-						RCAN1_uc002yuc.2_Intron|RCAN1_uc002yud.2_Intron	NM_004414	NP_004405			calcipressin 1 isoform a						blood circulation|calcium-mediated signaling|central nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36215818	36215819	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36215818_36215819delCA	uc002yuh.2	-						RUNX1_uc002yui.2_Intron|RUNX1_uc010gmu.2_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron|RUNX1_uc002yuo.1_Intron	NM_001001890	NP_001001890			runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36341697	36341697	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	36860770	36860770	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36860770delA	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	36872937	36872937	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36872937delA	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	37127325	37127325	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37127325delT	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				---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37595487	37595487	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37595487delT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119			pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
MORC3	23515	broad.mit.edu	37	21	37746690	37746690	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37746690delA	uc002yvi.2	+							NM_015358	NP_056173			MORC family CW-type zinc finger 3						cell aging|maintenance of protein location in nucleus|negative regulation of fibroblast proliferation|peptidyl-serine phosphorylation|protein stabilization	aggresome|intermediate filament cytoskeleton|PML body	ATP binding|zinc ion binding			ovary(2)	2																		---	---	---	---
PIGP	51227	broad.mit.edu	37	21	38439762	38439762	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38439762delT	uc002yvw.1	-						PIGP_uc002yvy.1_Intron|PIGP_uc002yvx.1_Intron	NM_153681	NP_710148			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity				0		Myeloproliferative disorder(46;0.0412)																---	---	---	---
TTC3	7267	broad.mit.edu	37	21	38460480	38460480	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38460480delT	uc002yvz.2	+						TTC3_uc011aee.1_Intron|TTC3_uc002ywa.2_Intron|TTC3_uc002ywb.2_Intron|TTC3_uc010gnf.2_Intron|TTC3_uc011aed.1_Intron|TTC3_uc010gne.1_Intron	NM_001001894	NP_001001894			tetratricopeptide repeat domain 3						protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(3)|ovary(2)|lung(2)|breast(2)	9		Myeloproliferative disorder(46;0.0412)																---	---	---	---
TTC3	7267	broad.mit.edu	37	21	38546044	38546044	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38546044delG	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)																---	---	---	---
DYRK1A	1859	broad.mit.edu	37	21	38760957	38760957	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38760957delT	uc002ywi.2	+						DYRK1A_uc002ywg.1_Intron|DYRK1A_uc010gno.1_Intron|DYRK1A_uc002ywh.1_Intron	NM_101395	NP_567824			dual-specificity tyrosine-(Y)-phosphorylation						nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4																		---	---	---	---
DYRK1A	1859	broad.mit.edu	37	21	38854151	38854153	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38854151_38854153delAAA	uc002ywk.2	+						DYRK1A_uc002ywh.1_Intron|DYRK1A_uc002ywi.2_Intron|DYRK1A_uc002ywj.2_Intron|DYRK1A_uc002ywl.2_Intron|DYRK1A_uc002ywm.2_Intron	NM_001396	NP_001387			dual-specificity tyrosine-(Y)-phosphorylation						nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	39351410	39351410	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39351410delC								KCNJ6 (62714 upstream) : DSCR4 (74904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	39687015	39687016	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39687015_39687016insA								KCNJ15 (13271 upstream) : ERG (64936 downstream)																																			---	---	---	---
NCRNA00114	400866	broad.mit.edu	37	21	40125377	40125378	+	5'Flank	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40125377_40125378delTC	uc010goa.2	-						NCRNA00114_uc011aen.1_Intron|NCRNA00114_uc002yxd.3_Intron	NR_027067				Homo sapiens chromosome 21 open reading frame 24 isoform 1 (C21orf24) mRNA, complete sequence.												0																		---	---	---	---
PSMG1	8624	broad.mit.edu	37	21	40553531	40553531	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40553531delA	uc002yxi.2	-						PSMG1_uc002yxj.2_Intron|PSMG1_uc010gob.2_Intron	NM_003720	NP_003711			Down syndrome critical region protein 2 isoform						proteasome assembly	endoplasmic reticulum	protein binding				0		Prostate(19;8.44e-08)																---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40605473	40605473	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40605473delA	uc002yxk.1	-						BRWD1_uc010goc.1_Intron|BRWD1_uc002yxl.2_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40642365	40642365	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40642365delA	uc002yxk.1	-						BRWD1_uc002yxl.2_Intron|BRWD1_uc010goe.1_Intron|BRWD1_uc010gof.1_Intron|BRWD1_uc010gog.1_Intron|BRWD1_uc010goh.1_Intron|BRWD1_uc010goi.1_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
B3GALT5	10317	broad.mit.edu	37	21	40981431	40981432	+	Intron	DEL	AA	-	-	rs72434862		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40981431_40981432delAA	uc002yyb.1	+						C21orf88_uc010gok.2_Intron|C21orf88_uc002yyd.3_Intron	NM_033173	NP_149363			UDP-Gal:betaGlcNAc beta						protein glycosylation	endoplasmic reticulum|Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			skin(1)	1		Prostate(19;2.55e-06)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	41106798	41106798	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41106798delT								B3GALT5 (71983 upstream) : IGSF5 (10536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	41188351	41188352	+	IGR	INS	-	GAGAG	GAGAG	rs143121776	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41188351_41188352insGAGAG								IGSF5 (14330 upstream) : PCP4 (50995 downstream)																																			---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41719226	41719231	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41719226_41719231delAAAAAA	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	42313030	42313030	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42313030delT								DSCAM (93991 upstream) : C21orf130 (200397 downstream)																																			---	---	---	---
BACE2	25825	broad.mit.edu	37	21	42580423	42580423	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42580423delG	uc002yyw.2	+						BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron	NM_012105	NP_036237			beta-site APP-cleaving enzyme 2 isoform A						membrane protein ectodomain proteolysis|negative regulation of amyloid precursor protein biosynthetic process|peptide hormone processing	cell surface|endoplasmic reticulum|endosome|Golgi apparatus|integral to membrane	aspartic-type endopeptidase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	42933542	42933543	+	IGR	INS	-	CT	CT	rs147949452	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42933542_42933543insCT								TMPRSS2 (30499 upstream) : NCRNA00111 (165919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	43145850	43145851	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43145850_43145851insC								NCRNA00112 (8109 upstream) : RIPK4 (13678 downstream)																																			---	---	---	---
RIPK4	54101	broad.mit.edu	37	21	43165934	43165935	+	Frame_Shift_Ins	INS	-	G	G	rs144324321		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43165934_43165935insG	uc002yzn.1	-	6	968_969	c.920_921insC	c.(919-921)CCGfs	p.P307fs		NM_020639	NP_065690	P57078	RIPK4_HUMAN	ankyrin repeat domain 3	307						cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7																		---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43258311	43258311	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43283957	43283959	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43283957_43283959delTTT	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																		---	---	---	---
C2CD2	25966	broad.mit.edu	37	21	43332940	43332941	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43332940_43332941insA	uc002yzw.2	-						C2CD2_uc002yzu.2_Intron|C2CD2_uc002yzv.2_Intron|C2CD2_uc002yzx.1_Intron	NM_015500	NP_056315			C2 calcium-dependent domain containing 2 isoform							cytosol|extracellular region|nucleus				ovary(1)	1																		---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43536464	43536464	+	Intron	DEL	A	-	-	rs60051992		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43536464delA	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zag.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																		---	---	---	---
UBASH3A	53347	broad.mit.edu	37	21	43826093	43826093	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43826093delG	uc002zbe.2	+						UBASH3A_uc002zbf.2_Intron|UBASH3A_uc010gpc.2_Intron|UBASH3A_uc010gpd.2_Intron|UBASH3A_uc010gpe.2_Intron	NM_018961	NP_061834			ubiquitin associated and SH3 domain containing,							cytosol|nucleus				ovary(3)	3																		---	---	---	---
SLC37A1	54020	broad.mit.edu	37	21	43940071	43940074	+	Intron	DEL	TGTT	-	-	rs11277768		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43940071_43940074delTGTT	uc002zbi.2	+						SLC37A1_uc002zbj.2_Intron	NM_018964	NP_061837			solute carrier family 37 member 1						carbohydrate transport|transmembrane transport	integral to membrane					0																		---	---	---	---
SLC37A1	54020	broad.mit.edu	37	21	43983674	43983675	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43983674_43983675insG	uc002zbi.2	+						SLC37A1_uc002zbj.2_Intron	NM_018964	NP_061837			solute carrier family 37 member 1						carbohydrate transport|transmembrane transport	integral to membrane					0																		---	---	---	---
PDE9A	5152	broad.mit.edu	37	21	44164467	44164467	+	Intron	DEL	G	-	-	rs7280880	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44164467delG	uc002zbm.2	+						PDE9A_uc002zbn.2_Intron|PDE9A_uc002zbo.2_Intron|PDE9A_uc002zbp.2_Intron|PDE9A_uc002zbq.2_Intron|PDE9A_uc002zbs.2_Intron|PDE9A_uc002zbr.2_Intron|PDE9A_uc002zbt.2_Intron|PDE9A_uc002zbu.2_Intron|PDE9A_uc002zbv.2_Intron|PDE9A_uc002zbw.2_Intron|PDE9A_uc002zbx.2_Intron|PDE9A_uc002zby.2_Intron|PDE9A_uc002zbz.2_Intron|PDE9A_uc002zca.2_Intron|PDE9A_uc002zcb.2_Intron|PDE9A_uc002zcc.2_Intron|PDE9A_uc002zcd.2_Intron|PDE9A_uc002zce.2_Intron|PDE9A_uc002zcf.2_Intron|PDE9A_uc002zcg.2_Intron|PDE9A_uc002zch.2_Intron|PDE9A_uc010gpf.1_Intron	NM_002606	NP_002597			phosphodiesterase 9A isoform a						platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
PDE9A	5152	broad.mit.edu	37	21	44195538	44195539	+	3'UTR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44195538_44195539delAA	uc002zbm.2	+	20					PDE9A_uc002zbn.2_3'UTR|PDE9A_uc002zbo.2_3'UTR|PDE9A_uc002zbp.2_3'UTR|PDE9A_uc002zbq.2_3'UTR|PDE9A_uc002zbs.2_3'UTR|PDE9A_uc002zbr.2_3'UTR|PDE9A_uc002zbt.2_3'UTR|PDE9A_uc002zbu.2_3'UTR|PDE9A_uc002zbv.2_3'UTR|PDE9A_uc002zbw.2_3'UTR|PDE9A_uc002zbx.2_3'UTR|PDE9A_uc002zby.2_3'UTR|PDE9A_uc002zbz.2_3'UTR|PDE9A_uc002zca.2_3'UTR|PDE9A_uc002zcb.2_3'UTR|PDE9A_uc002zcc.2_3'UTR|PDE9A_uc002zcd.2_3'UTR|PDE9A_uc002zce.2_3'UTR|PDE9A_uc002zcf.2_3'UTR|PDE9A_uc002zcg.2_3'UTR|PDE9A_uc002zch.2_3'UTR	NM_002606	NP_002597			phosphodiesterase 9A isoform a						platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	44388853	44388853	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44388853delT								NDUFV3 (59081 upstream) : PKNOX1 (5790 downstream)																																			---	---	---	---
CBS	875	broad.mit.edu	37	21	44476001	44476001	+	Intron	DEL	T	-	-	rs79861734		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44476001delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	44756088	44756096	+	IGR	DEL	CACCACCAA	-	-	rs72268009	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44756088_44756096delCACCACCAA								CRYAA (163175 upstream) : SIK1 (78302 downstream)																																			---	---	---	---
AGPAT3	56894	broad.mit.edu	37	21	45400764	45400764	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45400764delT	uc002zdv.2	+						AGPAT3_uc002zdw.2_Intron|AGPAT3_uc002zdx.2_Intron|AGPAT3_uc002zdy.2_Intron	NM_020132	NP_064517			1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)														---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45447264	45447264	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45447264delA	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron|TRAPPC10_uc002zdz.2_Intron	NM_003274	NP_003265			trafficking protein particle complex 10						vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45480829	45480829	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45480829delT	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron	NM_003274	NP_003265			trafficking protein particle complex 10						vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	45581867	45581867	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45581867delT								C21orf33 (16263 upstream) : ICOSLG (64857 downstream)																																			---	---	---	---
TRPM2	7226	broad.mit.edu	37	21	45793899	45793899	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45793899delT	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	45885463	45885464	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45885463_45885464delAC								LRRC3 (6733 upstream) : C21orf29 (32311 downstream)																																			---	---	---	---
C21orf67	84536	broad.mit.edu	37	21	46355248	46355249	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46355248_46355249insC	uc011afm.1	-						C21orf67_uc002zgj.3_Intron|C21orf67_uc002zgk.3_Intron	NR_027128				RecName: Full=Uncharacterized protein C21orf67;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	46678311	46678311	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46678311delT	uc002zgz.1	+											Homo sapiens C21orf89 protein (C21orf89) mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	46719327	46719327	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46719327delT								LOC642852 (2059 upstream) : COL18A1 (105770 downstream)																																			---	---	---	---
LSS	4047	broad.mit.edu	37	21	47637461	47637461	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47637461delT	uc002zij.2	-						LSS_uc011afv.1_Intron|LSS_uc002zil.2_Intron|LSS_uc002zik.2_Intron	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	47661927	47661927	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47661927delT	uc002zir.1	-						MCM3APAS_uc002zim.2_Intron|MCM3APAS_uc002zin.2_Intron|MCM3AP_uc002zio.1_Intron|MCM3AP_uc002zip.1_Intron|MCM3AP_uc002ziq.1_Intron|MCM3APAS_uc002zis.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	47782782	47782783	+	Intron	DEL	AA	-	-	rs77523108		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47782782_47782783delAA	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)																	---	---	---	---
PCNT	5116	broad.mit.edu	37	21	47821764	47821764	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47821764delT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	16237030	16237030	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16237030delT								None (None upstream) : POTEH (19302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	16361044	16361044	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16361044delT								POTEH (73107 upstream) : OR11H1 (87782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	16879003	16879003	+	IGR	DEL	G	-	-	rs56366933		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16879003delG								OR11H1 (429199 upstream) : CCT8L2 (192645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17042536	17042537	+	IGR	DEL	AT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17042536_17042537delAT								OR11H1 (592732 upstream) : CCT8L2 (29111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17414860	17414861	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17414860_17414861insC								HSFYL1 (104635 upstream) : GAB4 (27968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17655257	17655264	+	IGR	DEL	ACACACAC	-	-	rs113512986		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17655257_17655264delACACACAC								CECR4 (8923 upstream) : CECR1 (4928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17747344	17747345	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17747344_17747345insC								CECR1 (44606 upstream) : CECR2 (93494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17822279	17822290	+	IGR	DEL	AAGGAAGGAAGG	-	-	rs146543396		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17822279_17822290delAAGGAAGGAAGG								CECR1 (119541 upstream) : CECR2 (18549 downstream)																																			---	---	---	---
CECR2	27443	broad.mit.edu	37	22	17957131	17957132	+	Intron	INS	-	A	A	rs12157684	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17957131_17957132insA	uc010gqw.1	+						CECR2_uc010gqv.1_Intron|CECR2_uc002zml.2_Intron	NM_031413	NP_113601			cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)														---	---	---	---
CECR2	27443	broad.mit.edu	37	22	18016394	18016394	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18016394delT	uc010gqw.1	+						CECR2_uc010gqv.1_Intron|CECR2_uc002zml.2_Intron|CECR2_uc002zmn.2_5'Flank	NM_031413	NP_113601			cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)														---	---	---	---
SLC25A18	83733	broad.mit.edu	37	22	18046128	18046129	+	Intron	DEL	TT	-	-	rs71673871		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18046128_18046129delTT	uc002zmp.1	+						SLC25A18_uc010gqx.2_Intron|SLC25A18_uc002zmq.1_Intron	NM_031481	NP_113669			solute carrier							integral to membrane|mitochondrial inner membrane	binding|symporter activity				0				Lung(27;0.124)	L-Glutamic Acid(DB00142)													---	---	---	---
SLC25A18	83733	broad.mit.edu	37	22	18071940	18071940	+	Intron	DEL	T	-	-	rs142475005		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18071940delT	uc002zmp.1	+						SLC25A18_uc002zmq.1_Intron	NM_031481	NP_113669			solute carrier							integral to membrane|mitochondrial inner membrane	binding|symporter activity				0				Lung(27;0.124)	L-Glutamic Acid(DB00142)													---	---	---	---
ATP6V1E1	529	broad.mit.edu	37	22	18083727	18083727	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18083727delA	uc002zmr.1	-						ATP6V1E1_uc002zms.1_Intron|ATP6V1E1_uc002zmt.1_Intron	NM_001696	NP_001687			vacuolar H+ ATPase E1 isoform a						cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	apical plasma membrane|cytosol|endosome|proton-transporting two-sector ATPase complex, catalytic domain	protein binding|proton-transporting ATPase activity, rotational mechanism			large_intestine(1)|central_nervous_system(1)	2		all_epithelial(15;0.206)		Lung(27;0.19)														---	---	---	---
BCL2L13	23786	broad.mit.edu	37	22	18130199	18130199	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18130199delT	uc002zmw.2	+						BCL2L13_uc002zmu.2_Intron|BCL2L13_uc002zmv.2_Intron|BCL2L13_uc002zmx.2_Intron|BCL2L13_uc002zmy.2_Intron|BCL2L13_uc010gqy.2_Intron|BCL2L13_uc011agk.1_Intron	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)														---	---	---	---
BCL2L13	23786	broad.mit.edu	37	22	18205142	18205143	+	Intron	DEL	GG	-	-	rs113458410		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18205142_18205143delGG	uc002zmw.2	+						BCL2L13_uc002zmx.2_Intron|BCL2L13_uc002zmy.2_Intron|BCL2L13_uc010gqy.2_Intron|BCL2L13_uc011agk.1_Intron|BCL2L13_uc010gqz.2_Intron|BCL2L13_uc002zmz.2_Intron|BCL2L13_uc002zna.2_Intron	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)														---	---	---	---
BID	637	broad.mit.edu	37	22	18224871	18224871	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18224871delC	uc002znd.1	-						BID_uc002znc.1_Intron|BID_uc002zne.1_Intron|BID_uc010gra.1_Intron|BID_uc002znf.1_Intron|BID_uc010grb.1_Intron|BID_uc010grc.1_Intron	NM_001196	NP_001187			BH3 interacting domain death agonist isoform 2						activation of pro-apoptotic gene products|establishment of protein localization in membrane|induction of apoptosis by intracellular signals|induction of apoptosis via death domain receptors|neuron apoptosis|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria|release of cytochrome c from mitochondria	cytosol|membrane fraction|mitochondrial outer membrane	death receptor binding				0		all_epithelial(15;0.198)		Lung(27;0.0419)														---	---	---	---
MICAL3	57553	broad.mit.edu	37	22	18276852	18276853	+	Intron	INS	-	G	G	rs79449812	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18276852_18276853insG	uc002zng.3	-						MICAL3_uc011agl.1_Intron|MICAL3_uc010grd.1_5'Flank|MICAL3_uc010gre.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)														---	---	---	---
TUBA8	51807	broad.mit.edu	37	22	18570618	18570618	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18570618delA	uc002znr.2	+						PEX26_uc002znp.3_Intron|PEX26_uc002znq.3_Intron|PEX26_uc002znt.2_Intron	NM_018943	NP_061816			tubulin, alpha 8						microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0																		---	---	---	---
DGCR5	26220	broad.mit.edu	37	22	18976027	18976027	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18976027delA	uc002zom.1	+						DGCR5_uc002zon.1_Intron	NR_002733				Homo sapiens mRNA for KIAA1647 protein, partial cds.												0																		---	---	---	---
UFD1L	7353	broad.mit.edu	37	22	19443380	19443380	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19443380delG	uc002zpm.2	-						UFD1L_uc002zpo.2_Intron|UFD1L_uc011agy.1_Intron|UFD1L_uc002zpp.2_Intron	NM_005659	NP_005650			ubiquitin fusion degradation 1-like isoform A						skeletal system development|ubiquitin-dependent protein catabolic process	cytosol|nucleus	protein binding|ubiquitin-specific protease activity				0	Colorectal(54;0.0993)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	19610432	19610437	+	IGR	DEL	GTGTGT	-	-	rs71754184		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19610432_19610437delGTGTGT								LOC150185 (56070 upstream) : SEPT5 (91550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	19652767	19652768	+	IGR	DEL	AA	-	-	rs148492503		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19652767_19652768delAA								LOC150185 (98405 upstream) : SEPT5 (49219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	19677477	19677480	+	IGR	DEL	TTTT	-	-	rs34414365		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19677477_19677480delTTTT								LOC150185 (123115 upstream) : SEPT5 (24507 downstream)																																			---	---	---	---
C22orf25	128989	broad.mit.edu	37	22	20012580	20012580	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20012580delT	uc010grw.1	+						C22orf25_uc002zrb.1_Intron|C22orf25_uc002zrc.1_Intron|C22orf25_uc002zrd.1_Intron|C22orf25_uc002zre.2_Intron|C22orf25_uc010grx.2_Intron|C22orf25_uc011ahe.1_Intron|C22orf25_uc011ahf.1_Intron|C22orf25_uc011ahg.1_Intron|C22orf25_uc002zrg.2_Intron|C22orf25_uc011ahh.1_Intron|C22orf25_uc002zrf.2_Intron|C22orf25_uc011ahi.1_Intron	NM_152906	NP_690870			hypothetical protein LOC128989												0	Colorectal(54;0.0533)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	20060730	20060730	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20060730delT								C22orf25 (7283 upstream) : DGCR8 (7104 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	20185699	20185700	+	IGR	INS	-	TCT	TCT	rs150208796	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20185699_20185700insTCT								ZDHHC8 (50170 upstream) : LOC150197 (8155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	20212585	20212586	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20212585_20212586delCA								LOC150197 (16525 upstream) : RTN4R (16354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	20213247	20213248	+	IGR	INS	-	CA	CA	rs148153498	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20213247_20213248insCA								LOC150197 (17187 upstream) : RTN4R (15692 downstream)																																			---	---	---	---
KLHL22	84861	broad.mit.edu	37	22	20820090	20820090	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20820090delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	22	20944089	20944090	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20944089_20944090delAC								MED15 (2171 upstream) : POM121L4P (99753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	20955311	20955312	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20955311_20955312insT								MED15 (13393 upstream) : POM121L4P (88531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	21022401	21022401	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21022401delG								MED15 (80483 upstream) : POM121L4P (21442 downstream)																																			---	---	---	---
UBE2L3	7332	broad.mit.edu	37	22	21958126	21958127	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21958126_21958127delAA	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)																	---	---	---	---
PPIL2	23759	broad.mit.edu	37	22	22048659	22048659	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22048659delA	uc010gtj.1	+						PPIL2_uc002zvh.3_Intron|PPIL2_uc002zvi.3_Intron|PPIL2_uc002zvg.3_Intron|PPIL2_uc011aij.1_Intron|PPIL2_uc002zvk.3_Intron	NM_148175	NP_680480			peptidylprolyl isomerase-like 2 isoform a						blood coagulation|leukocyte migration|protein folding|protein polyubiquitination	Golgi lumen|nucleus|ubiquitin ligase complex	peptidyl-prolyl cis-trans isomerase activity|ubiquitin-ubiquitin ligase activity			ovary(2)	2	Colorectal(54;0.105)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	22226257	22226258	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22226257_22226258delTT								MAPK1 (4287 upstream) : PPM1F (47535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	22266435	22266437	+	IGR	DEL	AAA	-	-	rs8140372	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22266435_22266437delAAA								MAPK1 (44465 upstream) : PPM1F (7356 downstream)																																			---	---	---	---
PPM1F	9647	broad.mit.edu	37	22	22290680	22290680	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22290680delA	uc002zvp.1	-						PPM1F_uc011aik.1_Intron|PPM1F_uc002zvq.2_Intron|uc011ail.1_5'Flank	NM_014634	NP_055449			protein phosphatase 1F						apoptosis|protein dephosphorylation	protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			ovary(2)|large_intestine(1)|breast(1)|kidney(1)	5	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)														---	---	---	---
TOP3B	8940	broad.mit.edu	37	22	22320431	22320431	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22320431delT	uc002zvs.2	-						TOP3B_uc010gtm.1_Intron|TOP3B_uc002zvr.2_Intron|TOP3B_uc010gtl.2_Intron|TOP3B_uc002zvt.3_Intron	NM_003935	NP_003926			topoisomerase (DNA) III beta						DNA topological change	nucleus	ATP binding|DNA topoisomerase type I activity|protein binding			kidney(1)	1	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	22351713	22351713	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22351713delT	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	22418593	22418593	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22418593delT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	23283036	23283037	+	IGR	INS	-	AGG	AGG	rs138189965	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23283036_23283037insAGG								LOC96610 (17954 upstream) : RTDR1 (118557 downstream)																																			---	---	---	---
BCR	613	broad.mit.edu	37	22	23616489	23616489	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23616489delC	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								---	---	---	---
BCR	613	broad.mit.edu	37	22	23634615	23634615	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23634615delT	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.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	23829501	23829501	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23829501delT	uc010gtz.1	-											Homo sapiens hypothetical LOC388882, mRNA (cDNA clone MGC:46300 IMAGE:5164270), complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	23875615	23875633	+	IGR	DEL	GGGAGGCAGCGGCAGGAAG	-	-	rs67007208	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23875615_23875633delGGGAGGCAGCGGCAGGAAG								ZDHHC8P1 (130816 upstream) : IGLL1 (39682 downstream)																																			---	---	---	---
CABIN1	23523	broad.mit.edu	37	22	24480374	24480374	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24480374delT	uc002zzi.1	+						CABIN1_uc002zzj.1_Intron|CABIN1_uc002zzl.1_Intron	NM_012295	NP_036427			calcineurin binding protein 1						cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
UPB1	51733	broad.mit.edu	37	22	24914126	24914127	+	Intron	INS	-	A	A	rs113023158		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24914126_24914127insA	uc003aaf.2	+						UPB1_uc003aae.2_Intron|UPB1_uc011ajt.1_Intron	NM_016327	NP_057411			beta-ureidopropionase						pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	beta-ureidopropionase activity|metal ion binding			ovary(2)	2	Colorectal(2;0.0339)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	25108622	25108624	+	IGR	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25108622_25108624delAAA								POM121L10P (53508 upstream) : PIWIL3 (6377 downstream)																																			---	---	---	---
TMEM211	255349	broad.mit.edu	37	22	25336603	25336604	+	5'Flank	INS	-	CCTT	CCTT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25336603_25336604insCCTT	uc003abk.1	-							NM_001001663	NP_001001663			transmembrane protein 211							integral to membrane					0																		---	---	---	---
ADRBK2	157	broad.mit.edu	37	22	26020083	26020083	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26020083delT	uc003abx.3	+						ADRBK2_uc010gux.2_Intron|ADRBK2_uc003abw.2_Intron|ADRBK2_uc003aby.3_Intron	NM_005160	NP_005151			beta-adrenergic receptor kinase 2								ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	22	26131998	26131999	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26131998_26131999delTT								ADRBK2 (6742 upstream) : MYO18B (6121 downstream)																																			---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26243876	26243876	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26243876delT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997			myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26709561	26709570	+	Intron	DEL	CACACACACG	-	-	rs150855077	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26709561_26709570delCACACACACG	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																		---	---	---	---
ASPHD2	57168	broad.mit.edu	37	22	26826161	26826161	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26826161delG	uc003acg.2	+							NM_020437	NP_065170			aspartate beta-hydroxylase domain containing 2						peptidyl-amino acid modification	integral to endoplasmic reticulum membrane	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity			ovary(1)	1																		---	---	---	---
HPS4	89781	broad.mit.edu	37	22	26874207	26874208	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26874207_26874208insG	uc003acl.2	-						HPS4_uc003aci.2_Intron|HPS4_uc003acj.2_Intron|HPS4_uc003ack.2_Intron|HPS4_uc003acn.2_Intron|HPS4_uc010gvd.1_Intron|HPS4_uc003aco.1_Intron	NM_022081	NP_071364			light ear protein isoform a						lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0														Hermansky-Pudlak_syndrome				---	---	---	---
TPST2	8459	broad.mit.edu	37	22	26933832	26933832	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26933832delT	uc003acv.2	-						TPST2_uc003acw.2_Intron|TPST2_uc003acx.2_Intron	NM_003595	NP_003586			tyrosylprotein sulfotransferase 2						peptidyl-tyrosine sulfation	endoplasmic reticulum|Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity			central_nervous_system(1)	1																		---	---	---	---
TPST2	8459	broad.mit.edu	37	22	26976983	26976984	+	Intron	DEL	AT	-	-	rs56405869		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26976983_26976984delAT	uc003acx.2	-						TPST2_uc011akf.1_Intron	NM_003595	NP_003586			tyrosylprotein sulfotransferase 2						peptidyl-tyrosine sulfation	endoplasmic reticulum|Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	27365154	27365154	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27365154delA								MIAT (250205 upstream) : MN1 (779112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27409674	27409677	+	IGR	DEL	GAGA	-	-	rs72203124		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27409674_27409677delGAGA								MIAT (294725 upstream) : MN1 (734589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27437660	27437660	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27437660delT								MIAT (322711 upstream) : MN1 (706606 downstream)																																			---	---	---	---
TTC28	23331	broad.mit.edu	37	22	28871345	28871345	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28871345delA	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
TTC28	23331	broad.mit.edu	37	22	29005676	29005676	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29005676delT	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
TTC28	23331	broad.mit.edu	37	22	29069357	29069358	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29069357_29069358insA	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
CHEK2	11200	broad.mit.edu	37	22	29107168	29107168	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29107168delC	uc003adu.1	-						CHEK2_uc003ads.1_Intron|CHEK2_uc010gvh.1_Intron|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_Intron|CHEK2_uc010gvk.1_Intron|CHEK2_uc003adt.1_Intron|CHEK2_uc003adv.1_Intron|CHEK2_uc003adw.1_Intron|CHEK2_uc003adx.1_Intron|CHEK2_uc003ady.1_Intron|CHEK2_uc003adz.1_Intron	NM_007194	NP_009125			protein kinase CHK2 isoform a						cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20								F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				---	---	---	---
CCDC117	150275	broad.mit.edu	37	22	29181913	29181917	+	Intron	DEL	AAAAA	-	-	rs35631283		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29181913_29181917delAAAAA	uc003aeb.2	+						CCDC117_uc011aki.1_Intron|CCDC117_uc011akj.1_Intron|CCDC117_uc011akk.1_Intron	NM_173510	NP_775781			coiled-coil domain containing 117											breast(1)	1																		---	---	---	---
ZNRF3	84133	broad.mit.edu	37	22	29300074	29300074	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29300074delA	uc003aeg.2	+							NM_032173	NP_115549			zinc and ring finger 3							integral to membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
ZNRF3	84133	broad.mit.edu	37	22	29394285	29394285	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29394285delA	uc003aeg.2	+						ZNRF3_uc003aeh.1_Intron	NM_032173	NP_115549			zinc and ring finger 3							integral to membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
EWSR1	2130	broad.mit.edu	37	22	29669456	29669456	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29669456delT	uc003aet.2	+						EWSR1_uc003aes.3_Intron|EWSR1_uc003aev.2_Intron|EWSR1_uc003aew.2_Intron|EWSR1_uc003aex.2_Intron	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								---	---	---	---
NEFH	4744	broad.mit.edu	37	22	29880822	29880825	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29880822_29880825delTTTT	uc003afo.2	+							NM_021076	NP_066554			neurofilament, heavy polypeptide 200kDa						cell death|nervous system development	neurofilament					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	29902667	29902667	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29902667delA								NEFH (15392 upstream) : THOC5 (1490 downstream)																																			---	---	---	---
NF2	4771	broad.mit.edu	37	22	29997192	29997192	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29997192delT	uc003age.3	+						NF2_uc003afy.3_5'Flank|NF2_uc003afz.3_5'Flank|NF2_uc003agf.3_5'Flank|NF2_uc003agb.3_5'Flank|NF2_uc003agc.3_5'Flank|NF2_uc003agd.3_5'Flank|NF2_uc003agg.3_5'Flank|NF2_uc003aga.3_5'Flank|NF2_uc003agh.3_5'Flank|NF2_uc003agi.3_5'Flank|NF2_uc003agj.3_5'Flank	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	p.?(1)		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				---	---	---	---
NF2	4771	broad.mit.edu	37	22	30071803	30071804	+	Intron	INS	-	AC	AC	rs145350766	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30071803_30071804insAC	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|NF2_uc010gvp.2_Intron|NF2_uc011akq.1_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	p.?(1)		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				---	---	---	---
CABP7	164633	broad.mit.edu	37	22	30114308	30114309	+	5'Flank	INS	-	CTTAA	CTTAA	rs143107131	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30114308_30114309insCTTAA	uc003agl.2	+							NM_182527	NP_872333			calcium binding protein 7							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding				0			OV - Ovarian serous cystadenocarcinoma(5;0.00442)|Epithelial(10;0.215)|all cancers(5;0.233)															---	---	---	---
Unknown	0	broad.mit.edu	37	22	30787106	30787106	+	IGR	DEL	A	-	-	rs34042272		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30787106delA								RNF215 (3804 upstream) : SEC14L2 (5827 downstream)																																	OREG0026459	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PES1	23481	broad.mit.edu	37	22	30989481	30989481	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30989481delA	uc003aij.1	-						PES1_uc003aik.1_5'Flank|PES1_uc003ail.1_5'Flank|PES1_uc003aim.1_5'Flank|PES1_uc003ain.1_Intron|PES1_uc003aio.1_Intron	NM_014303	NP_055118			pescadillo homolog 1, containing BRCT domain						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																		---	---	---	---
OSBP2	23762	broad.mit.edu	37	22	31228445	31228445	+	Intron	DEL	T	-	-	rs71861196		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31228445delT	uc003aiy.1	+						OSBP2_uc011ala.1_Intron|OSBP2_uc010gwc.1_Intron|OSBP2_uc003aix.1_Intron|OSBP2_uc011alb.1_Intron|OSBP2_uc003aiz.1_Intron|OSBP2_uc003aja.1_Intron|OSBP2_uc011alc.1_Intron	NM_030758	NP_110385			oxysterol binding protein 2 isoform a						lipid transport	membrane	lipid binding			breast(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	31540589	31540592	+	IGR	DEL	AAAC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31540589_31540592delAAAC								PLA2G3 (4120 upstream) : RNF185 (15546 downstream)																																			---	---	---	---
RNF185	91445	broad.mit.edu	37	22	31590717	31590717	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31590717delA	uc003akb.2	+						RNF185_uc010gwh.2_Intron|RNF185_uc011alm.1_Intron|RNF185_uc003akc.2_Intron|RNF185_uc003ake.2_Intron	NM_152267	NP_689480			ring finger protein 185 isoform 1							integral to membrane	zinc ion binding				0																		---	---	---	---
PATZ1	23598	broad.mit.edu	37	22	31726485	31726485	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31726485delA	uc003akq.2	-						PATZ1_uc003akp.2_Intron|PATZ1_uc003akr.2_Intron	NM_014323	NP_055138			POZ (BTB) and AT hook containing zinc finger 1						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/PATZ1(2)	soft_tissue(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	31761554	31761555	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31761554_31761555delGA								PATZ1 (19305 upstream) : DRG1 (33984 downstream)																																			---	---	---	---
SFI1	9814	broad.mit.edu	37	22	31920415	31920415	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31920415delT	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468			spindle assembly associated Sfi1 homolog isoform						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1																		---	---	---	---
SFI1	9814	broad.mit.edu	37	22	31955417	31955417	+	Intron	DEL	A	-	-	rs11912981	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31955417delA	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468			spindle assembly associated Sfi1 homolog isoform						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	32070401	32070402	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32070401_32070402delTT								PISD (12200 upstream) : C22orf30 (1840 downstream)																																			---	---	---	---
C22orf30	253143	broad.mit.edu	37	22	32135986	32135986	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32135986delA	uc003alp.3	-							NM_173566	NP_775837			hypothetical protein LOC253143												0																		---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32188633	32188633	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32188633delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	32712684	32712684	+	IGR	DEL	T	-	-	rs35348888		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32712684delT								SLC5A4 (61366 upstream) : RFPL3 (38188 downstream)																																			---	---	---	---
C22orf28	51493	broad.mit.edu	37	22	32794130	32794131	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32794130_32794131delTT	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																		---	---	---	---
BPIL2	254240	broad.mit.edu	37	22	32812067	32812070	+	Intron	DEL	TTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32812067_32812070delTTTT	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	33176966	33176969	+	Intron	DEL	TCCT	-	-	rs68188956		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33176966_33176969delTCCT	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																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33239916	33239917	+	Intron	INS	-	TG	TG	rs146581623	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33239916_33239917insTG	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron|TIMP3_uc003anb.2_Intron	NM_003490	NP_003481			synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33299186	33299186	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33299186delC	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	33519480	33519480	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33519480delT								SYN3 (65103 upstream) : LARGE (149583 downstream)																																			---	---	---	---
LARGE	9215	broad.mit.edu	37	22	33833454	33833454	+	Intron	DEL	T	-	-	rs78077172		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33833454delT	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	33952698	33952699	+	Intron	DEL	AA	-	-	rs112690181		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33952698_33952699delAA	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	34257390	34257391	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34257390_34257391delAC	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	35111864	35111865	+	IGR	INS	-	TCC	TCC	rs12166611	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35111864_35111865insTCC								LARGE (793280 upstream) : ISX (350264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35291180	35291180	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35291180delT								LARGE (972596 upstream) : ISX (170949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	36107646	36107647	+	IGR	INS	-	TTCC	TTCC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36107646_36107647insTTCC								APOL6 (43191 upstream) : APOL5 (6272 downstream)																																			---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36234720	36234720	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36234720delA	uc003aon.3	-						RBM9_uc003aol.3_Intron|RBM9_uc003aoj.3_Intron|RBM9_uc003aok.3_Intron|RBM9_uc003aoh.3_Intron|RBM9_uc003aom.3_Intron|RBM9_uc010gwu.2_Intron|RBM9_uc003aoo.3_Intron|RBM9_uc003aop.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																		---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36239034	36239034	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36239034delA	uc003aon.3	-						RBM9_uc003aol.3_5'Flank|RBM9_uc003aoj.3_5'Flank|RBM9_uc003aok.3_5'Flank|RBM9_uc003aoh.3_5'Flank|RBM9_uc003aom.3_5'Flank|RBM9_uc010gwu.2_Intron|RBM9_uc003aoo.3_Intron|RBM9_uc003aop.3_5'Flank	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																		---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36412257	36412257	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36412257delA	uc003aon.3	-						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	36670540	36670540	+	IGR	DEL	A	-	-	rs150921751		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36670540delA								APOL1 (6964 upstream) : MYH9 (6784 downstream)																																			---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36698531	36698531	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36698531delA	uc003apg.2	-						MYH9_uc003aph.1_Intron	NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
Unknown	0	broad.mit.edu	37	22	37194595	37194595	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37194595delG								IFT27 (22481 upstream) : PVALB (2151 downstream)																																			---	---	---	---
NCF4	4689	broad.mit.edu	37	22	37260746	37260746	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37260746delT	uc003apy.3	+						NCF4_uc003apz.3_Intron	NM_000631	NP_000622			neutrophil cytosolic factor 4 isoform 1						cell communication|immune response|oxidation-reduction process	cytosol|NADPH oxidase complex	phosphatidylinositol binding|protein dimerization activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	37361062	37361062	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37361062delA								CSF2RB (24585 upstream) : C22orf33 (26099 downstream)																																			---	---	---	---
SSTR3	6753	broad.mit.edu	37	22	37608277	37608278	+	5'Flank	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37608277_37608278delGA	uc003ara.2	-						SSTR3_uc003arb.2_5'UTR	NM_001051	NP_001042			somatostatin receptor 3						G-protein signaling, coupled to cyclic nucleotide second messenger|induction of apoptosis by hormones|negative regulation of cell proliferation	integral to plasma membrane|nonmotile primary cilium	somatostatin receptor activity			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	37752508	37752508	+	5'Flank	DEL	A	-	-	rs111666604		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37752508delA	uc003arg.2	-											Homo sapiens cDNA FLJ40468 fis, clone TESTI2042400.																														---	---	---	---
TRIOBP	11078	broad.mit.edu	37	22	38161836	38161836	+	Intron	DEL	G	-	-	rs63153461		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38161836delG	uc003atr.2	+						TRIOBP_uc003atu.2_Intron|TRIOBP_uc003atw.2_Intron|TRIOBP_uc003atx.1_Intron|TRIOBP_uc010gxh.2_Intron	NM_001039141	NP_001034230			TRIO and F-actin binding protein isoform 6						actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)																	---	---	---	---
EIF3L	51386	broad.mit.edu	37	22	38282201	38282202	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38282201_38282202delAA	uc003auf.2	+						EIF3L_uc003aue.1_Intron|EIF3L_uc011ann.1_Intron|EIF3L_uc003aug.2_Intron|EIF3L_uc003auh.2_Intron	NM_016091	NP_057175			eukaryotic translation initiation factor 3							eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)	1																		---	---	---	---
MICALL1	85377	broad.mit.edu	37	22	38305373	38305373	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38305373delT	uc003aui.2	+							NM_033386	NP_203744			molecule interacting with Rab13							cytoplasm|cytoskeleton	protein binding|zinc ion binding			breast(1)	1	Melanoma(58;0.045)																	---	---	---	---
C22orf23	84645	broad.mit.edu	37	22	38343084	38343084	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	38613649	38613649	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38613649delA	uc003avi.1	+											Homo sapiens cDNA clone IMAGE:40131522.																														---	---	---	---
KDELR3	11015	broad.mit.edu	37	22	38877028	38877028	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38877028delA	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)																	---	---	---	---
NPTXR	23467	broad.mit.edu	37	22	39215271	39215271	+	3'UTR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39215271delT	uc003awk.2	-	5						NM_014293	NP_055108			neuronal pentraxin receptor							integral to membrane	metal ion binding			central_nervous_system(2)|skin(1)	3	Melanoma(58;0.04)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	39301132	39301132	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39301132delT								CBX6 (32874 upstream) : APOBEC3A (52395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	39455528	39455529	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39455528_39455529insT								APOBEC3F (3555 upstream) : APOBEC3G (17496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	39570631	39570631	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39570631delT								CBX7 (22093 upstream) : PDGFB (49056 downstream)																																			---	---	---	---
PDGFB	5155	broad.mit.edu	37	22	39621797	39621797	+	Frame_Shift_Del	DEL	G	-	-	rs67510150		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39621797delG	uc003axf.2	-	6	1646	c.657delC	c.(655-657)CCCfs	p.P219fs	PDGFB_uc003axe.2_Frame_Shift_Del_p.P204fs	NM_002608	NP_002599	P01127	PDGFB_HUMAN	platelet-derived growth factor beta isoform 1	219					activation of protein kinase B activity|cellular response to mycophenolic acid|embryonic placenta development|heart development|hemopoiesis|metanephric glomerular mesangial cell development|monocyte chemotaxis|negative regulation of phosphatidylinositol biosynthetic process|negative regulation of platelet activation|negative regulation of transcription, DNA-dependent|paracrine signaling|peptidyl-serine phosphorylation|peptidyl-tyrosine phosphorylation|platelet activation|platelet degranulation|positive regulation of blood vessel endothelial cell migration|positive regulation of calcium ion import|positive regulation of cell division|positive regulation of chemotaxis|positive regulation of cyclin-dependent protein kinase activity|positive regulation of DNA biosynthetic process|positive regulation of DNA replication|positive regulation of endothelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|positive regulation of glomerular filtration|positive regulation of glomerular mesangial cell proliferation|positive regulation of MAP kinase activity|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of mitosis|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein autophosphorylation|positive regulation of protein tyrosine kinase activity|positive regulation of reactive oxygen species metabolic process|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription, DNA-dependent|reactive oxygen species metabolic process|transforming growth factor beta receptor signaling pathway	basolateral plasma membrane|cell surface|endoplasmic reticulum lumen|extracellular region|Golgi membrane|platelet alpha granule lumen	collagen binding|eukaryotic cell surface binding|growth factor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein heterodimerization activity|protein homodimerization activity|superoxide-generating NADPH oxidase activator activity	p.P219P(1)	COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(1)	373	Melanoma(58;0.04)				Becaplermin(DB00102)			T	COL1A1	DFSP								---	---	---	---
RPL3	6122	broad.mit.edu	37	22	39718123	39718124	+	5'Flank	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39718123_39718124insT	uc003axi.2	-						RPL3_uc003axh.2_5'Flank|RPL3_uc003axj.2_5'Flank|RPL3_uc011aoj.1_5'Flank	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	39821565	39821565	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39821565delT	uc003axt.2	+						TAB1_uc003axr.2_Intron|TAB1_uc011aok.1_Intron|TAB1_uc003axu.1_Intron	NM_006116	NP_006107			mitogen-activated protein kinase kinase kinase 7						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																		---	---	---	---
CACNA1I	8911	broad.mit.edu	37	22	40014157	40014157	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40014157delT	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)													---	---	---	---
FAM83F	113828	broad.mit.edu	37	22	40396178	40396179	+	Intron	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40396178_40396179insG	uc003ayk.1	+							NM_138435	NP_612444			hypothetical protein LOC113828											breast(1)	1																		---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40708460	40708460	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40708460delT	uc011aor.1	+						TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Intron|TNRC6B_uc003ayo.2_Intron	NM_001162501	NP_001155973			trinucleotide repeat containing 6B isoform 1						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
MKL1	57591	broad.mit.edu	37	22	40840774	40840774	+	Intron	DEL	A	-	-	rs34631881		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40840774delA	uc003ayv.1	-						MKL1_uc003ayw.1_Intron|MKL1_uc010gye.1_Intron|MKL1_uc010gyf.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								---	---	---	---
SLC25A17	10478	broad.mit.edu	37	22	41190631	41190632	+	Intron	DEL	AT	-	-	rs79609780		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41190631_41190632delAT	uc003azc.2	-						SLC25A17_uc010gyg.2_Intron|SLC25A17_uc011aou.1_Intron|SLC25A17_uc003azd.2_Intron|SLC25A17_uc011aov.1_Intron	NM_006358	NP_006349			solute carrier family 25 (mitochondrial carrier;						fatty acid alpha-oxidation	integral to plasma membrane|mitochondrial inner membrane|peroxisomal membrane	adenine nucleotide transmembrane transporter activity|protein binding				0																		---	---	---	---
SLC25A17	10478	broad.mit.edu	37	22	41195143	41195143	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41195143delT	uc003azc.2	-						SLC25A17_uc010gyg.2_Intron|SLC25A17_uc011aou.1_Intron|SLC25A17_uc003azd.2_Intron|SLC25A17_uc011aov.1_Intron	NM_006358	NP_006349			solute carrier family 25 (mitochondrial carrier;						fatty acid alpha-oxidation	integral to plasma membrane|mitochondrial inner membrane|peroxisomal membrane	adenine nucleotide transmembrane transporter activity|protein binding				0																		---	---	---	---
XPNPEP3	63929	broad.mit.edu	37	22	41338762	41338762	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41338762delT	uc011aoy.1	+							NM_022098				X-prolyl aminopeptidase (aminopeptidase P) 3,						cellular process	mitochondrion	aminopeptidase activity|manganese ion binding|metallopeptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	41407900	41407901	+	IGR	DEL	AA	-	-	rs75579152		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41407900_41407901delAA								RBX1 (39234 upstream) : MIR1281 (80616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	41585708	41585708	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41585708delT	uc003azm.2	-											Homo sapiens, clone IMAGE:5580334, mRNA.																														---	---	---	---
RANGAP1	5905	broad.mit.edu	37	22	41650191	41650191	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41650191delA	uc003azs.2	-						RANGAP1_uc003azt.2_Intron|RANGAP1_uc003azu.2_Intron|RANGAP1_uc003azr.2_5'Flank|RANGAP1_uc010gyk.2_5'Flank|RANGAP1_uc011aoz.1_Intron	NM_002883	NP_002874			Ran GTPase activating protein 1						mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0																		---	---	---	---
RANGAP1	5905	broad.mit.edu	37	22	41676099	41676099	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41676099delA	uc003azs.2	-						RANGAP1_uc003azt.2_Intron|RANGAP1_uc003azu.2_Intron|RANGAP1_uc011aoz.1_Intron	NM_002883	NP_002874			Ran GTPase activating protein 1						mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0																		---	---	---	---
ZC3H7B	23264	broad.mit.edu	37	22	41753526	41753526	+	3'UTR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41753526delG	uc003azw.2	+	23					ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060			zinc finger CCCH-type containing 7B						interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
PHF5A	84844	broad.mit.edu	37	22	41864427	41864427	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41864427delC	uc003bab.2	-						ACO2_uc003bac.2_5'Flank|ACO2_uc003bad.2_5'Flank	NM_032758	NP_116147			PHD-finger 5A						nuclear mRNA splicing, via spliceosome|positive regulation of transcription, DNA-dependent	nuclear speck|U12-type spliceosomal complex|U2 snRNP	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
NHP2L1	4809	broad.mit.edu	37	22	42076373	42076373	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42076373delG	uc003bat.2	-						NHP2L1_uc003bau.2_Intron|NHP2L1_uc003bav.2_Intron|NHP2L1_uc003baw.2_Intron	NM_005008	NP_004999			NHP2 non-histone chromosome protein 2-like 1						nuclear mRNA splicing, via spliceosome|ribosome biogenesis	box C/D snoRNP complex|nucleoplasm|spliceosomal complex	protein binding|RNA binding				0																		---	---	---	---
MEI1	150365	broad.mit.edu	37	22	42166141	42166141	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42166141delA	uc003baz.1	+						WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|MEI1_uc011apd.1_Intron|MEI1_uc003bbb.1_Intron|MEI1_uc003bbc.1_Intron|MEI1_uc010gym.1_Intron|MEI1_uc003bbd.1_Intron	NM_152513	NP_689726			meiosis defective 1								binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
WBP2NL	164684	broad.mit.edu	37	22	42312934	42312935	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42312934_42312935delAA	uc011ape.1	+						LOC339674_uc003bba.1_Intron	NM_152613	NP_689826			WBP2 N-terminal like						egg activation|male pronucleus assembly|meiosis	perinuclear theca	WW domain binding			ovary(2)	2																		---	---	---	---
SERHL	94009	broad.mit.edu	37	22	42916608	42916609	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42916608_42916609insA	uc011apm.1	+						RRP7A_uc003bcq.2_5'Flank					RecName: Full=Serine hydrolase-like protein;          EC=3.1.-.-;												0																		---	---	---	---
SERHL2	253190	broad.mit.edu	37	22	42962565	42962565	+	Intron	DEL	A	-	-	rs147819513		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42962565delA	uc003bcr.2	+						SERHL_uc011apm.1_Intron|SERHL2_uc011apn.1_Intron|SERHL2_uc010gyz.2_Intron|SERHL2_uc010gyy.2_Intron|SERHL2_uc011apo.1_Intron|RRP7B_uc003bcs.2_Intron	NM_014509	NP_055324			serine hydrolase-like 2							perinuclear region of cytoplasm|peroxisome	hydrolase activity				0																		---	---	---	---
POLDIP3	84271	broad.mit.edu	37	22	42998570	42998570	+	Intron	DEL	T	-	-	rs79254789		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42998570delT	uc003bcu.2	-						POLDIP3_uc011app.1_Intron|POLDIP3_uc003bcv.2_Intron|POLDIP3_uc011apq.1_Intron|POLDIP3_uc010gza.2_Intron|POLDIP3_uc011apr.1_Intron|POLDIP3_uc010gzb.1_Intron	NM_032311	NP_115687			DNA polymerase delta interacting protein 3						positive regulation of translation	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
CYB5R3	1727	broad.mit.edu	37	22	43032223	43032223	+	Intron	DEL	A	-	-	rs71852267		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43032223delA	uc003bcz.2	-						CYB5R3_uc010gzc.1_Intron|CYB5R3_uc003bcw.2_Intron|CYB5R3_uc011aps.1_Intron|CYB5R3_uc003bcy.2_Intron|CYB5R3_uc003bcx.2_Intron	NM_000398	NP_000389			cytochrome b5 reductase 3 isoform m						blood circulation|cholesterol biosynthetic process|water-soluble vitamin metabolic process	endoplasmic reticulum membrane|hemoglobin complex|mitochondrial outer membrane	cytochrome-b5 reductase activity			skin(1)	1					NADH(DB00157)													---	---	---	---
PACSIN2	11252	broad.mit.edu	37	22	43395675	43395675	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43395675delA	uc003bdg.3	-							NM_007229	NP_009160			protein kinase C and casein kinase substrate in						actin cytoskeleton organization|endocytosis	cytoplasmic membrane-bounded vesicle	transporter activity				0		Glioma(61;0.222)																---	---	---	---
TTLL1	25809	broad.mit.edu	37	22	43442684	43442684	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43442684delT	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)														---	---	---	---
SCUBE1	80274	broad.mit.edu	37	22	43676496	43676497	+	Intron	INS	-	CC	CC	rs145767429	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43676496_43676497insCC	uc003bdt.1	-						SCUBE1_uc003bdu.1_Intron|uc003bdv.2_Intron	NM_173050	NP_766638			signal peptide, CUB domain, EGF-like 1						adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	43774979	43774979	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43774979delA								SCUBE1 (35624 upstream) : MPPED1 (33041 downstream)																																			---	---	---	---
MPPED1	758	broad.mit.edu	37	22	43828698	43828699	+	Intron	INS	-	GAGA	GAGA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43828698_43828699insGAGA	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)																---	---	---	---
MPPED1	758	broad.mit.edu	37	22	43895661	43895663	+	Intron	DEL	GGT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43895661_43895663delGGT	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	44134261	44134262	+	Intron	DEL	CA	-	-	rs144479768		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44134261_44134262delCA	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)																---	---	---	---
SULT4A1	25830	broad.mit.edu	37	22	44249820	44249820	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44249820delA	uc003bee.1	-						SULT4A1_uc003bef.1_Intron|SULT4A1_uc011aqb.1_Intron	NM_014351	NP_055166			sulfotransferase family 4A, member 1						3'-phosphoadenosine 5'-phosphosulfate metabolic process|steroid metabolic process|xenobiotic metabolic process	cytosol	sulfotransferase activity				0		Ovarian(80;0.024)|all_neural(38;0.0416)		Colorectal(1;0.00242)|READ - Rectum adenocarcinoma(1;0.0419)														---	---	---	---
SAMM50	25813	broad.mit.edu	37	22	44371821	44371821	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44371821delA	uc003bej.2	+						SAMM50_uc011aqd.1_Intron|SAMM50_uc003bek.2_5'UTR	NM_015380	NP_056195			sorting and assembly machinery component 50						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)																---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44505610	44505610	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44505610delT	uc003ben.2	+						PARVB_uc003bem.2_Intron|PARVB_uc010gzn.2_Intron|PARVB_uc003beo.2_Intron	NM_013327	NP_037459			parvin, beta isoform b						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)																---	---	---	---
PARVG	64098	broad.mit.edu	37	22	44591962	44591962	+	Intron	DEL	A	-	-	rs34401197		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44591962delA	uc011aqe.1	+						PARVG_uc003bep.2_Intron|PARVG_uc011aqf.1_Intron|PARVG_uc003beq.2_Intron|PARVG_uc003ber.2_Intron	NM_001137605	NP_001131077			parvin, gamma						cell-matrix adhesion	cytoplasm|cytoskeleton|focal adhesion	actin binding				0		Ovarian(80;0.024)|all_neural(38;0.0299)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	44793327	44793335	+	IGR	DEL	CTCACAGGT	-	-	rs67504592		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44793327_44793335delCTCACAGGT								KIAA1644 (84596 upstream) : LDOC1L (95115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	44909801	44909801	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44909801delT								LDOC1L (15796 upstream) : NCRNA00207 (55418 downstream)																																			---	---	---	---
FAM118A	55007	broad.mit.edu	37	22	45704770	45704770	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45704770delA	uc003bfz.3	+						FAM118A_uc003bga.3_5'Flank	NM_001104595	NP_001098065			hypothetical protein LOC55007							integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)														---	---	---	---
SMC1B	27127	broad.mit.edu	37	22	45752384	45752384	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45752384delT	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	45772597	45772597	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45772597delT	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)														---	---	---	---
SMC1B	27127	broad.mit.edu	37	22	45797770	45797770	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45797770delT	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)														---	---	---	---
FBLN1	2192	broad.mit.edu	37	22	45937984	45937984	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45937984delA	uc003bgj.1	+						FBLN1_uc003bgg.1_Intron|FBLN1_uc003bgh.2_Intron|FBLN1_uc010gzz.2_Intron|FBLN1_uc003bgi.1_Intron	NM_006486	NP_006477			fibulin 1 isoform D						interspecies interaction between organisms	extracellular space|soluble fraction	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)														---	---	---	---
ATXN10	25814	broad.mit.edu	37	22	46085990	46085990	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46085990delA	uc003bgm.1	+						ATXN10_uc011aqt.1_Intron|ATXN10_uc003bgn.1_Intron	NM_013236	NP_037368			ataxin 10						cell death|neuron projection development	dendrite|neuronal cell body|perinuclear region of cytoplasm				ovary(1)|kidney(1)	2		Ovarian(80;0.00973)|all_neural(38;0.0417)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0223)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	46378986	46378987	+	IGR	INS	-	GGAT	GGAT	rs140223755	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46378986_46378987insGGAT								WNT7B (5978 upstream) : LOC730668 (23509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	46528160	46528160	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46528160delT								LOC400931 (18354 upstream) : PPARA (18339 downstream)																																			---	---	---	---
PPARA	5465	broad.mit.edu	37	22	46626949	46626949	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46626949delT	uc003bgw.1	+						PPARA_uc003bgx.1_Intron|PPARA_uc010hab.1_Intron|PPARA_uc003bhb.1_Intron|PPARA_uc010hac.1_Intron	NM_005036	NP_005027			peroxisome proliferative activated receptor,						fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)													---	---	---	---
TRMU	55687	broad.mit.edu	37	22	46751234	46751235	+	Intron	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46751234_46751235insTG	uc003bhp.2	+						TRMU_uc003bhq.2_Intron|TRMU_uc003bhs.2_Intron|TRMU_uc003bhr.2_Intron|TRMU_uc003bht.2_Intron|TRMU_uc003bhu.2_Intron|TRMU_uc003bhv.2_Intron	NM_018006	NP_060476			tRNA 5-methylaminomethyl-2-thiouridylate							mitochondrion	ATP binding|sulfurtransferase activity|tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity|tRNA binding			ovary(1)	1		Ovarian(80;0.00965)|Breast(42;0.0194)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00449)|LUAD - Lung adenocarcinoma(64;0.248)												OREG0026654	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46931227	46931227	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46931227delC	uc003bhw.1	-	1	1841	c.1841delG	c.(1840-1842)GGCfs	p.G614fs		NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	614	Extracellular (Potential).|Cadherin 4.				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
GRAMD4	23151	broad.mit.edu	37	22	47068271	47068271	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47068271delG	uc003bhx.2	+						GRAMD4_uc010had.2_Intron|GRAMD4_uc003bhy.2_5'Flank	NM_015124	NP_055939			death-inducing-protein						apoptosis	integral to membrane|mitochondrial membrane				ovary(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)														---	---	---	---
CERK	64781	broad.mit.edu	37	22	47120920	47120920	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47120920delA	uc003bia.2	-							NM_022766	NP_073603			ceramide kinase						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|ceramide metabolic process	integral to membrane of membrane fraction|membrane|nucleus	ATP binding|ceramide kinase activity|diacylglycerol kinase activity|magnesium ion binding			skin(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	47684064	47684065	+	IGR	INS	-	ATCCATCC	ATCCATCC	rs12166451		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47684064_47684065insATCCATCC								TBC1D22A (114342 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	47684093	47684094	+	IGR	INS	-	TCCC	TCCC	rs6008119	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47684093_47684094insTCCC								TBC1D22A (114371 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48058986	48058988	+	Intron	DEL	AAA	-	-	rs35691662		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48058986_48058988delAAA	uc003bik.1	+											Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	48665863	48665863	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48665863delG								None (None upstream) : FAM19A5 (219425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48791334	48791335	+	IGR	INS	-	CA	CA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48791334_48791335insCA								None (None upstream) : FAM19A5 (93953 downstream)																																			---	---	---	---
FAM19A5	25817	broad.mit.edu	37	22	49036724	49036724	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49036724delG	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436			family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)														---	---	---	---
FAM19A5	25817	broad.mit.edu	37	22	49093420	49093421	+	Intron	INS	-	TGA	TGA	rs147993243		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49093420_49093421insTGA	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436			family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	49150265	49150266	+	IGR	INS	-	GTGTGTGCAC	GTGTGTGCAC	rs149910124		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49150265_49150266insGTGTGTGCAC								FAM19A5 (2523 upstream) : C22orf34 (657910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49155395	49155396	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49155395_49155396delAC								FAM19A5 (7653 upstream) : C22orf34 (652780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49197752	49197753	+	IGR	DEL	TG	-	-	rs113043536		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49197752_49197753delTG								FAM19A5 (50010 upstream) : C22orf34 (610423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49435381	49435382	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49435381_49435382delCA								FAM19A5 (287639 upstream) : C22orf34 (372794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49764552	49764552	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49764552delC								FAM19A5 (616810 upstream) : C22orf34 (43624 downstream)																																			---	---	---	---
BRD1	23774	broad.mit.edu	37	22	50200647	50200648	+	Intron	DEL	AA	-	-	rs10572848		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50200647_50200648delAA	uc003biv.2	-						BRD1_uc011arf.1_Intron|BRD1_uc011arg.1_Intron|BRD1_uc011arh.1_Intron|BRD1_uc003biu.3_Intron	NM_014577	NP_055392			bromodomain containing protein 1						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)														---	---	---	---
ODF3B	440836	broad.mit.edu	37	22	50971706	50971706	+	5'Flank	DEL	A	-	-	rs131795	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50971706delA	uc003bmh.2	-						ODF3B_uc003bmg.2_5'Flank	NM_001014440	NP_001014440			outer dense fiber of sperm tails 3B												0																		---	---	---	---
MAPK8IP2	23542	broad.mit.edu	37	22	51048477	51048477	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51048477delA	uc003bmx.2	+						MAPK8IP2_uc003bmy.2_Intron|MAPK8IP2_uc011asc.1_Intron	NM_012324	NP_036456			mitogen-activated protein kinase 8 interacting						behavioral fear response|dendrite morphogenesis|MAPKKK cascade|nonassociative learning|positive regulation of anti-apoptosis|regulation of excitatory postsynaptic membrane potential|regulation of JNK cascade|regulation of receptor activity|regulation of synaptic transmission, glutamatergic|signal complex assembly|social behavior	cytoplasm|postsynaptic density	beta-amyloid binding|kinesin binding|MAP-kinase scaffold activity|protein kinase activator activity|protein kinase binding			large_intestine(2)|central_nervous_system(1)	3		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		OV - Ovarian serous cystadenocarcinoma(4;1.28e-70)|Epithelial(4;3.46e-65)|GBM - Glioblastoma multiforme(4;4.83e-06)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
ARSA	410	broad.mit.edu	37	22	51063978	51063978	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51063978delG	uc003bnb.3	-						ARSA_uc003bna.3_Intron|ARSA_uc003bnc.3_Intron|ARSA_uc003bnd.3_Intron|ARSA_uc003bmz.3_Intron	NM_001085426	NP_001078895			arylsulfatase A isoform a precursor							lysosome	arylsulfatase activity|calcium ion binding|cerebroside-sulfatase activity			pancreas(1)|skin(1)	2		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	640905	640906	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:640905_640906insTG								SHOX (20760 upstream) : CRLF2 (673981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	686017	686018	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:686017_686018insC								SHOX (65872 upstream) : CRLF2 (628869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	849604	849605	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:849604_849605delTT								SHOX (229459 upstream) : CRLF2 (465282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	866731	866731	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:866731delG								SHOX (246586 upstream) : CRLF2 (448156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	1211255	1211256	+	IGR	INS	-	GT	GT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1211255_1211256insGT								SHOX (591110 upstream) : CRLF2 (103631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	1227446	1227457	+	IGR	DEL	ACAGGTACAGGT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1227446_1227457delACAGGTACAGGT								SHOX (607301 upstream) : CRLF2 (87430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	1244235	1244236	+	IGR	INS	-	AC	AC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1244235_1244236insAC								SHOX (624090 upstream) : CRLF2 (70651 downstream)																																			---	---	---	---
IL3RA	3563	broad.mit.edu	37	X	1454623	1454624	+	5'Flank	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1454623_1454624delTT	uc004cps.2	+							NM_002183	NP_002174			interleukin 3 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)													---	---	---	---
IL3RA	3563	broad.mit.edu	37	X	1497742	1497744	+	Intron	DEL	ATT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1497742_1497744delATT	uc004cps.2	+						IL3RA_uc011mhd.1_Intron	NM_002183	NP_002174			interleukin 3 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)													---	---	---	---
ASMTL	8623	broad.mit.edu	37	X	1530077	1530077	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1530077delA	uc004cpx.1	-						NCRNA00105_uc004cpv.2_Intron|NCRNA00105_uc004cpw.2_Intron|ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183			acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
ASMTL	8623	broad.mit.edu	37	X	1543451	1543454	+	Intron	DEL	ATCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1543451_1543454delATCT	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183			acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	1807603	1807603	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1807603delG								ASMT (45630 upstream) : DHRSX (329954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	1946700	1946701	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1946700_1946701insT								ASMT (184727 upstream) : DHRSX (190856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	2029691	2029692	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2029691_2029692delCT								ASMT (267718 upstream) : DHRSX (107865 downstream)																																			---	---	---	---
DHRSX	207063	broad.mit.edu	37	X	2200422	2200423	+	Intron	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2200422_2200423delAC	uc004cqf.3	-							NM_145177	NP_660160			dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)																---	---	---	---
DHRSX	207063	broad.mit.edu	37	X	2326869	2326869	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2326869delA	uc004cqf.3	-							NM_145177	NP_660160			dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)																---	---	---	---
CD99	4267	broad.mit.edu	37	X	2638662	2638669	+	Intron	DEL	TTTTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2638662_2638669delTTTTTTTT	uc004cqm.2	+						CD99_uc010nda.2_Intron|CD99_uc004cqn.2_Intron|CD99_uc004cqo.2_Intron	NM_002414	NP_002405			CD99 antigen isoform a precursor						cell adhesion	cytoplasm|integral to plasma membrane				skin(1)	1																		---	---	---	---
XG	7499	broad.mit.edu	37	X	2667341	2667342	+	5'Flank	INS	-	TGTTTC	TGTTTC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2667341_2667342insTGTTTC	uc011mhg.1	+						XG_uc010ndb.2_5'Flank|XG_uc004cqp.2_5'Flank	NM_175569	NP_780778			XG glycoprotein isoform 1 precursor							integral to membrane|plasma membrane				ovary(1)	1		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)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	3058317	3058318	+	IGR	DEL	AC	-	-	rs112567288		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3058317_3058318delAC								ARSF (27570 upstream) : MXRA5 (168293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	3064446	3064448	+	IGR	DEL	CTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3064446_3064448delCTC								ARSF (33699 upstream) : MXRA5 (162163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	3097381	3097381	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3097381delA								ARSF (66634 upstream) : MXRA5 (129230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	3182163	3182163	+	IGR	DEL	T	-	-	rs34519843		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3182163delT								ARSF (151416 upstream) : MXRA5 (44448 downstream)																																			---	---	---	---
PRKX	5613	broad.mit.edu	37	X	3539377	3539379	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3539377_3539379delAAA	uc010nde.2	-							NM_005044	NP_005035			protein kinase, X-linked								ATP binding|cAMP-dependent protein kinase activity			skin(2)|lung(1)	3		all_lung(23;0.000396)|Lung NSC(23;0.00123)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	3635686	3635686	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3635686delA								PRKX (4025 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	4735365	4735366	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:4735365_4735366insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	4949821	4949821	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:4949821delA								None (None upstream) : NLGN4X (858263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	4960160	4960161	+	IGR	INS	-	TTGT	TTGT	rs144619677		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:4960160_4960161insTTGT								None (None upstream) : NLGN4X (847923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	5581383	5581383	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5581383delA								None (None upstream) : NLGN4X (226701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	5708287	5708287	+	IGR	DEL	A	-	-	rs11796584		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5708287delA								None (None upstream) : NLGN4X (99797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	6233302	6233302	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6233302delT								NLGN4X (86596 upstream) : VCX3A (218358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	6451442	6451443	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6451442_6451443insC								NLGN4X (304736 upstream) : VCX3A (217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	6961281	6961281	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6961281delG								VCX3A (508122 upstream) : HDHD1A (5680 downstream)																																			---	---	---	---
HDHD1A	8226	broad.mit.edu	37	X	7032088	7032089	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7032088_7032089delTC	uc004crv.2	-						HDHD1A_uc011mhm.1_Intron|HDHD1A_uc011mhn.1_Intron|HDHD1A_uc010ndl.2_Intron|HDHD1A_uc011mho.1_Intron	NM_012080	NP_036212			haloacid dehalogenase-like hydrolase domain						nucleotide metabolic process		metal ion binding|phosphatase activity				0		Colorectal(8;0.0114)|Medulloblastoma(8;0.184)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	7824545	7824545	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7824545delT								VCX (12362 upstream) : PNPLA4 (42259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	7853113	7853113	+	IGR	DEL	A	-	-	rs34968282		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7853113delA								VCX (40930 upstream) : PNPLA4 (13691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	7943286	7943287	+	IGR	INS	-	TGTG	TGTG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7943286_7943287insTGTG								PNPLA4 (47506 upstream) : MIR651 (151719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	8072551	8072551	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8072551delC								PNPLA4 (176771 upstream) : MIR651 (22455 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	8203270	8203270	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8203270delT								VCX2 (63962 upstream) : VCX3B (229601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	8232568	8232571	+	IGR	DEL	ACAC	-	-	rs35999603		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8232568_8232571delACAC								VCX2 (93260 upstream) : VCX3B (200300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	8343786	8343787	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8343786_8343787insTG								VCX2 (204478 upstream) : VCX3B (89084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	8890303	8890303	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8890303delT								FAM9A (120879 upstream) : FAM9B (102736 downstream)																																			---	---	---	---
FAM9B	171483	broad.mit.edu	37	X	9000595	9000597	+	Intron	DEL	GGG	-	-	rs111614282		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9000595_9000597delGGG	uc011mhu.1	-						FAM9B_uc011mhv.1_Intron|FAM9B_uc004csh.2_Intron	NM_205849	NP_995321			family with sequence similarity 9, member B							nucleus					0		Hepatocellular(5;0.219)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	9218805	9218806	+	IGR	INS	-	GT	GT	rs144734680		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9218805_9218806insGT								FAM9B (86158 upstream) : TBL1X (212529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	9296176	9296177	+	IGR	DEL	GC	-	-	rs10856478		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9296176_9296177delGC								FAM9B (163529 upstream) : TBL1X (135158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	9305647	9305647	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9305647delA								FAM9B (173000 upstream) : TBL1X (125688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	9349894	9349895	+	IGR	INS	-	AGGCCCCACCCC	AGGCCCCACCCC	rs113300267		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9349894_9349895insAGGCCCCACCCC								FAM9B (217247 upstream) : TBL1X (81440 downstream)																																			---	---	---	---
TBL1X	6907	broad.mit.edu	37	X	9667894	9667894	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9667894delC	uc010ndq.2	+						TBL1X_uc004csq.3_Intron|TBL1X_uc010ndr.2_Intron|TBL1X_uc004csr.2_Intron|TBL1X_uc004css.2_Intron	NM_001139466	NP_001132938			transducin beta-like 1X isoform a						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|sensory perception of sound|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein C-terminus binding|protein domain specific binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Hepatocellular(5;0.000888)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	10408318	10408320	+	IGR	DEL	CTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10408318_10408320delCTC								CLCN4 (202621 upstream) : MID1 (5277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	11087131	11087131	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11087131delA	uc004cuh.2	-						uc004cui.1_Intron					Homo sapiens clone IMAGE:4081578, mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	11695901	11695902	+	IGR	DEL	TT	-	-	rs150226379		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11695901_11695902delTT								ARHGAP6 (12080 upstream) : MSL3 (80376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	12059675	12059676	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12059675_12059676delTT								MSL3 (265805 upstream) : FRMPD4 (96909 downstream)																																			---	---	---	---
FRMPD4	9758	broad.mit.edu	37	X	12280559	12280560	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12280559_12280560insT	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																		---	---	---	---
FRMPD4	9758	broad.mit.edu	37	X	12400716	12400717	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12400716_12400717insA	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																		---	---	---	---
FRMPD4	9758	broad.mit.edu	37	X	12704199	12704199	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12704199delT	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																		---	---	---	---
TLR8	51311	broad.mit.edu	37	X	12939876	12939876	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12939876delA	uc004cve.2	+	2	2785	c.2717delA	c.(2716-2718)GAAfs	p.E906fs	TLR8_uc004cvd.2_Frame_Shift_Del_p.E924fs	NM_138636	NP_619542	Q9NR97	TLR8_HUMAN	toll-like receptor 8 precursor	906	Cytoplasmic (Potential).|TIR.				cellular response to mechanical stimulus|defense response to virus|I-kappaB kinase/NF-kappaB cascade|immunoglobulin mediated immune response|inflammatory response|innate immune response|positive regulation of innate immune response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process	endosome membrane	DNA binding|double-stranded RNA binding|single-stranded RNA binding|transmembrane receptor activity			ovary(4)|lung(2)|large_intestine(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	13000460	13000461	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13000460_13000461insT								TLR8 (59174 upstream) : FAM9C (53276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	13335955	13335956	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13335955_13335956delTT								FAM9C (273155 upstream) : ATXN3L (814 downstream)																																			---	---	---	---
GPM6B	2824	broad.mit.edu	37	X	13864598	13864599	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13864598_13864599insT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	13962554	13962554	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13962554delA								GPM6B (5723 upstream) : GEMIN8 (62292 downstream)																																			---	---	---	---
GEMIN8	54960	broad.mit.edu	37	X	14039512	14039512	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14039512delA	uc004cwb.2	-						GEMIN8_uc004cwc.2_Intron|GEMIN8_uc004cwd.2_Intron	NM_017856	NP_060326			gem (nuclear organelle) associated protein 8						spliceosomal snRNP assembly	Cajal body|cytoplasm|SMN complex|spliceosomal complex	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	14146362	14146362	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14146362delT								GEMIN8 (98327 upstream) : GLRA2 (401058 downstream)																																			---	---	---	---
GLRA2	2742	broad.mit.edu	37	X	14577880	14577880	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14577880delT	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)													---	---	---	---
GLRA2	2742	broad.mit.edu	37	X	14674043	14674043	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14674043delT	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)													---	---	---	---
MOSPD2	158747	broad.mit.edu	37	X	14902295	14902295	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14902295delA	uc004cwi.2	+						MOSPD2_uc004cwj.2_5'Flank	NM_152581	NP_689794			motile sperm domain containing 2							integral to membrane	structural molecule activity			lung(1)	1	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	15067064	15067065	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15067064_15067065delAA								MOSPD2 (127609 upstream) : ASB9 (195046 downstream)																																			---	---	---	---
ASB11	140456	broad.mit.edu	37	X	15315432	15315432	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15315432delA	uc004cwp.1	-						ASB11_uc004cwo.1_Intron|ASB11_uc010nes.1_Intron|ASB11_uc010net.1_Intron	NM_080873	NP_543149			ankyrin repeat and SOCS box-containing protein						intracellular signal transduction					breast(2)|skin(1)	3	Hepatocellular(33;0.183)																	---	---	---	---
CTPS2	56474	broad.mit.edu	37	X	16661494	16661494	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16661494delT	uc004cxk.2	-						CTPS2_uc004cxl.2_Intron|CTPS2_uc004cxm.2_Intron	NM_001144002	NP_001137474			cytidine triphosphate synthase II						glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine nucleotide biosynthetic process	cytosol	ATP binding|CTP synthase activity			ovary(1)	1	Hepatocellular(33;0.0997)																	---	---	---	---
SYAP1	94056	broad.mit.edu	37	X	16735162	16735163	+	5'Flank	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16735162_16735163delAA	uc004cxp.2	+						SYAP1_uc004cxo.2_5'Flank|SYAP1_uc011miv.1_5'Flank	NM_032796	NP_116185			SYAP1 protein											skin(1)	1	Hepatocellular(33;0.0997)																	---	---	---	---
RBBP7	5931	broad.mit.edu	37	X	16867569	16867569	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16867569delT	uc004cxt.2	-						RBBP7_uc004cxs.1_Intron|RBBP7_uc004cxu.2_Intron	NM_002893	NP_002884			retinoblastoma binding protein 7						cell proliferation|cellular heat acclimation|CenH3-containing nucleosome assembly at centromere|DNA replication|multicellular organismal development|negative regulation of cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex|NuRD complex	protein binding			upper_aerodigestive_tract(1)|ovary(1)	2	Hepatocellular(33;0.0997)																	---	---	---	---
REPS2	9185	broad.mit.edu	37	X	17088011	17088011	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17088011delT	uc004cxv.1	+						REPS2_uc004cxw.1_Intron|REPS2_uc011miw.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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	17344038	17344038	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17344038delT								REPS2 (172635 upstream) : NHS (49505 downstream)																																			---	---	---	---
NHS	4810	broad.mit.edu	37	X	17534897	17534898	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17534897_17534898delCA	uc004cxx.2	+						NHS_uc011mix.1_Intron	NM_198270	NP_938011			Nance-Horan syndrome protein isoform 1							nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)																	---	---	---	---
NHS	4810	broad.mit.edu	37	X	17551387	17551387	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17551387delT	uc004cxx.2	+						NHS_uc011mix.1_Intron	NM_198270	NP_938011			Nance-Horan syndrome protein isoform 1							nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)																	---	---	---	---
NHS	4810	broad.mit.edu	37	X	17665272	17665272	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17665272delA	uc004cxx.2	+						NHS_uc011mix.1_Intron|NHS_uc004cxy.2_Intron|NHS_uc004cxz.2_Intron	NM_198270	NP_938011			Nance-Horan syndrome protein isoform 1							nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	17913488	17913488	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17913488delA								RAI2 (34031 upstream) : BEND2 (267565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	17976962	17976962	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17976962delC								RAI2 (97505 upstream) : BEND2 (204091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	18385818	18385818	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18385818delA								SCML2 (12974 upstream) : CDKL5 (57907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	18420858	18420858	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18420858delG								SCML2 (48014 upstream) : CDKL5 (22867 downstream)																																			---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18613312	18613312	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18613312delA	uc004cym.2	+						CDKL5_uc004cyn.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18620742	18620742	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18620742delT	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)																	---	---	---	---
RS1	6247	broad.mit.edu	37	X	18692498	18692498	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18692498delT	uc004cyo.2	-							NM_000330	NP_000321			X-linked juvenile retinoschisis protein						cell adhesion|multicellular organismal development|response to stimulus|visual perception	extracellular space				ovary(2)	2	Hepatocellular(33;0.183)																	---	---	---	---
PPEF1	5475	broad.mit.edu	37	X	18741106	18741108	+	Intron	DEL	ATT	-	-	rs111289404		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18741106_18741108delATT	uc004cyq.2	+						PPEF1_uc004cyp.2_Intron|PPEF1_uc004cyr.2_Intron|PPEF1_uc004cys.2_Intron|PPEF1_uc011mja.1_Intron	NM_006240	NP_006231			protein phosphatase with EF hand calcium-binding						detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity				0	Hepatocellular(33;0.183)																	---	---	---	---
PPEF1	5475	broad.mit.edu	37	X	18827526	18827527	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18827526_18827527insA	uc004cyq.2	+						PPEF1_uc004cyp.2_Intron|PPEF1_uc004cyr.2_Intron|PPEF1_uc004cys.2_Intron|PPEF1_uc011mja.1_Intron|PPEF1_uc011mjb.1_Intron	NM_006240	NP_006231			protein phosphatase with EF hand calcium-binding						detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity				0	Hepatocellular(33;0.183)																	---	---	---	---
PPEF1	5475	broad.mit.edu	37	X	18845705	18845706	+	3'UTR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18845705_18845706insA	uc004cyq.2	+	19					PPEF1_uc004cyp.2_3'UTR|PPEF1_uc004cyr.2_3'UTR|PPEF1_uc004cys.2_3'UTR|PPEF1_uc011mja.1_3'UTR|PPEF1_uc011mjb.1_3'UTR	NM_006240	NP_006231			protein phosphatase with EF hand calcium-binding						detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity				0	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	18884862	18884862	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18884862delA								PPEF1 (38830 upstream) : PHKA2 (25555 downstream)																																			---	---	---	---
GPR64	10149	broad.mit.edu	37	X	19046358	19046359	+	Splice_Site	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19046358_19046359insA	uc004cyx.2	-	10	523	c.359_splice	c.e10-1	p.A120_splice	GPR64_uc004cyy.2_Splice_Site_p.A117_splice|GPR64_uc004cyz.2_Splice_Site_p.A106_splice|GPR64_uc004czb.2_Splice_Site_p.A120_splice|GPR64_uc004czc.2_Splice_Site_p.A104_splice|GPR64_uc004czd.2_Splice_Site_p.A96_splice|GPR64_uc004cze.2_Splice_Site_p.A90_splice|GPR64_uc004czf.2_Splice_Site_p.A82_splice|GPR64_uc004cza.2_Splice_Site_p.A98_splice|GPR64_uc004cyw.2_Splice_Site_p.A104_splice|GPR64_uc010nfj.2_Splice_Site_p.A90_splice	NM_001079858	NP_001073327			G protein-coupled receptor 64 isoform 1						neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	19215350	19215352	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19215350_19215352delTTT								GPR64 (74673 upstream) : PDHA1 (146659 downstream)																																			---	---	---	---
CXorf23	256643	broad.mit.edu	37	X	19953721	19953721	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19953721delA	uc004czp.2	-						CXorf23_uc010nfn.2_Intron|CXorf23_uc011mjg.1_Intron|CXorf23_uc004czo.2_Intron	NM_198279	NP_938020			hypothetical protein LOC256643							mitochondrion				lung(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	20000668	20000679	+	IGR	DEL	CACACACACACA	-	-	rs72097944		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20000668_20000679delCACACACACACA								CXorf23 (12286 upstream) : LOC729609 (4256 downstream)																																			---	---	---	---
EIF1AX	1964	broad.mit.edu	37	X	20154350	20154351	+	Intron	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20154350_20154351delCA	uc004czt.2	-						SCARNA9L_uc010nfp.2_RNA	NM_001412	NP_001403			X-linked eukaryotic translation initiation							cytosol	translation initiation factor activity			ovary(1)	1																		---	---	---	---
RPS6KA3	6197	broad.mit.edu	37	X	20253005	20253006	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20253005_20253006delAA	uc004czu.2	-						RPS6KA3_uc004czv.2_Intron|RPS6KA3_uc011mjl.1_Intron|RPS6KA3_uc011mjm.1_Intron	NM_004586	NP_004577			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|skeletal system development|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 serine/threonine kinase activity			central_nervous_system(4)|stomach(1)|ovary(1)|lung(1)|breast(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	20701913	20701913	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20701913delT								RPS6KA3 (416390 upstream) : CNKSR2 (691067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	21059234	21059236	+	IGR	DEL	TTG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21059234_21059236delTTG								RPS6KA3 (773711 upstream) : CNKSR2 (333744 downstream)																																			---	---	---	---
SMPX	23676	broad.mit.edu	37	X	21740119	21740119	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21740119delA	uc004daa.2	-							NM_014332	NP_055147			small muscle protein, X-linked						striated muscle contraction						0																		---	---	---	---
YY2	404281	broad.mit.edu	37	X	21863335	21863335	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21863335delT	uc010nfq.2	+	3	468	c.271delT	c.(271-273)TTTfs	p.F91fs	MBTPS2_uc004dae.2_Frame_Shift_Del_p.F91fs|MBTPS2_uc004dab.2_Frame_Shift_Del_p.F91fs	NM_206923	NP_996806	O15391	TYY2_HUMAN	YY2 transcription factor	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	DNA binding|zinc ion binding			breast(1)|skin(1)	2																		---	---	---	---
SMS	6611	broad.mit.edu	37	X	21966116	21966116	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21966116delT	uc004dag.2	+						SMS_uc011mjq.1_Intron|SMS_uc004daf.1_Intron	NM_004595	NP_004586			spermine synthase						methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)													---	---	---	---
SMS	6611	broad.mit.edu	37	X	21985522	21985522	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21985522delT	uc004dag.2	+						SMS_uc011mjq.1_Intron|SMS_uc004daf.1_Intron	NM_004595	NP_004586			spermine synthase						methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)													---	---	---	---
PRDX4	10549	broad.mit.edu	37	X	23695924	23695924	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23695924delA	uc004dam.2	+							NM_006406	NP_006397			peroxiredoxin 4						cell redox homeostasis|I-kappaB phosphorylation		thioredoxin peroxidase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
PRDX4	10549	broad.mit.edu	37	X	23696384	23696384	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23696384delA	uc004dam.2	+							NM_006406	NP_006397			peroxiredoxin 4						cell redox homeostasis|I-kappaB phosphorylation		thioredoxin peroxidase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
ACOT9	23597	broad.mit.edu	37	X	23722754	23722754	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23722754delA	uc004dap.2	-						ACOT9_uc004dan.2_Intron|ACOT9_uc004dao.2_Intron|ACOT9_uc004daq.2_Intron|ACOT9_uc004dar.2_Intron|ACOT9_uc011mjt.1_Intron|ACOT9_uc004das.2_Intron	NM_001033583	NP_001028755			acyl-Coenzyme A thioesterase 2, mitochondrial						acyl-CoA metabolic process	mitochondrion	acetyl-CoA hydrolase activity|carboxylesterase activity			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	24117711	24117711	+	IGR	DEL	T	-	-	rs67991022		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24117711delT								EIF2S3 (20786 upstream) : ZFX (50051 downstream)																																			---	---	---	---
POLA1	5422	broad.mit.edu	37	X	24735994	24735994	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24735994delT	uc004dbl.2	+						POLA1_uc004dbm.2_Intron|POLA1_uc004dbn.2_Intron	NM_016937	NP_058633			DNA-directed DNA polymerase alpha 1						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	25269958	25269958	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25269958delT								ARX (235893 upstream) : MAGEB18 (886505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	25413314	25413317	+	IGR	DEL	GAGA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25413314_25413317delGAGA								ARX (379249 upstream) : MAGEB18 (743146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	25924923	25924923	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25924923delA								ARX (890858 upstream) : MAGEB18 (231540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	26008449	26008449	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26008449delA								ARX (974384 upstream) : MAGEB18 (148014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	26236299	26236299	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26236299delT								MAGEB6 (22537 upstream) : VENTXP1 (340155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	27417497	27417497	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27417497delA	uc004dbt.2	-											Homo sapiens cDNA clone IMAGE:4824334.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	27519310	27519311	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27519310_27519311delTC								SMEK3P (37852 upstream) : DCAF8L2 (245615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	27519403	27519404	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27519403_27519404delTG								SMEK3P (37945 upstream) : DCAF8L2 (245522 downstream)																																			---	---	---	---
DCAF8L2	347442	broad.mit.edu	37	X	27766493	27766495	+	In_Frame_Del	DEL	TCT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27766493_27766495delTCT	uc011mjy.1	+	1	1568_1570	c.1481_1483delTCT	c.(1480-1485)ATCTTC>ATC	p.F496del		NM_001136533	NP_001130005			DDB1 and CUL4 associated factor 8-like 2											central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	27985102	27985102	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27985102delC								MAGEB10 (144340 upstream) : DCAF8L1 (11008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	28202545	28202545	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:28202545delT								DCAF8L1 (202979 upstream) : IL1RAPL1 (403136 downstream)																																			---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	29935792	29935792	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29935792delT	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	30045536	30045536	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30045536delA								IL1RAPL1 (71519 upstream) : MAGEB2 (188139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	30283438	30283438	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30283438delT								MAGEB1 (13284 upstream) : NR0B1 (39102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	31085364	31085365	+	IGR	DEL	AT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31085364_31085365delAT								TAB3 (92163 upstream) : FTHL17 (3993 downstream)																																			---	---	---	---
DMD	1756	broad.mit.edu	37	X	31144834	31144834	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31144834delA	uc004dda.1	-						DMD_uc004dcq.1_Intron|DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc004dcm.1_Intron|DMD_uc004dcn.1_Intron|DMD_uc004dco.1_Intron|DMD_uc004dcp.1_Intron|DMD_uc011mkb.1_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	31164567	31164568	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31164567_31164568insA	uc004dda.1	-						DMD_uc004dcq.1_Intron|DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc004dcm.1_Intron|DMD_uc004dcn.1_Intron|DMD_uc004dco.1_Intron|DMD_uc004dcp.1_Intron|DMD_uc011mkb.1_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	31195898	31195898	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31195898delA	uc004dda.1	-						DMD_uc004dcq.1_Intron|DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc004dcm.1_Intron|DMD_uc004dcn.1_Intron|DMD_uc004dco.1_Intron|DMD_uc004dcp.1_Intron|DMD_uc011mkb.1_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	31497362	31497362	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31497362delT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	33942103	33942104	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:33942103_33942104delGA								DMD (584377 upstream) : FAM47A (205771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	34283926	34283926	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34283926delT								FAM47A (133498 upstream) : TMEM47 (361257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	34374220	34374220	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34374220delT								FAM47A (223792 upstream) : TMEM47 (270963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	34735503	34735513	+	IGR	DEL	TTTTTTTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34735503_34735513delTTTTTTTTTTT								TMEM47 (60098 upstream) : FAM47B (225418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	34789702	34789702	+	IGR	DEL	A	-	-	rs66610386		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34789702delA								TMEM47 (114297 upstream) : FAM47B (171229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	34932057	34932057	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34932057delA								TMEM47 (256652 upstream) : FAM47B (28874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	35525378	35525378	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35525378delT								FAM47B (562344 upstream) : MAGEB16 (291081 downstream)																																			---	---	---	---
CXorf22	170063	broad.mit.edu	37	X	36005773	36005774	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36005773_36005774insA	uc004ddj.2	+						CXorf22_uc010ngv.2_Intron	NM_152632	NP_689845			hypothetical protein LOC170063											large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	36050425	36050425	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36050425delA								CXorf22 (42157 upstream) : CXorf59 (14628 downstream)																																			---	---	---	---
CXorf59	286464	broad.mit.edu	37	X	36074039	36074039	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36074039delT	uc004ddk.1	+							NM_173695	NP_775966			hypothetical protein LOC286464							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
CXorf59	286464	broad.mit.edu	37	X	36118114	36118114	+	Intron	DEL	T	-	-	rs67232822		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36118114delT	uc004ddk.1	+							NM_173695	NP_775966			hypothetical protein LOC286464							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
CXorf30	645090	broad.mit.edu	37	X	36360739	36360739	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36360739delT	uc011mkc.1	+							NM_001098843	NP_001092313			hypothetical protein LOC645090											lung(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	36975143	36975143	+	IGR	DEL	A	-	-	rs60267092	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36975143delA								CXorf30 (571710 upstream) : FAM47C (51327 downstream)																																			---	---	---	---
LANCL3	347404	broad.mit.edu	37	X	37447665	37447665	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37447665delA	uc011mkd.1	+						LANCL3_uc004ddp.1_Intron	NM_198511	NP_940913			LanC lantibiotic synthetase component C-like 3								catalytic activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	37715569	37715569	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37715569delA								DYNLT3 (8680 upstream) : CXorf27 (134501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	37810301	37810301	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37810301delA								DYNLT3 (103412 upstream) : CXorf27 (39769 downstream)																																			---	---	---	---
RPGR	6103	broad.mit.edu	37	X	38162057	38162057	+	Intron	DEL	T	-	-	rs35450787		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38162057delT	uc004ded.1	-						RPGR_uc004deb.2_Intron|RPGR_uc004dea.2_Intron|RPGR_uc004dec.2_Intron|RPGR_uc004dee.1_Intron	NM_001034853	NP_001030025			retinitis pigmentosa GTPase regulator isoform C						intracellular protein transport|response to stimulus|visual perception	Golgi apparatus|photoreceptor outer segment	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	38404117	38404117	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38404117delT								OTC (123415 upstream) : TSPAN7 (16614 downstream)																																			---	---	---	---
TSPAN7	7102	broad.mit.edu	37	X	38440748	38440748	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38440748delC	uc004deg.3	+						TSPAN7_uc011mkj.1_Intron|TSPAN7_uc011mkk.1_Intron	NM_004615	NP_004606			tetraspanin 7						interspecies interaction between organisms	integral to plasma membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	38707440	38707440	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38707440delA								MID1IP1 (41659 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	39633158	39633158	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39633158delC								MID1IP1 (967377 upstream) : BCOR (277343 downstream)																																			---	---	---	---
BCOR	54880	broad.mit.edu	37	X	39951717	39951717	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39951717delA	uc004den.3	-						BCOR_uc004dep.3_Intron|BCOR_uc004deo.3_Intron|BCOR_uc004dem.3_Intron|BCOR_uc004deq.3_Intron	NM_001123385	NP_001116857			BCL-6 interacting corepressor isoform c						heart development|histone H2A monoubiquitination|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4																		---	---	---	---
BCOR	54880	broad.mit.edu	37	X	39975750	39975750	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39975750delA	uc004dep.3	-						BCOR_uc004deo.3_Intron	NM_001123383	NP_001116855			BCL-6 interacting corepressor isoform a						heart development|histone H2A monoubiquitination|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	40151786	40151787	+	IGR	DEL	CT	-	-	rs71892386		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40151786_40151787delCT								BCOR (115204 upstream) : ATP6AP2 (288429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	40245303	40245303	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40245303delT								BCOR (208721 upstream) : ATP6AP2 (194913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	40316620	40316620	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40316620delT								BCOR (280038 upstream) : ATP6AP2 (123596 downstream)																																			---	---	---	---
MED14	9282	broad.mit.edu	37	X	40588551	40588551	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40588551delT	uc004dex.3	-						MED14_uc010nhe.1_Intron	NM_004229	NP_004220			mediator complex subunit 14						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(2)|kidney(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	40618309	40618310	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40618309_40618310insA								MED14 (23173 upstream) : LOC100132831 (72160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	40792538	40792538	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40792538delT								LOC100132831 (100089 upstream) : USP9X (152350 downstream)																																			---	---	---	---
USP9X	8239	broad.mit.edu	37	X	40950465	40950466	+	Intron	INS	-	CT	CT	rs112038131		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40950465_40950466insCT	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679			ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6																		---	---	---	---
USP9X	8239	broad.mit.edu	37	X	40973899	40973900	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40973899_40973900insT	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679			ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6																		---	---	---	---
USP9X	8239	broad.mit.edu	37	X	41043078	41043078	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41043078delT	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679			ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6																		---	---	---	---
USP9X	8239	broad.mit.edu	37	X	41059834	41059834	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41059834delA	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679			ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6																		---	---	---	---
USP9X	8239	broad.mit.edu	37	X	41083888	41083889	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41083888_41083889insA	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679			ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6																		---	---	---	---
NYX	60506	broad.mit.edu	37	X	41324444	41324444	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41324444delT	uc004dfh.2	+						NYX_uc011mku.1_Intron	NM_022567	NP_072089			nyctalopin precursor						response to stimulus|visual perception	intracellular|proteinaceous extracellular matrix				lung(2)	2																		---	---	---	---
CASK	8573	broad.mit.edu	37	X	41649373	41649373	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41649373delT	uc004dfl.3	-						CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron	NM_003688	NP_003679			calcium/calmodulin-dependent serine protein						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	41981576	41981576	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41981576delA								CASK (199289 upstream) : PPP1R2P9 (655043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42083231	42083231	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42083231delT								CASK (300944 upstream) : PPP1R2P9 (553388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42091975	42091976	+	IGR	INS	-	TGTG	TGTG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42091975_42091976insTGTG								CASK (309688 upstream) : PPP1R2P9 (544643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42290686	42290687	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42290686_42290687delAA								CASK (508399 upstream) : PPP1R2P9 (345932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42419984	42419984	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42419984delT								CASK (637697 upstream) : PPP1R2P9 (216635 downstream)																																			---	---	---	---
PPP1R2P9	80316	broad.mit.edu	37	X	42640106	42640106	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42640106delA	uc004dfv.2	-							NR_002191				RecName: Full=Putative type-1 protein phosphatase inhibitor 4;          Short=I-4; AltName: Full=Protein phosphatase 1, regulatory subunit 2 pseudogene 9;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	42837158	42837158	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42837158delT								PPP1R2P9 (199672 upstream) : MAOA (678251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42967112	42967113	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42967112_42967113delTG								PPP1R2P9 (329626 upstream) : MAOA (548296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	43162375	43162375	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43162375delT								PPP1R2P9 (524889 upstream) : MAOA (353034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	44529972	44529972	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44529972delA								FUNDC1 (127751 upstream) : DUSP21 (173277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	44648056	44648056	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44648056delA								FUNDC1 (245835 upstream) : DUSP21 (55193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	44723634	44723634	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44723634delT								DUSP21 (19502 upstream) : KDM6A (8789 downstream)																																			---	---	---	---
KDM6A	7403	broad.mit.edu	37	X	44822743	44822744	+	Intron	DEL	TC	-	-	rs111397439		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44822743_44822744delTC	uc004dge.3	+						KDM6A_uc010nhk.2_Intron|KDM6A_uc011mkz.1_Intron|KDM6A_uc011mla.1_Intron|KDM6A_uc011mlb.1_Intron|KDM6A_uc011mlc.1_Intron	NM_021140	NP_066963			ubiquitously transcribed tetratricopeptide						histone H3-K4 methylation		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	p.0(14)|p.0?(6)		kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84								D|N|F|S		renal|oesophageal SCC|MM								---	---	---	---
KDM6A	7403	broad.mit.edu	37	X	44851802	44851802	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44851802delT	uc004dge.3	+						KDM6A_uc010nhk.2_Intron|KDM6A_uc011mkz.1_Intron|KDM6A_uc011mla.1_Intron|KDM6A_uc011mlb.1_Intron|KDM6A_uc011mlc.1_Intron	NM_021140	NP_066963			ubiquitously transcribed tetratricopeptide						histone H3-K4 methylation		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	p.?(1)		kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84								D|N|F|S		renal|oesophageal SCC|MM								---	---	---	---
KDM6A	7403	broad.mit.edu	37	X	44938317	44938317	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44938317delA	uc004dge.3	+						KDM6A_uc010nhk.2_Intron|KDM6A_uc011mkz.1_Intron|KDM6A_uc011mla.1_Intron|KDM6A_uc011mlb.1_Intron|KDM6A_uc011mlc.1_Intron|KDM6A_uc011mld.1_Intron	NM_021140	NP_066963			ubiquitously transcribed tetratricopeptide						histone H3-K4 methylation		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84								D|N|F|S		renal|oesophageal SCC|MM								---	---	---	---
Unknown	0	broad.mit.edu	37	X	45074622	45074625	+	IGR	DEL	AAAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45074622_45074625delAAAA								CXorf36 (14476 upstream) : MIR221 (530960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	45735312	45735313	+	IGR	DEL	CA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45735312_45735313delCA								MIR222 (128782 upstream) : ZNF673 (571311 downstream)																																			---	---	---	---
PHF16	9767	broad.mit.edu	37	X	46865418	46865419	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46865418_46865419insA	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	46961727	46961727	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46961727delT								RGN (9015 upstream) : NDUFB11 (39889 downstream)																																			---	---	---	---
UBA1	7317	broad.mit.edu	37	X	47066042	47066043	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47066042_47066043insT	uc004dhj.3	+						UBA1_uc004dhk.3_Intron|UBA1_uc004dhm.2_5'Flank	NM_153280	NP_695012			ubiquitin-activating enzyme E1						cell death|protein modification process		ATP binding|ligase activity|protein binding|small protein activating enzyme activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	47206918	47206919	+	IGR	INS	-	TCCC	TCCC	rs58715425		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47206918_47206919insTCCC								USP11 (99192 upstream) : ZNF157 (23080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	47218693	47218694	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47218693_47218694delTT								USP11 (110967 upstream) : ZNF157 (11305 downstream)																																			---	---	---	---
CFP	5199	broad.mit.edu	37	X	47483958	47483959	+	Intron	DEL	CC	-	-	rs72201747		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47483958_47483959delCC	uc004dig.3	-						CFP_uc004dih.2_Intron|CFP_uc004dii.1_3'UTR|CFP_uc010nhu.2_3'UTR	NM_001145252	NP_001138724			complement factor properdin precursor						complement activation, alternative pathway|defense response to bacterium	extracellular space				breast(2)|lung(1)	3																		---	---	---	---
CFP	5199	broad.mit.edu	37	X	47492427	47492427	+	5'Flank	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47492427delT	uc004dih.2	-							NM_002621	NP_002612			complement factor properdin precursor						complement activation, alternative pathway|defense response to bacterium	extracellular space				breast(2)|lung(1)	3																		---	---	---	---
ELK1	2002	broad.mit.edu	37	X	47500596	47500596	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47500596delG	uc004dik.3	-						ELK1_uc010nhv.2_Intron|ELK1_uc010nhw.2_5'UTR|ELK1_uc004dil.3_Intron	NM_001114123	NP_001107595			ELK1 protein						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	47561410	47561410	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47561410delA								LOC100133957 (41634 upstream) : ZNF81 (134891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	47583505	47583505	+	RNA	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47583505delC	uc004dio.1	+	2		c.775delC								Homo sapiens cDNA FLJ36789 fis, clone ADRGL2004459.																														---	---	---	---
ZNF81	347344	broad.mit.edu	37	X	47760261	47760261	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47760261delT	uc010nhy.1	+							NM_007137	NP_009068			zinc finger protein 81							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(315;0.0973)																---	---	---	---
ZNF182	7569	broad.mit.edu	37	X	47842981	47842981	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47842981delA	uc004dir.2	-						ZNF182_uc004dis.2_Intron|ZNF182_uc004dit.2_Intron|ZNF182_uc011mlu.1_Intron|ZNF630_uc010nhz.1_Intron	NM_006962	NP_008893			zinc finger protein 21 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3																		---	---	---	---
ZNF630	57232	broad.mit.edu	37	X	47875098	47875098	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47875098delA	uc010nhz.1	-											Homo sapiens cDNA FLJ20573 fis, clone REC01089, highly similar to ZN84_HUMAN ZINC FINGER PROTEIN 84.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	48138042	48138043	+	IGR	DEL	TT	-	-	rs34358005		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48138042_48138043delTT								SSX1 (11163 upstream) : SSX3 (67820 downstream)																																			---	---	---	---
SSX3	10214	broad.mit.edu	37	X	48209231	48209231	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48209231delT	uc004djd.1	-						SSX3_uc004dje.2_Intron	NM_021014	NP_066294			synovial sarcoma, X breakpoint 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0																		---	---	---	---
PORCN	64840	broad.mit.edu	37	X	48373146	48373146	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48373146delG	uc010nie.1	+						PORCN_uc004djr.1_Intron|PORCN_uc004djs.1_Intron|PORCN_uc004djt.1_Intron|PORCN_uc011mlx.1_Intron|PORCN_uc004dju.1_Intron|PORCN_uc004djv.1_Intron|PORCN_uc004djw.1_Intron	NM_203475	NP_982301			porcupine isoform D						Wnt receptor signaling pathway	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
WDR13	64743	broad.mit.edu	37	X	48462533	48462533	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48462533delA	uc004dkh.1	+						WDR13_uc004dki.1_Intron|WDR13_uc004dkj.1_Intron|WDR13_uc004dkk.1_Intron|WDR13_uc004dkl.3_Intron	NM_017883	NP_060353			WD repeat domain 13 protein							cytoplasm|nucleus				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	48505002	48505002	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48505002delA								WDR13 (41428 upstream) : WAS (37184 downstream)																																			---	---	---	---
GATA1	2623	broad.mit.edu	37	X	48648141	48648142	+	Intron	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48648141_48648142insC	uc004dkq.3	+							NM_002049	NP_002040			GATA binding protein 1						basophil differentiation|eosinophil differentiation|erythrocyte development|megakaryocyte differentiation|platelet aggregation|platelet formation|positive regulation of anti-apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|regulation of glycoprotein biosynthetic process|transcription from RNA polymerase II promoter	nuclear membrane|nucleolus|nucleoplasm	C2H2 zinc finger domain binding|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(246)|lung(2)	248								Mis|F		megakaryoblastic leukemia of Downs Syndrome								---	---	---	---
GRIPAP1	56850	broad.mit.edu	37	X	48837297	48837298	+	Intron	DEL	AA	-	-	rs78899852		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48837297_48837298delAA	uc004dly.1	-						GRIPAP1_uc004dlz.2_Intron|GRIPAP1_uc004dma.2_Intron	NM_020137	NP_064522			GRIP1 associated protein 1 isoform 1							early endosome				breast(2)|kidney(1)	3																		---	---	---	---
TFE3	7030	broad.mit.edu	37	X	48887952	48887952	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48887952delC	uc004dmb.3	-	10	1683	c.1445delG	c.(1444-1446)GGAfs	p.G482fs	TFE3_uc004dmc.3_Frame_Shift_Del_p.G377fs	NM_006521	NP_006512	P19532	TFE3_HUMAN	transcription factor E3	482					humoral immune response|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding		ASPSCR1/TFE3(161)|PRCC/TFE3(25)|SFPQ/TFE3(6)|NONO/TFE3(2)|CLTC/TFE3(2)	soft_tissue(120)|kidney(76)|central_nervous_system(1)	197								T	SFPQ|ASPSCR1|PRCC|NONO|CLTC	papillary renal|alveolar soft part sarcoma|renal								---	---	---	---
PRAF2	11230	broad.mit.edu	37	X	48931311	48931311	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48931311delC	uc004dmi.2	-						PRAF2_uc004dmh.2_5'Flank|PRAF2_uc011mmt.1_Intron	NM_007213	NP_009144			PRA1 domain family, member 2						L-glutamate transport|protein transport	endosome membrane|integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	49401127	49401128	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49401127_49401128insA								GAGE1 (30169 upstream) : PAGE1 (50928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	49425024	49425025	+	IGR	DEL	AC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49425024_49425025delAC								GAGE1 (54066 upstream) : PAGE1 (27031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	49433107	49433107	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49433107delG								GAGE1 (62149 upstream) : PAGE1 (18949 downstream)																																			---	---	---	---
CLCN5	1184	broad.mit.edu	37	X	49685154	49685154	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49685154delA	uc004dor.1	+						CLCN5_uc004doq.1_5'Flank	NM_001127899	NP_001121371			chloride channel 5 isoform a						excretion	apical part of cell|endosome membrane|Golgi membrane|integral to plasma membrane	antiporter activity|ATP binding			ovary(2)|lung(1)|central_nervous_system(1)	4	Ovarian(276;0.236)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	50673857	50673858	+	IGR	INS	-	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50673857_50673858insC								BMP15 (14251 upstream) : NUDT10 (401225 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	51493256	51493260	+	IGR	DEL	TTTTT	-	-	rs72152130		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51493256_51493260delTTTTT								GSPT2 (4227 upstream) : MAGED1 (52895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	51742008	51742008	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51742008delT								MAGED1 (96560 upstream) : MAGED4 (62917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	52020993	52020993	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:52020993delT								MAGED4B (208625 upstream) : XAGE2 (91085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	52642704	52642704	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:52642704delT								XAGE1D (398753 upstream) : SSX8 (9281 downstream)																																			---	---	---	---
GPR173	54328	broad.mit.edu	37	X	53105735	53105735	+	5'UTR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53105735delC	uc004dru.2	+	2						NM_018969	NP_061842			G protein-coupled receptor 173							integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1																		---	---	---	---
TSPYL2	64061	broad.mit.edu	37	X	53112052	53112052	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53112052delG	uc004drw.2	+	1	504	c.372delG	c.(370-372)TCGfs	p.S124fs	TSPYL2_uc004drv.2_Frame_Shift_Del_p.S124fs|TSPYL2_uc004drx.1_5'Flank	NM_022117	NP_071400	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	124					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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	53204496	53204496	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53204496delT								TSPYL2 (86775 upstream) : KDM5C (965 downstream)																																			---	---	---	---
WNK3	65267	broad.mit.edu	37	X	54263350	54263351	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54263350_54263351insA	uc004dtd.1	-						WNK3_uc004dtc.1_Intron	NM_001002838	NP_001002838			WNK lysine deficient protein kinase 3 isoform 2						intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11																		---	---	---	---
WNK3	65267	broad.mit.edu	37	X	54298879	54298879	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54298879delA	uc004dtd.1	-						WNK3_uc004dtc.1_Intron	NM_001002838	NP_001002838			WNK lysine deficient protein kinase 3 isoform 2						intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11																		---	---	---	---
WNK3	65267	broad.mit.edu	37	X	54340638	54340638	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54340638delA	uc004dtd.1	-						WNK3_uc004dtc.1_Intron	NM_001002838	NP_001002838			WNK lysine deficient protein kinase 3 isoform 2						intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	54444929	54444929	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54444929delA								WNK3 (60491 upstream) : TSR2 (21924 downstream)																																			---	---	---	---
FGD1	2245	broad.mit.edu	37	X	54508146	54508146	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54508146delT	uc004dtg.2	-							NM_004463	NP_004454			faciogenital dysplasia protein						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|organ morphogenesis|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|Golgi apparatus|lamellipodium|nucleus|plasma membrane|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
GNL3L	54552	broad.mit.edu	37	X	54563218	54563220	+	Intron	DEL	AAA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54563218_54563220delAAA	uc004dth.1	+						GNL3L_uc004dti.2_Intron	NM_019067	NP_061940			guanine nucleotide binding protein-like 3						ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1																		---	---	---	---
GNL3L	54552	broad.mit.edu	37	X	54576639	54576640	+	Intron	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54576639_54576640delGA	uc004dth.1	+						GNL3L_uc004dti.2_Intron	NM_019067	NP_061940			guanine nucleotide binding protein-like 3						ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1																		---	---	---	---
GNL3L	54552	broad.mit.edu	37	X	54589053	54589053	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54589053delA	uc004dth.1	+	16					GNL3L_uc004dti.2_RNA	NM_019067	NP_061940			guanine nucleotide binding protein-like 3						ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	54829702	54829703	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54829702_54829703delAG								ITIH5L (5029 upstream) : MAGED2 (4468 downstream)																																			---	---	---	---
RRAGB	10325	broad.mit.edu	37	X	55753729	55753729	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55753729delT	uc004dup.2	+						RRAGB_uc004duq.2_Intron	NM_016656	NP_057740			Ras-related GTP binding B long isoform						cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade|signal transduction	Golgi apparatus|lysosome|nucleus	GTP binding|protein binding				0																		---	---	---	---
LOC550643	550643	broad.mit.edu	37	X	56788722	56788723	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56788722_56788723insT	uc004dut.3	+							NR_015367				Homo sapiens hypothetical protein LOC550643, mRNA (cDNA clone IMAGE:5285100).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	57071438	57071439	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57071438_57071439insT								SPIN3 (49450 upstream) : SPIN2B (74677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	57141821	57141821	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57141821delT								SPIN3 (119833 upstream) : SPIN2B (4295 downstream)																																			---	---	---	---
FAAH2	158584	broad.mit.edu	37	X	57462791	57462791	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57462791delA	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	58288714	58288714	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:58288714delA								ZXDA (351647 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	64116342	64116342	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64116342delT								MTMR8 (501031 upstream) : ZC4H2 (19920 downstream)																																			---	---	---	---
ZC4H2	55906	broad.mit.edu	37	X	64248417	64248419	+	Intron	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64248417_64248419delTTT	uc004dvv.2	-							NM_018684	NP_061154			zinc finger, C4H2 domain containing								metal ion binding|protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	64826016	64826017	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64826016_64826017delTT	uc004dwe.2	+											Homo sapiens cDNA clone IMAGE:30330955.																														---	---	---	---
MSN	4478	broad.mit.edu	37	X	64898072	64898074	+	Intron	DEL	CTC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64898072_64898074delCTC	uc004dwf.2	+						MSN_uc010nkp.1_5'Flank	NM_002444	NP_002435			moesin						leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking	apical plasma membrane|cytoskeleton|extrinsic to membrane|microvillus membrane|nucleolus	cell adhesion molecule binding|receptor binding|structural constituent of cytoskeleton		MSN/ALK(6)	haematopoietic_and_lymphoid_tissue(6)|ovary(3)|lung(1)	10								T	ALK	ALCL								---	---	---	---
Unknown	0	broad.mit.edu	37	X	65379571	65379571	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65379571delA								VSIG4 (119604 upstream) : HEPH (3092 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	66657285	66657286	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66657285_66657286delTC								EDA2R (798177 upstream) : AR (106588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	66707658	66707658	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66707658delA								EDA2R (848550 upstream) : AR (56216 downstream)																																			---	---	---	---
OPHN1	4983	broad.mit.edu	37	X	67372297	67372298	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67372297_67372298delTT	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																		---	---	---	---
OPHN1	4983	broad.mit.edu	37	X	67414807	67414808	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67414807_67414808insA	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																		---	---	---	---
OPHN1	4983	broad.mit.edu	37	X	67506998	67506999	+	Intron	INS	-	GAAA	GAAA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67506998_67506999insGAAA	uc004dww.3	-						OPHN1_uc011mpg.1_Intron|OPHN1_uc004dwx.2_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																		---	---	---	---
STARD8	9754	broad.mit.edu	37	X	67875063	67875064	+	Intron	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67875063_67875064delTG	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																		---	---	---	---
STARD8	9754	broad.mit.edu	37	X	67910278	67910278	+	Intron	DEL	C	-	-	rs75534839		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67910278delC	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	68052927	68052927	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68052927delG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	68367969	68367969	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68367969delA								EFNB1 (301940 upstream) : PJA1 (12613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	68699821	68699822	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68699821_68699822insA								PJA1 (314481 upstream) : FAM155B (25256 downstream)																																			---	---	---	---
EDA	1896	broad.mit.edu	37	X	69049119	69049119	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69049119delT	uc004dxs.2	+						EDA_uc004dxr.2_Intron|EDA_uc011mpj.1_Intron|EDA_uc004dxn.1_Intron|EDA_uc004dxm.1_Intron|EDA_uc004dxp.1_Intron|EDA_uc004dxq.1_Intron	NM_001399	NP_001390			ectodysplasin A isoform EDA-A1						cell differentiation|ectoderm development|immune response|positive regulation of NF-kappaB transcription factor activity|signal transduction	collagen|cytoskeleton|membrane fraction	tumor necrosis factor receptor binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
EDA	1896	broad.mit.edu	37	X	69062667	69062668	+	Intron	INS	-	CT	CT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69062667_69062668insCT	uc004dxs.2	+						EDA_uc004dxr.2_Intron|EDA_uc011mpj.1_Intron|EDA_uc004dxn.1_Intron|EDA_uc004dxm.1_Intron|EDA_uc004dxp.1_Intron|EDA_uc004dxq.1_Intron	NM_001399	NP_001390			ectodysplasin A isoform EDA-A1						cell differentiation|ectoderm development|immune response|positive regulation of NF-kappaB transcription factor activity|signal transduction	collagen|cytoskeleton|membrane fraction	tumor necrosis factor receptor binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	69305733	69305734	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69305733_69305734delTT								OTUD6A (21704 upstream) : IGBP1 (47565 downstream)																																			---	---	---	---
ARR3	407	broad.mit.edu	37	X	69497549	69497549	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69497549delC	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																		---	---	---	---
DLG3	1741	broad.mit.edu	37	X	69719610	69719610	+	Intron	DEL	A	-	-	rs79608588		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69719610delA	uc004dyi.1	+						DLG3_uc004dyj.1_Intron|DLG3_uc011mpn.1_Intron	NM_021120	NP_066943			synapse-associated protein 102 isoform a						axon guidance|negative regulation of cell proliferation|synaptic transmission	plasma membrane	guanylate kinase activity			large_intestine(1)|pancreas(1)	2	Renal(35;0.156)																	---	---	---	---
SLC7A3	84889	broad.mit.edu	37	X	70149334	70149334	+	Intron	DEL	C	-	-	rs113661998		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70149334delC	uc004dyn.2	-						SLC7A3_uc004dyo.2_Intron	NM_032803	NP_116192			solute carrier family 7 (cationic amino acid						cellular nitrogen compound metabolic process	integral to membrane|plasma membrane				ovary(1)|kidney(1)	2	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)													---	---	---	---
SNX12	29934	broad.mit.edu	37	X	70278622	70278622	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70278622delA	uc004dyp.1	-							NM_013346				sorting nexin 12						cell communication|protein transport	membrane	phosphatidylinositol binding|protein binding				0	Renal(35;0.156)																	---	---	---	---
MED12	9968	broad.mit.edu	37	X	70352599	70352603	+	Intron	DEL	TCTCC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70352599_70352603delTCTCC	uc004dyy.2	+						MED12_uc011mpq.1_Intron|MED12_uc004dyz.2_Intron|MED12_uc004dza.2_Intron|MED12_uc010nla.2_Intron	NM_005120	NP_005111			mediator complex subunit 12						androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)																	---	---	---	---
BCYRN1	618	broad.mit.edu	37	X	70556996	70556996	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70556996delT	uc011mpt.1	-							NR_001568				Homo sapiens brain cytoplasmic RNA 1 (non-protein coding) (BCYRN1), non-coding RNA.												0																		---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70617339	70617339	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70617339delT	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron|TAF1_uc004dzv.3_Intron	NM_138923	NP_620278			TBP-associated factor 1 isoform 2						G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)																---	---	---	---
NHSL2	340527	broad.mit.edu	37	X	71295790	71295790	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71295790delT	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-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71492424delA								PIN4 (7612 upstream) : RPS4X (30 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	73003071	73003071	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73003071delT								CHIC1 (96136 upstream) : TSIX (8969 downstream)																																			---	---	---	---
NCRNA00182	100302692	broad.mit.edu	37	X	73428598	73428598	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73428598delA	uc010nlq.1	-						uc004ebq.1_Intron					Homo sapiens cDNA FLJ33139 fis, clone UTERU1000109.												0																		---	---	---	---
NCRNA00182	100302692	broad.mit.edu	37	X	73503507	73503507	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73503507delA	uc010nlq.1	-						NCRNA00182_uc004ebr.1_Intron					Homo sapiens cDNA FLJ33139 fis, clone UTERU1000109.												0																		---	---	---	---
NCRNA00182	100302692	broad.mit.edu	37	X	73506654	73506655	+	Intron	DEL	AA	-	-	rs71700920		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73506654_73506655delAA	uc010nlq.1	-						NCRNA00182_uc004ebr.1_Intron					Homo sapiens cDNA FLJ33139 fis, clone UTERU1000109.												0																		---	---	---	---
ZCCHC13	389874	broad.mit.edu	37	X	73524621	73524621	+	3'UTR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73524621delC	uc004ebs.3	+	1						NM_203303	NP_976048			zinc finger, CCHC domain containing 13								nucleic acid binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	73555293	73555294	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73555293_73555294delAA								ZCCHC13 (30425 upstream) : SLC16A2 (85791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	73637565	73637565	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73637565delT								ZCCHC13 (112697 upstream) : SLC16A2 (3520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	74823602	74823603	+	IGR	INS	-	GT	GT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74823602_74823603insGT								ZDHHC15 (80265 upstream) : MAGEE2 (179220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	75853934	75853934	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75853934delT								MAGEE1 (202190 upstream) : MIR384 (285764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	76234500	76234500	+	Intron	DEL	A	-	-	rs113143693		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76234500delA	uc010nlv.1	-											Homo sapiens cDNA FLJ25017 fis, clone CBL01605.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	76437744	76437744	+	IGR	DEL	T	-	-	rs151224368	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76437744delT								MIR325 (211818 upstream) : FGF16 (271903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	76442435	76442435	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76442435delA								MIR325 (216509 upstream) : FGF16 (267212 downstream)																																			---	---	---	---
ATRX	546	broad.mit.edu	37	X	76763680	76763680	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76763680delA	uc004ecp.3	-	35					ATRX_uc004ecq.3_3'UTR|ATRX_uc004eco.3_3'UTR	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	77227855	77227855	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77227855delT	uc004ecx.3	+						ATP7A_uc004ecw.2_Intron|PGAM4_uc004ecy.1_5'Flank	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																		---	---	---	---
CYSLTR1	10800	broad.mit.edu	37	X	77574380	77574381	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77574380_77574381delTT	uc004edb.2	-						CYSLTR1_uc010nma.2_Intron|CYSLTR1_uc010nmb.2_Intron	NM_006639	NP_006630			cysteinyl leukotriene receptor 1						elevation of cytosolic calcium ion concentration|respiratory gaseous exchange	integral to plasma membrane|membrane fraction	leukotriene receptor activity			ovary(1)	1					Amlexanox(DB01025)|Cinalukast(DB00587)|Montelukast(DB00471)|Nedocromil(DB00716)|Pranlukast(DB01411)|Zafirlukast(DB00549)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	77659855	77659855	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77659855delA								CYSLTR1 (76768 upstream) : ZCCHC5 (251711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	78272206	78272207	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78272206_78272207insA								P2RY10 (54769 upstream) : GPR174 (154262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	79403553	79403553	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79403553delA								TBX22 (116285 upstream) : FAM46D (187450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	79728801	79728801	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79728801delT								FAM46D (27991 upstream) : BRWD3 (202882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	79805572	79805572	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79805572delT								FAM46D (104762 upstream) : BRWD3 (126111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	79816596	79816596	+	IGR	DEL	A	-	-	rs75574361		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79816596delA								FAM46D (115786 upstream) : BRWD3 (115087 downstream)																																			---	---	---	---
BRWD3	254065	broad.mit.edu	37	X	79947491	79947491	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
BRWD3	254065	broad.mit.edu	37	X	80065199	80065200	+	5'UTR	INS	-	GA	GA			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80065199_80065200insGA	uc004edt.2	-	1					BRWD3_uc004edo.2_5'Flank|BRWD3_uc004edp.2_5'Flank|BRWD3_uc004edq.2_5'Flank|BRWD3_uc010nmj.1_5'Flank|BRWD3_uc004edr.2_5'Flank|BRWD3_uc004eds.2_5'Flank|BRWD3_uc004edu.2_5'UTR|BRWD3_uc004edv.2_5'UTR|BRWD3_uc004edw.2_5'UTR|BRWD3_uc004edx.2_5'UTR|BRWD3_uc004edy.2_5'UTR|BRWD3_uc004edz.2_5'UTR|BRWD3_uc004eea.2_5'UTR|BRWD3_uc004eeb.2_5'UTR	NM_153252	NP_694984			bromodomain and WD repeat domain containing 3											ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	80304754	80304754	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80304754delT								BRWD3 (239521 upstream) : HMGN5 (64446 downstream)																																			---	---	---	---
HMGN5	79366	broad.mit.edu	37	X	80373886	80373886	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80373886delA	uc004eee.1	-							NM_030763	NP_110390			high-mobility group nucleosome binding domain 5						chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleolus	chromatin binding|DNA binding			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	81025057	81025060	+	IGR	DEL	AAAA	-	-	rs72009522		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:81025057_81025060delAAAA								SH3BGRL (471015 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	81541420	81541420	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:81541420delT								SH3BGRL (987378 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	82166647	82166647	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82166647delT								None (None upstream) : POU3F4 (596622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	82555421	82555421	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82555421delA								None (None upstream) : POU3F4 (207848 downstream)																																			---	---	---	---
HDX	139324	broad.mit.edu	37	X	83727114	83727114	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83727114delA	uc004eek.1	-						HDX_uc011mqv.1_Intron|HDX_uc004eel.1_Intron	NM_144657	NP_653258			highly divergent homeobox							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	83784592	83784593	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83784592_83784593insA								HDX (27134 upstream) : UBE2DNL (404564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	84235811	84235812	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84235811_84235812insA								UBE2DNL (45916 upstream) : APOOL (23093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	84905347	84905347	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84905347delT								POF1B (270599 upstream) : MIR1321 (185438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	84923374	84923375	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84923374_84923375insT								POF1B (288626 upstream) : MIR1321 (167410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	84995865	84995866	+	IGR	DEL	CA	-	-	rs111898274		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84995865_84995866delCA								POF1B (361117 upstream) : MIR1321 (94919 downstream)																																			---	---	---	---
DACH2	117154	broad.mit.edu	37	X	85474259	85474259	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85474259delT	uc004eew.2	+						DACH2_uc004eex.2_Intron|DACH2_uc010nmq.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																		---	---	---	---
DACH2	117154	broad.mit.edu	37	X	85631154	85631155	+	Intron	INS	-	TG	TG	rs72353234		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85631154_85631155insTG	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	86680694	86680695	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86680694_86680695insT								DACH2 (593089 upstream) : KLHL4 (92020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87220007	87220008	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87220007_87220008insA								KLHL4 (294957 upstream) : CPXCR1 (782218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87353782	87353782	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87353782delT								KLHL4 (428732 upstream) : CPXCR1 (648444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87699547	87699548	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87699547_87699548insT								KLHL4 (774497 upstream) : CPXCR1 (302678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87988920	87988920	+	IGR	DEL	T	-	-	rs34254354		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87988920delT								None (None upstream) : CPXCR1 (13306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	88287128	88287128	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:88287128delT								CPXCR1 (277345 upstream) : TGIF2LX (889812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	88429035	88429042	+	IGR	DEL	TTTTTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:88429035_88429042delTTTTTTTT								CPXCR1 (419252 upstream) : TGIF2LX (747898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	89749593	89749593	+	IGR	DEL	T	-	-	rs35209089		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89749593delT								TGIF2LX (571713 upstream) : PABPC5 (940004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	90105820	90105820	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:90105820delA								TGIF2LX (927940 upstream) : PABPC5 (583777 downstream)																																			---	---	---	---
PCDH11X	27328	broad.mit.edu	37	X	91735518	91735519	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91735518_91735519delTT	uc004efk.1	+						PCDH11X_uc004efl.1_Intron|PCDH11X_uc004efo.1_Intron|PCDH11X_uc010nmv.1_Intron|PCDH11X_uc004efm.1_Intron|PCDH11X_uc004efn.1_Intron	NM_032968	NP_116750			protocadherin 11 X-linked isoform c						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	93720492	93720492	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:93720492delA								FAM133A (753231 upstream) : MIR548M (597648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	94009051	94009052	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:94009051_94009052delAG								None (None upstream) : MIR548M (309088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	94148472	94148472	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:94148472delT								None (None upstream) : MIR548M (169668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	94317955	94317956	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:94317955_94317956insA								None (None upstream) : MIR548M (184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	94465292	94465292	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:94465292delA								MIR548M (147067 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	95006313	95006314	+	IGR	INS	-	TGTGTGTGTGTG	TGTGTGTGTGTG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95006313_95006314insTGTGTGTGTGTG								MIR548M (688088 upstream) : LOC643486 (585772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	95929221	95929222	+	IGR	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95929221_95929222delTC								LOC643486 (336320 upstream) : DIAPH2 (10440 downstream)																																			---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	95990724	95990724	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95990724delT	uc004efu.3	+						DIAPH2_uc004eft.3_Intron|DIAPH2_uc004efs.2_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																		---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96492582	96492583	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96492582_96492583insT	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																		---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96498670	96498670	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96498670delT	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																		---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96653591	96653592	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96653591_96653592insT	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	97111241	97111243	+	IGR	DEL	TTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:97111241_97111243delTTT								DIAPH2 (255645 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	97357133	97357133	+	IGR	DEL	G	-	-	rs144712223		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:97357133delG								DIAPH2 (501537 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	97977473	97977474	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:97977473_97977474delAA								None (None upstream) : LOC442459 (739126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	98677047	98677047	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:98677047delT								None (None upstream) : LOC442459 (39553 downstream)																																			---	---	---	---
LOC442459	442459	broad.mit.edu	37	X	98930711	98930712	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:98930711_98930712insT	uc011mrd.1	-							NR_024608				Homo sapiens DNA repair protein mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	99476539	99476539	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99476539delA								LOC442459 (281698 upstream) : PCDH19 (70111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	99506524	99506524	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99506524delA								LOC442459 (311683 upstream) : PCDH19 (40126 downstream)																																			---	---	---	---
SYTL4	94121	broad.mit.edu	37	X	99930891	99930892	+	3'UTR	DEL	AT	-	-	rs67841104		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99930891_99930892delAT	uc004egd.3	-	19					SYTL4_uc004egc.2_3'UTR|SYTL4_uc010nnb.2_3'UTR|SYTL4_uc010nnc.2_3'UTR|SYTL4_uc004ege.3_3'UTR|SYTL4_uc004egf.3_3'UTR	NM_080737	NP_542775			synaptotagmin-like 4						exocytosis|intracellular protein transport	extrinsic to membrane|plasma membrane|synaptic vesicle|transport vesicle membrane	neurexin binding|phospholipid binding|Rab GTPase binding|transporter activity|zinc ion binding			ovary(2)	2					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
SYTL4	94121	broad.mit.edu	37	X	99940302	99940302	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99940302delA	uc004egd.3	-						SYTL4_uc010nnb.2_Intron|SYTL4_uc010nnc.2_Intron|SYTL4_uc004ege.3_Intron|SYTL4_uc004egf.3_Intron|SYTL4_uc004egg.3_3'UTR	NM_080737	NP_542775			synaptotagmin-like 4						exocytosis|intracellular protein transport	extrinsic to membrane|plasma membrane|synaptic vesicle|transport vesicle membrane	neurexin binding|phospholipid binding|Rab GTPase binding|transporter activity|zinc ion binding			ovary(2)	2					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
SYTL4	94121	broad.mit.edu	37	X	99961586	99961587	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99961586_99961587insA	uc004egd.3	-						SYTL4_uc010nnc.2_Intron|SYTL4_uc004ege.3_Intron|SYTL4_uc004egf.3_Intron|SYTL4_uc004egg.3_Intron	NM_080737	NP_542775			synaptotagmin-like 4						exocytosis|intracellular protein transport	extrinsic to membrane|plasma membrane|synaptic vesicle|transport vesicle membrane	neurexin binding|phospholipid binding|Rab GTPase binding|transporter activity|zinc ion binding			ovary(2)	2					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
NOX1	27035	broad.mit.edu	37	X	100111569	100111570	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100111569_100111570delTT	uc004egj.2	-						uc010nnf.2_Intron|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																		---	---	---	---
TMEM35	59353	broad.mit.edu	37	X	100350525	100350525	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100350525delA	uc004egw.2	+	2					CENPI_uc011mrg.1_5'Flank	NM_021637	NP_067650			transmembrane protein 35							cytoplasmic membrane-bounded vesicle|integral to membrane|peroxisomal membrane					0																		---	---	---	---
CENPI	2491	broad.mit.edu	37	X	100381989	100381989	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100381989delA	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																		---	---	---	---
DRP2	1821	broad.mit.edu	37	X	100483895	100483895	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100483895delA	uc004egz.2	+						DRP2_uc011mrh.1_Intron	NM_001939	NP_001930			dystrophin related protein 2						central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2																		---	---	---	---
DRP2	1821	broad.mit.edu	37	X	100512635	100512636	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100512635_100512636delAA	uc004egz.2	+						DRP2_uc011mrh.1_Intron	NM_001939	NP_001930			dystrophin related protein 2						central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	100736122	100736122	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100736122delA	uc004eho.1	+											Homo sapiens cDNA FLJ39636 fis, clone SMINT2002976.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	101029405	101029407	+	IGR	DEL	CTA	-	-	rs58889212		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101029405_101029407delCTA								ARMCX2 (114542 upstream) : NXF5 (57678 downstream)																																			---	---	---	---
NXF5	55998	broad.mit.edu	37	X	101093566	101093566	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
NXF4	55999	broad.mit.edu	37	X	101804818	101804818	+	5'Flank	DEL	C	-	-	rs112443744		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101804818delC	uc004ejf.1	+							NR_002216				Homo sapiens cDNA FLJ42710 fis, clone BRAMY3007609, moderately similar to Homo sapiens nuclear RNA export factor 2 (NXF2).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	101878948	101878948	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101878948delT								ARMCX5 (19865 upstream) : GPRASP1 (27346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	101880962	101880962	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101880962delT								ARMCX5 (21879 upstream) : GPRASP1 (25332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	102139510	102139510	+	RNA	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102139510delT	uc004ejq.1	+	8		c.1277delT								Homo sapiens cDNA clone IMAGE:5576940.																														---	---	---	---
RAB9B	51209	broad.mit.edu	37	X	103075912	103075913	+	Intron	DEL	AT	-	-	rs66817909		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103075912_103075913delAT	uc004eli.1	-											Homo sapiens mRNA for RAB9-like protein, complete cds.						Golgi to endosome transport|protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|protein binding			lung(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	103167151	103167151	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103167151delT								RAB9B (79993 upstream) : TMSB15B (6328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	103527274	103527274	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103527274delA								ESX1 (27686 upstream) : IL1RAPL2 (283722 downstream)																																			---	---	---	---
IL1RAPL2	26280	broad.mit.edu	37	X	103812773	103812773	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103812773delT	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																		---	---	---	---
IL1RAPL2	26280	broad.mit.edu	37	X	104619159	104619159	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104619159delT	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																		---	---	---	---
NRK	203447	broad.mit.edu	37	X	105156736	105156736	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105156736delA	uc004emd.2	+	14	2641	c.2338delA	c.(2338-2340)AAAfs	p.K780fs	NRK_uc010npc.1_Frame_Shift_Del_p.K448fs	NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase	780							ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14															HNSCC(51;0.14)			---	---	---	---
Unknown	0	broad.mit.edu	37	X	105229283	105229283	+	IGR	DEL	T	-	-	rs66843950		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105229283delT								NRK (26687 upstream) : SERPINA7 (47914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	105747480	105747480	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105747480delT								MUM1L1 (294532 upstream) : CXorf57 (107680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	105846499	105846499	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105846499delA								MUM1L1 (393551 upstream) : CXorf57 (8661 downstream)																																			---	---	---	---
RNF128	79589	broad.mit.edu	37	X	105970804	105970804	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105970804delA	uc004eml.2	+						RNF128_uc004emk.2_Intron	NM_194463	NP_919445			ring finger protein 128 isoform 1							endomembrane system|integral to membrane|perinuclear region of cytoplasm	zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	106286324	106286325	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106286324_106286325delTT								MORC4 (42882 upstream) : RBM41 (21325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	106295108	106295109	+	IGR	INS	-	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106295108_106295109insG								MORC4 (51666 upstream) : RBM41 (12541 downstream)																																			---	---	---	---
TEX13B	56156	broad.mit.edu	37	X	107224932	107224933	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107224932_107224933delCT	uc004enn.1	-	2	518_519	c.425_426delAG	c.(424-426)GAGfs	p.E142fs		NM_031273	NP_112563	Q9BXU2	TX13B_HUMAN	testis expressed 13B	142										ovary(1)	1																		---	---	---	---
COL4A6	1288	broad.mit.edu	37	X	107560634	107560634	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107560634delA	uc004enw.3	-						COL4A6_uc004env.3_Intron|COL4A6_uc011msn.1_Intron|COL4A6_uc010npk.2_Intron|COL4A6_uc004enx.2_Intron|COL4A6_uc004eny.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	107665429	107665430	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107665429_107665430insA	uc004enw.3	-						COL4A6_uc004env.3_Intron|COL4A6_uc011msn.1_Intron|COL4A6_uc010npk.2_Intron|COL4A6_uc004enx.2_Intron|COL4A6_uc004eny.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				---	---	---	---
COL4A5	1287	broad.mit.edu	37	X	107931673	107931673	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107931673delT	uc004enz.1	+						COL4A5_uc011mso.1_Intron|COL4A5_uc011msp.1_Intron	NM_033380	NP_203699			type IV collagen alpha 5 isoform 2 precursor						axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
Unknown	0	broad.mit.edu	37	X	107992033	107992033	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107992033delA								IRS4 (12426 upstream) : GUCY2F (624103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	108608448	108608448	+	IGR	DEL	T	-	-	rs112394319		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108608448delT								IRS4 (628841 upstream) : GUCY2F (7688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	108788585	108788586	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108788585_108788586insA								NXT2 (672 upstream) : KCNE1L (78345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	109090917	109090920	+	IGR	DEL	TGTG	-	-	rs112490147		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109090917_109090920delTGTG								ACSL4 (114296 upstream) : TMEM164 (154943 downstream)																																			---	---	---	---
TMEM164	84187	broad.mit.edu	37	X	109287654	109287654	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109287654delT	uc004eom.2	+						TMEM164_uc004eol.2_Intron|TMEM164_uc010npq.2_Intron	NM_032227	NP_115603			transmembrane protein 164 isoform b							integral to membrane				large_intestine(1)|lung(1)|skin(1)	3																		---	---	---	---
TMEM164	84187	broad.mit.edu	37	X	109311928	109311928	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109311928delT	uc004eom.2	+						TMEM164_uc004eol.2_Intron|TMEM164_uc010npq.2_Intron	NM_032227	NP_115603			transmembrane protein 164 isoform b							integral to membrane				large_intestine(1)|lung(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	109714902	109714902	+	IGR	DEL	A	-	-	rs10708315		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109714902delA								RGAG1 (15341 upstream) : TDGF3 (48638 downstream)																																			---	---	---	---
CHRDL1	91851	broad.mit.edu	37	X	110035534	110035534	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110035534delA	uc004eou.3	-						CHRDL1_uc004eov.2_5'Flank|CHRDL1_uc004eow.2_Intron|CHRDL1_uc010nps.2_Intron|CHRDL1_uc004eot.2_Intron|CHRDL1_uc011mss.1_Intron|CHRDL1_uc004eox.3_Intron	NM_001143981	NP_001137453			chordin-like 1 isoform 1 precursor						BMP signaling pathway|cell differentiation|nervous system development|ossification	extracellular region					0																		---	---	---	---
PAK3	5063	broad.mit.edu	37	X	110416183	110416184	+	Intron	DEL	TC	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110416183_110416184delTC	uc004epa.2	+						PAK3_uc010npt.1_Intron|PAK3_uc010npu.1_Intron|PAK3_uc004eoy.1_Intron|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)			---	---	---	---
Unknown	0	broad.mit.edu	37	X	110681087	110681088	+	IGR	DEL	TT	-	-	rs72356622		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110681087_110681088delTT								DCX (25681 upstream) : ALG13 (243325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	110903656	110903656	+	IGR	DEL	T	-	-	rs113467632		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110903656delT								DCX (248250 upstream) : ALG13 (20757 downstream)																																			---	---	---	---
TRPC5	7224	broad.mit.edu	37	X	111119264	111119264	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111119264delA	uc004epl.1	-						TRPC5_uc004epm.1_Intron	NM_012471	NP_036603			transient receptor potential cation channel,						axon guidance	calcium channel complex|integral to plasma membrane	protein binding|store-operated calcium channel activity			urinary_tract(1)	1																		---	---	---	---
ZCCHC16	340595	broad.mit.edu	37	X	111378944	111378944	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111378944delT	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	111997013	111997013	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111997013delT								LHFPL1 (73638 upstream) : AMOT (21093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	113187375	113187375	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113187375delT								None (None upstream) : HTR2C (631176 downstream)																																			---	---	---	---
HTR2C	3358	broad.mit.edu	37	X	113983566	113983566	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113983566delA	uc004epu.1	+						HTR2C_uc010nqc.1_Intron|HTR2C_uc004epv.1_Intron	NM_000868	NP_000859			5-hydroxytryptamine (serotonin) receptor 2C						cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)													---	---	---	---
HTR2C	3358	broad.mit.edu	37	X	114124145	114124145	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114124145delT	uc004epu.1	+						HTR2C_uc010nqc.1_Intron|HTR2C_uc004epv.1_Intron	NM_000868	NP_000859			5-hydroxytryptamine (serotonin) receptor 2C						cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)													---	---	---	---
HTR2C	3358	broad.mit.edu	37	X	114131959	114131960	+	Intron	DEL	TT	-	-	rs76291749		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114131959_114131960delTT	uc004epu.1	+						HTR2C_uc010nqc.1_Intron|HTR2C_uc004epv.1_Intron	NM_000868	NP_000859			5-hydroxytryptamine (serotonin) receptor 2C						cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)													---	---	---	---
HTR2C	3358	broad.mit.edu	37	X	114134740	114134740	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114134740delA	uc004epu.1	+						HTR2C_uc010nqc.1_Intron|HTR2C_uc004epv.1_Intron	NM_000868	NP_000859			5-hydroxytryptamine (serotonin) receptor 2C						cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	114545809	114545809	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114545809delT								LUZP4 (3690 upstream) : PLS3 (249397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	114721158	114721159	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114721158_114721159delAA								LUZP4 (179039 upstream) : PLS3 (74047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	114771979	114771980	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114771979_114771980delAA	uc004eqc.1	-											Homo sapiens cDNA FLJ45456 fis, clone BRSTN2009917.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	114899621	114899621	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114899621delC								PLS3 (14631 upstream) : AGTR2 (402337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	115008900	115008900	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115008900delA								PLS3 (123910 upstream) : AGTR2 (293058 downstream)																																			---	---	---	---
AGTR2	186	broad.mit.edu	37	X	115303402	115303402	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115303402delT	uc004eqh.3	+							NM_000686	NP_000677			angiotensin II receptor, type 2						behavior|blood vessel remodeling|brain development|G-protein signaling, coupled to cGMP nucleotide second messenger|intracellular protein kinase cascade|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of heart rate|negative regulation of nerve growth factor receptor signaling pathway|nitric oxide mediated signal transduction|positive regulation of apoptosis|positive regulation of nitric-oxide synthase activity|positive regulation of phosphoprotein phosphatase activity|positive regulation of vasodilation|regulation of systemic arterial blood pressure by circulatory renin-angiotensin		angiotensin type II receptor activity|receptor antagonist activity			ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	115804917	115804919	+	IGR	DEL	GTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115804917_115804919delGTT								CXorf61 (210780 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	116695748	116695749	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:116695748_116695749delAA								None (None upstream) : KLHL13 (336028 downstream)																																			---	---	---	---
KLHL13	90293	broad.mit.edu	37	X	117035915	117035915	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117035915delA	uc004eql.2	-						KLHL13_uc004eqk.2_Intron|KLHL13_uc011mtn.1_Intron|KLHL13_uc011mto.1_Intron|KLHL13_uc011mtp.1_Intron|KLHL13_uc004eqm.2_Intron|KLHL13_uc011mtq.1_Intron	NM_033495	NP_277030			kelch-like 13						cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex				kidney(1)|skin(1)	2																		---	---	---	---
WDR44	54521	broad.mit.edu	37	X	117520201	117520201	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117520201delT	uc004eqn.2	+						WDR44_uc004eqo.2_Intron|WDR44_uc011mtr.1_Intron|MIR1277_hsa-mir-1277|MI0006419_5'Flank	NM_019045	NP_061918			WD repeat domain 44 protein							cytosol|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm				lung(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	117857708	117857708	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117857708delA								DOCK11 (37585 upstream) : IL13RA1 (3851 downstream)																																			---	---	---	---
IL13RA1	3597	broad.mit.edu	37	X	117937894	117937894	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117937894delT	uc004eqt.1	+							NM_001560	NP_001551			interleukin 13 receptor, alpha 1 precursor							interleukin-13 receptor complex	cytokine receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	117952270	117952271	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117952270_117952271delTT								IL13RA1 (12811 upstream) : ZCCHC12 (5516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	118012394	118012394	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118012394delT								ZCCHC12 (51464 upstream) : LONRF3 (96319 downstream)																																			---	---	---	---
KIAA1210	57481	broad.mit.edu	37	X	118280860	118280860	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118280860delA	uc004era.3	-							NM_020721	NP_065772			hypothetical protein LOC57481											ovary(4)|skin(1)	5																		---	---	---	---
CXorf56	63932	broad.mit.edu	37	X	118694020	118694020	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118694020delA	uc004erk.1	-						CXorf56_uc004erj.1_Intron|CXorf56_uc011mtu.1_Intron	NM_022101	NP_071384			hypothetical protein LOC63932								protein binding				0																		---	---	---	---
NKRF	55922	broad.mit.edu	37	X	118728143	118728143	+	5'Flank	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118728143delA	uc004erq.2	-						NKRF_uc004err.2_Intron	NM_017544	NP_060014			transcription factor NRF						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|double-stranded RNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SEPT6	23157	broad.mit.edu	37	X	118771659	118771660	+	Intron	INS	-	CCAT	CCAT			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118771659_118771660insCCAT	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	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																		---	---	---	---
SEPT6	23157	broad.mit.edu	37	X	118795233	118795233	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118795233delA	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	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	118840129	118840129	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118840129delA								SEPT6 (12796 upstream) : ANKRD58 (52447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	118946216	118946216	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118946216delA								RPL39 (20610 upstream) : UPF3B (21773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	119449322	119449323	+	IGR	DEL	AC	-	-	rs72374130		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119449322_119449323delAC								FAM70A (3931 upstream) : ATP1B4 (46617 downstream)																																			---	---	---	---
ATP1B4	23439	broad.mit.edu	37	X	119494220	119494224	+	5'Flank	DEL	TTTTT	-	-	rs111649085		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119494220_119494224delTTTTT	uc004esr.2	+						ATP1B4_uc004esq.2_5'Flank|ATP1B4_uc011mtx.1_5'Flank|ATP1B4_uc011mty.1_5'Flank	NM_001142447	NP_001135919			ATPase, (Na+)/K+ transporting, beta 4						ATP biosynthetic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to plasma membrane|nuclear inner membrane	sodium:potassium-exchanging ATPase activity			ovary(1)|skin(1)	2																		---	---	---	---
LAMP2	3920	broad.mit.edu	37	X	119580473	119580474	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119580473_119580474delAA	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																		---	---	---	---
LAMP2	3920	broad.mit.edu	37	X	119586410	119586411	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119586410_119586411insT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	119941214	119941214	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119941214delT								C1GALT1C1 (177273 upstream) : CT47B1 (65240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	120320319	120320319	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120320319delT								GLUD2 (136525 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	120593871	120593871	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120593871delT								GLUD2 (410077 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	122123583	122123584	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122123583_122123584insA								None (None upstream) : GRIA3 (194512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	122728194	122728195	+	IGR	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122728194_122728195insA								MIR220A (32139 upstream) : THOC2 (6218 downstream)																																			---	---	---	---
THOC2	57187	broad.mit.edu	37	X	122747885	122747885	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122747885delA	uc004etu.2	-						THOC2_uc010nqt.1_Intron|THOC2_uc004etw.1_Intron	NM_001081550	NP_001075019			THO complex 2						intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3																		---	---	---	---
XIAP	331	broad.mit.edu	37	X	123037470	123037471	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123037470_123037471delTT	uc010nqu.2	+						XIAP_uc004etx.2_Intron|XIAP_uc010nqv.2_Intron	NM_001167	NP_001158			baculoviral IAP repeat-containing protein 4						anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus	cytosol	caspase inhibitor activity|ligase activity|protein binding|zinc ion binding			ovary(1)|lung(1)	2														X-linked_Lymphoproliferative_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	X	124292789	124292790	+	IGR	DEL	AA	-	-	rs66827552		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124292789_124292790delAA								ODZ1 (195123 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	124325773	124325773	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124325773delT								ODZ1 (228107 upstream) : DCAF12L2 (972741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	124916246	124916246	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124916246delT								ODZ1 (818580 upstream) : DCAF12L2 (382268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	124943763	124943763	+	IGR	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124943763delC								ODZ1 (846097 upstream) : DCAF12L2 (354751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	125124929	125124929	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125124929delT								None (None upstream) : DCAF12L2 (173585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	125839748	125839748	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125839748delA								DCAF12L1 (152906 upstream) : CXorf64 (113999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	126404072	126404072	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:126404072delA								CXorf64 (448306 upstream) : ACTRT1 (780871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	126757566	126757566	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:126757566delA								CXorf64 (801800 upstream) : ACTRT1 (427377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	127166043	127166044	+	IGR	DEL	TG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127166043_127166044delTG								None (None upstream) : ACTRT1 (18899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	127218290	127218290	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127218290delA								ACTRT1 (31908 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	127310471	127310471	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127310471delT								ACTRT1 (124089 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	128042240	128042243	+	IGR	DEL	AAGA	-	-	rs11408448	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128042240_128042243delAAGA								ACTRT1 (855858 upstream) : SMARCA1 (538237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	128140526	128140526	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128140526delT								ACTRT1 (954144 upstream) : SMARCA1 (439954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	128155770	128155771	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128155770_128155771delTT								ACTRT1 (969388 upstream) : SMARCA1 (424709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	128205577	128205577	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128205577delT								None (None upstream) : SMARCA1 (374903 downstream)																																			---	---	---	---
SMARCA1	6594	broad.mit.edu	37	X	128582727	128582727	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128582727delA	uc004eun.3	-						SMARCA1_uc004eup.3_Intron|SMARCA1_uc011muk.1_Intron|SMARCA1_uc011mul.1_Intron	NM_003069	NP_003060			SWI/SNF-related matrix-associated						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	128740973	128740980	+	IGR	DEL	AAGGAAGT	-	-	rs72146220		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128740973_128740980delAAGGAAGT								OCRL (14445 upstream) : APLN (38346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	128771058	128771058	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128771058delG								OCRL (44530 upstream) : APLN (8268 downstream)																																			---	---	---	---
ZDHHC9	51114	broad.mit.edu	37	X	128976077	128976077	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128976077delA	uc004euv.2	-						ZDHHC9_uc004euw.2_Intron|ZDHHC9_uc004eux.1_Intron|ZDHHC9_uc004euy.1_Intron	NM_001008222	NP_001008223			zinc finger, DHHC domain containing 9							endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
UTP14A	10813	broad.mit.edu	37	X	129054164	129054165	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129054164_129054165delAA	uc004euz.2	+						UTP14A_uc011mup.1_Intron|UTP14A_uc011muq.1_Intron|UTP14A_uc004eva.1_5'Flank	NM_006649	NP_006640			UTP14, U3 small nucleolar ribonucleoprotein,						rRNA processing	nucleolus|small-subunit processome	protein binding			ovary(2)	2																		---	---	---	---
AIFM1	9131	broad.mit.edu	37	X	129285123	129285123	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129285123delT	uc004evg.2	-						AIFM1_uc011mus.1_Intron|AIFM1_uc004evh.2_Intron|AIFM1_uc004evi.2_Intron|AIFM1_uc004evk.2_Intron	NM_004208	NP_004199			programmed cell death 8 isoform 1						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																		---	---	---	---
RBMX2	51634	broad.mit.edu	37	X	129536209	129536209	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129536209delC	uc004evt.2	+							NM_016024	NP_057108			RNA binding motif protein, X-linked 2								nucleotide binding|RNA binding			breast(3)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	129739344	129739344	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129739344delT								FAM45B (108612 upstream) : ENOX2 (18015 downstream)																																			---	---	---	---
ARHGAP36	158763	broad.mit.edu	37	X	130194759	130194779	+	Intron	DEL	TTAGGCTCAATTGCTTACATG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130194759_130194779delTTAGGCTCAATTGCTTACATG	uc004evz.2	+						ARHGAP36_uc004ewa.2_Intron	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	130828698	130828698	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130828698delA								IGSF1 (115825 upstream) : LOC286467 (7981 downstream)																																			---	---	---	---
LOC286467	286467	broad.mit.edu	37	X	130926215	130926217	+	Intron	DEL	GAG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130926215_130926217delGAG	uc004ewi.2	-						LOC286467_uc004ewj.1_Intron	NR_026975				Homo sapiens cDNA FLJ40592 fis, clone THYMU2010192.												0																		---	---	---	---
HS6ST2	90161	broad.mit.edu	37	X	131890848	131890849	+	Intron	INS	-	GTGT	GTGT	rs3065679		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131890848_131890849insGTGT	uc011mve.1	-						HS6ST2_uc011mvb.1_Intron|HS6ST2_uc011mvc.1_Intron|HS6ST2_uc011mvd.1_Intron	NM_147175	NP_671704			heparan sulfate 6-O-sulfotransferase 2 isoform							integral to membrane	sulfotransferase activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
HS6ST2	90161	broad.mit.edu	37	X	132004976	132004976	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132004976delA	uc011mve.1	-						HS6ST2_uc011mvb.1_Intron|HS6ST2_uc011mvc.1_Intron|HS6ST2_uc011mvd.1_Intron	NM_147175	NP_671704			heparan sulfate 6-O-sulfotransferase 2 isoform							integral to membrane	sulfotransferase activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	132135261	132135261	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132135261delA								HS6ST2 (39838 upstream) : USP26 (23793 downstream)																																			---	---	---	---
GPC4	2239	broad.mit.edu	37	X	132532853	132532854	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132532853_132532854insA	uc004exc.1	-						GPC4_uc011mvg.1_Intron	NM_001448	NP_001439			glypican 4 precursor						anatomical structure morphogenesis|cell proliferation	anchored to membrane|external side of plasma membrane|extracellular space|insoluble fraction|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	132623232	132623233	+	IGR	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132623232_132623233delAA								GPC4 (74027 upstream) : GPC3 (46543 downstream)																																			---	---	---	---
GPC3	2719	broad.mit.edu	37	X	132809688	132809688	+	Intron	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132809688delG	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				---	---	---	---
Unknown	0	broad.mit.edu	37	X	133287797	133287797	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133287797delA								GPC3 (168131 upstream) : MIR363 (15611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	133308707	133308707	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133308707delT								MIR106A (4399 upstream) : CCDC160 (62370 downstream)																																			---	---	---	---
PHF6	84295	broad.mit.edu	37	X	133554599	133554599	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133554599delA	uc004exj.2	+						PHF6_uc004exk.2_Intron|PHF6_uc011mvk.1_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)																	---	---	---	---
MOSPD1	56180	broad.mit.edu	37	X	134039234	134039234	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134039234delA	uc004eyb.2	-						MOSPD1_uc010nrv.2_Intron|MOSPD1_uc011mvr.1_Intron	NM_019556	NP_062456			motile sperm domain containing 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	integral to membrane|nucleus|perinuclear region of cytoplasm	structural molecule activity			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	134065621	134065621	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134065621delA								MOSPD1 (16324 upstream) : LOC644538 (59347 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	134095181	134095181	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134095181delA								MOSPD1 (45884 upstream) : LOC644538 (29787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	134120728	134120729	+	IGR	DEL	TC	-	-	rs72453313		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134120728_134120729delTC								MOSPD1 (71431 upstream) : LOC644538 (4239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	134594015	134594015	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134594015delT								NCRNA00086 (33791 upstream) : DDX26B (60540 downstream)																																			---	---	---	---
SLC9A6	10479	broad.mit.edu	37	X	135071960	135071960	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135071960delT	uc004ezj.2	+						SLC9A6_uc004ezk.2_Intron|SLC9A6_uc011mvx.1_Intron	NM_006359	NP_006350			solute carrier family 9 (sodium/hydrogen						regulation of pH	early endosome membrane|endoplasmic reticulum membrane|integral to membrane|microsome|plasma membrane|recycling endosome membrane	sodium:hydrogen antiporter activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
GPR112	139378	broad.mit.edu	37	X	135424898	135424898	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135424898delA	uc004ezu.1	+						GPR112_uc010nsb.1_Intron|GPR112_uc010nsc.1_5'Flank	NM_153834	NP_722576			G-protein coupled receptor 112						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)																	---	---	---	---
CD40LG	959	broad.mit.edu	37	X	135732733	135732734	+	Intron	DEL	AA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135732733_135732734delAA	uc004faa.2	+						CD40LG_uc010nsd.2_Intron|CD40LG_uc010nse.1_Intron	NM_000074	NP_000065			CD40 ligand						anti-apoptosis|B cell proliferation|inflammatory response|isotype switching|leukocyte cell-cell adhesion|platelet activation|positive regulation of endothelial cell apoptosis|positive regulation of interleukin-12 production	extracellular space|integral to plasma membrane|soluble fraction	CD40 receptor binding|cytokine activity|tumor necrosis factor receptor binding			skin(1)	1	Acute lymphoblastic leukemia(192;0.000127)				Atorvastatin(DB01076)									Immune_Deficiency_with_Hyper-IgM				---	---	---	---
Unknown	0	broad.mit.edu	37	X	135745815	135745816	+	IGR	DEL	TT	-	-	rs111330065		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135745815_135745816delTT								CD40LG (3267 upstream) : ARHGEF6 (1898 downstream)																																			---	---	---	---
ARHGEF6	9459	broad.mit.edu	37	X	135759864	135759864	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135759864delA	uc004fab.2	-						ARHGEF6_uc011mwd.1_Intron|ARHGEF6_uc011mwe.1_Intron	NM_004840	NP_004831			Rac/Cdc42 guanine nucleotide exchange factor 6						apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ARHGEF6	9459	broad.mit.edu	37	X	135790933	135790933	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135790933delA	uc004fab.2	-						ARHGEF6_uc011mwd.1_Intron|ARHGEF6_uc011mwe.1_Intron	NM_004840	NP_004831			Rac/Cdc42 guanine nucleotide exchange factor 6						apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ARHGEF6	9459	broad.mit.edu	37	X	135846328	135846328	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135846328delA	uc004fab.2	-						ARHGEF6_uc011mwd.1_Intron|ARHGEF6_uc011mwe.1_Intron	NM_004840	NP_004831			Rac/Cdc42 guanine nucleotide exchange factor 6						apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	136045668	136045668	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136045668delA	uc004fai.1	+											Homo sapiens cDNA FLJ31132 fis, clone IMR322000953.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	136722281	136722282	+	IGR	DEL	GA	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136722281_136722282delGA								ZIC3 (68024 upstream) : LOC158696 (974610 downstream)																																			---	---	---	---
FGF13	2258	broad.mit.edu	37	X	138266813	138266814	+	Intron	INS	-	AC	AC			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138266813_138266814insAC	uc004faq.2	-						FGF13_uc004far.2_Intron|FGF13_uc011mwj.1_Intron|FGF13_uc011mwk.1_Intron	NM_001139502	NP_001132974			fibroblast growth factor 13 isoform 3						cell-cell signaling|MAPKKK cascade|nervous system development	cytoplasm|nucleus	growth factor activity|protein kinase activator activity			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	138503969	138503969	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138503969delA								FGF13 (216784 upstream) : F9 (108926 downstream)																																			---	---	---	---
MCF2	4168	broad.mit.edu	37	X	138678635	138678636	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138678635_138678636insA	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)																	---	---	---	---
MCF2	4168	broad.mit.edu	37	X	138745736	138745740	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138745736_138745740delTTTTT	uc011mwn.1	-						MCF2_uc004faw.2_Intron|MCF2_uc011mwo.1_Intron					SubName: Full=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	138840030	138840030	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									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	138920571	138920571	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138920571delA								ATP11C (6124 upstream) : MIR505 (85736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	138989907	138989907	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138989907delA								ATP11C (75460 upstream) : MIR505 (16400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	139028686	139028686	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139028686delT								MIR505 (22296 upstream) : CXorf66 (9199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	139161152	139161152	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139161152delA								CXorf66 (113475 upstream) : SOX3 (424000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	139551653	139551653	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139551653delA								CXorf66 (503976 upstream) : SOX3 (33499 downstream)																																			---	---	---	---
SPANXC	64663	broad.mit.edu	37	X	140442077	140442077	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140442077delA	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	141562420	141562421	+	IGR	DEL	CT	-	-	rs34938741		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141562420_141562421delCT								MAGEC2 (269344 upstream) : SPANXN4 (551283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	142394032	142394033	+	IGR	INS	-	A	A	rs112997999		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142394032_142394033insA								SPANXN4 (271967 upstream) : SPANXN3 (202532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	142402740	142402740	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142402740delT								SPANXN4 (280675 upstream) : SPANXN3 (193825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	142527974	142527975	+	IGR	DEL	CT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142527974_142527975delCT								SPANXN4 (405909 upstream) : SPANXN3 (68590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	143059047	143059047	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:143059047delA								UBE2NL (90692 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	143080455	143080456	+	IGR	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:143080455_143080456insT								UBE2NL (112100 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	143406602	143406602	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:143406602delT								UBE2NL (438247 upstream) : SPANXN1 (922505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	143410959	143410959	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:143410959delA								UBE2NL (442604 upstream) : SPANXN1 (918148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	143926816	143926826	+	IGR	DEL	TTTTTTTTTTT	-	-	rs72003959		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:143926816_143926826delTTTTTTTTTTT								UBE2NL (958461 upstream) : SPANXN1 (402281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	144064908	144064908	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144064908delA								None (None upstream) : SPANXN1 (264199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	144309820	144309820	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144309820delT								None (None upstream) : SPANXN1 (19287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	145190925	145190925	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145190925delT								MIR891A (81535 upstream) : CXorf51 (700377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	145279512	145279512	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145279512delA								MIR891A (170122 upstream) : CXorf51 (611790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	145460694	145460694	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145460694delA								MIR891A (351304 upstream) : CXorf51 (430608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	145572682	145572682	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145572682delA								MIR891A (463292 upstream) : CXorf51 (318620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	146524595	146524595	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146524595delA								MIR514-3 (158349 upstream) : ASFMR1 (466354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	146665596	146665596	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146665596delT								MIR514-3 (299350 upstream) : ASFMR1 (325353 downstream)																																			---	---	---	---
FMR1	2332	broad.mit.edu	37	X	147008432	147008432	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147008432delA	uc010nst.2	+						FMR1_uc011mwz.1_Intron|FMR1_uc004fcj.2_Intron|FMR1_uc004fck.3_Intron|FMR1_uc004fcl.3_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	147015725	147015725	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147015725delT	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				---	---	---	---
Unknown	0	broad.mit.edu	37	X	147492315	147492315	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147492315delT								FMR1NB (384135 upstream) : AFF2 (89824 downstream)																																			---	---	---	---
AFF2	2334	broad.mit.edu	37	X	147710622	147710623	+	Intron	INS	-	TG	TG	rs72303223		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147710622_147710623insTG	uc004fcp.2	+						AFF2_uc004fco.2_Intron|AFF2_uc004fcq.2_Intron|AFF2_uc004fcr.2_Intron|AFF2_uc011mxb.1_Intron|AFF2_uc004fcs.2_Intron	NM_002025	NP_002016			fragile X mental retardation 2						brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MAGEA11	4110	broad.mit.edu	37	X	148794754	148794754	+	Intron	DEL	C	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148794754delC	uc004fdq.2	+						HSFX2_uc004fdl.2_Intron|HSFX1_uc004fdm.2_Intron|MAGEA11_uc004fdr.2_Intron	NM_005366	NP_005357			melanoma antigen family A, 11 isoform a							cytoplasm|nucleus	protein binding			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	148882785	148882785	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148882785delT								HSFX1 (24268 upstream) : MAGEA8 (127211 downstream)																																			---	---	---	---
MAGEA8	4107	broad.mit.edu	37	X	149013887	149013888	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149013887_149013888insT	uc004fdw.1	+	3	1056_1057	c.841_842insT	c.(841-843)CTTfs	p.L281fs		NM_005364	NP_005355	P43361	MAGA8_HUMAN	melanoma antigen family A, 8	281	MAGE.										0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
LOC100272228	100272228	broad.mit.edu	37	X	149191909	149191910	+	Intron	INS	-	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149191909_149191910insT	uc004fea.2	+											Homo sapiens cDNA FLJ30251 fis, clone BRACE2002394.												0																		---	---	---	---
LOC100272228	100272228	broad.mit.edu	37	X	149305624	149305624	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149305624delT	uc004fea.2	+											Homo sapiens cDNA FLJ30251 fis, clone BRACE2002394.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	149513329	149513329	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149513329delT								MIR2114 (117011 upstream) : MAMLD1 (16507 downstream)																																			---	---	---	---
CD99L2	83692	broad.mit.edu	37	X	149949158	149949158	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149949158delA	uc004fel.2	-						CD99L2_uc004fek.2_Intron|CD99L2_uc004fem.2_Intron|CD99L2_uc004fen.2_Intron|CD99L2_uc004feo.2_Intron|CD99L2_uc011myb.1_Intron	NM_031462	NP_113650			CD99 antigen-like 2 isoform E3'-E4'-E3-E4						cell adhesion	cell junction|integral to membrane				large_intestine(2)|ovary(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	150102675	150102676	+	IGR	INS	-	TG	TG			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150102675_150102676insTG								CD99L2 (35496 upstream) : HMGB3 (49087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	150312549	150312549	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150312549delA								HMGB3 (153303 upstream) : GPR50 (32510 downstream)																																			---	---	---	---
PASD1	139135	broad.mit.edu	37	X	150816900	150816901	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150816900_150816901delTT	uc004fev.3	+							NM_173493	NP_775764			PAS domain containing 1							nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	150976371	150976371	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150976371delA								CNGA2 (62335 upstream) : MAGEA4 (104625 downstream)																																			---	---	---	---
GABRE	2564	broad.mit.edu	37	X	151133902	151133902	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151133902delA	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)																	---	---	---	---
GABRA3	2556	broad.mit.edu	37	X	151380591	151380592	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151380591_151380592insA	uc010ntk.1	-							NM_000808	NP_000799			gamma-aminobutyric acid A receptor, alpha 3						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)				Alprazolam(DB00404)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	152469086	152469086	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152469086delA								PNMA6A (225685 upstream) : MAGEA1 (12436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	152695540	152695541	+	IGR	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152695540_152695541delTT								ZFP92 (8455 upstream) : TREX2 (14638 downstream)																																			---	---	---	---
ATP2B3	492	broad.mit.edu	37	X	152836319	152836320	+	Intron	DEL	TT	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152836319_152836320delTT	uc004fht.1	+						ATP2B3_uc004fhs.1_Intron|ATP2B3_uc010nuf.1_Intron|ATP2B3_uc004fhu.1_Intron	NM_001001344	NP_001001344			plasma membrane calcium ATPase 3 isoform 3b						ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MECP2	4204	broad.mit.edu	37	X	153325950	153325950	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153325950delA	uc004fjv.2	-						MECP2_uc004fjw.2_Intron	NM_004992	NP_004983			methyl CpG binding protein 2 isoform 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
GAB3	139716	broad.mit.edu	37	X	153936879	153936880	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153936879_153936880insA	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)																	---	---	---	---
MPP1	4354	broad.mit.edu	37	X	154009645	154009645	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154009645delA	uc004fmp.1	-						MPP1_uc010nvg.1_Intron|MPP1_uc011mzv.1_Intron|MPP1_uc004fmq.1_Intron|MPP1_uc011mzw.1_Intron	NM_002436	NP_002427			palmitoylated membrane protein 1						regulation of neutrophil chemotaxis|signal transduction	integral to plasma membrane|membrane fraction|stereocilium	guanylate kinase activity|protein binding			ovary(2)|central_nervous_system(1)	3	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)																	---	---	---	---
F8	2157	broad.mit.edu	37	X	154074505	154074506	+	Intron	INS	-	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154074505_154074506insA	uc004fmt.2	-						F8_uc004fms.2_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)													---	---	---	---
F8	2157	broad.mit.edu	37	X	154132429	154132429	+	Intron	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154132429delA	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)													---	---	---	---
F8	2157	broad.mit.edu	37	X	154148489	154148489	+	Intron	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154148489delT	uc004fmt.2	-							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)													---	---	---	---
F8	2157	broad.mit.edu	37	X	154158195	154158195	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154158195delT	uc004fmt.2	-	14	4041	c.3870delA	c.(3868-3870)AAAfs	p.K1290fs		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	1290	B.				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)													---	---	---	---
MTCP1NB	100272147	broad.mit.edu	37	X	154290070	154290070	+	3'UTR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154290070delA	uc004fmy.2	-	3						NM_001018024	NP_001018024			mature T-cell proliferation 1 neighbor						cell proliferation	mitochondrion				lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9924110	9924110	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9924110delT								TTTY22 (273256 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9964997	9964997	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9964997delT								TTTY22 (314143 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9972620	9972620	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9972620delA								TTTY22 (321766 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	10000017	10000017	+	IGR	DEL	G	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10000017delG								TTTY22 (349163 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	10038945	10038945	+	IGR	DEL	A	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10038945delA								TTTY22 (388091 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	10071231	10071232	+	IGR	DEL	AG	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10071231_10071232delAG								TTTY22 (420377 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13619591	13619591	+	IGR	DEL	T	-	-			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13619591delT								None (None upstream) : None (None downstream)																																			---	---	---	---
MORN1	79906	broad.mit.edu	37	1	2303936	2303936	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2303936G>A	uc001ajb.1	-	8	750	c.729C>T	c.(727-729)CAC>CAT	p.H243H	MORN1_uc009vld.2_Silent_p.H219H|MORN1_uc001ajd.1_Silent_p.H243H	NM_024848	NP_079124	Q5T089	MORN1_HUMAN	MORN repeat containing 1	243										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)														---	---	---	---
RER1	11079	broad.mit.edu	37	1	2334500	2334500	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2334500G>A	uc001aje.1	+	7	719	c.528G>A	c.(526-528)CCG>CCA	p.P176P	RER1_uc001ajf.1_3'UTR	NM_007033	NP_008964	O15258	RER1_HUMAN	RER1 retention in endoplasmic reticulum 1	176				HAATKGILVAMVCTFFDAFNVPVFWPILVMYFIMLFCITMK RQIKHMIKYRYIPFTHGKRRYRGKEDAGKAFAS -> DASV CGDGRCSCKAGGGRQCPVLAADAALTFSPHLKACGYQGHPC GYGLYFLRRFQRPGVLADSGDVLHHALLYHDEEANQAHD (in Ref. 2; AAC72940).	retrograde vesicle-mediated transport, Golgi to ER	integral to Golgi membrane					0	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.28e-37)|OV - Ovarian serous cystadenocarcinoma(86;8.29e-23)|GBM - Glioblastoma multiforme(42;4.71e-08)|Colorectal(212;4.73e-05)|COAD - Colon adenocarcinoma(227;0.00021)|Kidney(185;0.00116)|BRCA - Breast invasive adenocarcinoma(365;0.00459)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0182)|Lung(427;0.204)														---	---	---	---
ARHGEF16	27237	broad.mit.edu	37	1	3395142	3395142	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3395142C>T	uc001akg.3	+	12	2028	c.1780C>T	c.(1780-1782)CGC>TGC	p.R594C	ARHGEF16_uc001aki.2_Missense_Mutation_p.R306C|ARHGEF16_uc001akj.2_Missense_Mutation_p.R306C|ARHGEF16_uc010nzh.1_Missense_Mutation_p.R298C	NM_014448	NP_055263	Q5VV41	ARHGG_HUMAN	Rho guanine exchange factor 16	594	PH.				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)														---	---	---	---
MEGF6	1953	broad.mit.edu	37	1	3431982	3431982	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3431982G>A	uc001akl.2	-	6	941	c.714C>T	c.(712-714)GAC>GAT	p.D238D	MEGF6_uc001akk.2_Silent_p.D133D	NM_001409	NP_001400	O75095	MEGF6_HUMAN	EGF-like-domain, multiple 3 precursor	238	EGF-like 4.|EGF-like 3.					extracellular region	calcium ion binding			large_intestine(1)	1	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)														---	---	---	---
KIAA0562	9731	broad.mit.edu	37	1	3765295	3765295	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3765295C>T	uc001aky.2	-	3	523	c.164G>A	c.(163-165)CGA>CAA	p.R55Q	KIAA0562_uc010nzm.1_RNA|KIAA0562_uc001akz.2_Missense_Mutation_p.R55Q	NM_014704	NP_055519	O60308	CE104_HUMAN	glycine-, glutamate-,	55						centriole	binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_epithelial(116;3.96e-21)|all_lung(118;2.74e-08)|Lung NSC(185;6.4e-06)|Breast(487;0.00066)|Renal(390;0.00121)|Hepatocellular(190;0.00335)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.031)|Lung SC(97;0.0548)|Medulloblastoma(700;0.212)		Epithelial(90;6.85e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.59e-22)|GBM - Glioblastoma multiforme(42;3.16e-16)|Colorectal(212;2.01e-05)|COAD - Colon adenocarcinoma(227;7.99e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000389)|Kidney(185;0.000513)|STAD - Stomach adenocarcinoma(132;0.00709)|KIRC - Kidney renal clear cell carcinoma(229;0.00714)|Lung(427;0.137)														---	---	---	---
DFFB	1677	broad.mit.edu	37	1	3789133	3789133	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3789133A>G	uc001alc.2	+	6	1102	c.779A>G	c.(778-780)CAC>CGC	p.H260R	DFFB_uc001ale.2_RNA|DFFB_uc009vlp.2_RNA|DFFB_uc001alb.2_RNA|DFFB_uc010nzn.1_Missense_Mutation_p.H284R|DFFB_uc009vlq.2_RNA|DFFB_uc009vlr.2_Missense_Mutation_p.H211R|DFFB_uc001ald.2_Missense_Mutation_p.H196R	NM_004402	NP_004393	O76075	DFFB_HUMAN	DNA fragmentation factor, 40 kD, beta	260					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)														---	---	---	---
CHD5	26038	broad.mit.edu	37	1	6169955	6169955	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6169955G>A	uc001amb.1	-	38	5578	c.5478C>T	c.(5476-5478)AAC>AAT	p.N1826N	CHD5_uc001alz.1_Silent_p.N683N|CHD5_uc001ama.1_RNA	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	1826					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)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7721916	7721916	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7721916C>T	uc001aoi.2	+	8	1002	c.795C>T	c.(793-795)ACC>ACT	p.T265T		NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	265					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	8384692	8384692	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8384692C>T	uc001apb.2	+	1	303	c.303C>T	c.(301-303)TAC>TAT	p.Y101Y		NM_001080397	NP_001073866	Q9Y2W3	S45A1_HUMAN	DNB5	101	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)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8420774	8420774	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8420774C>T	uc001ape.2	-	19	3603	c.2793G>A	c.(2791-2793)CCG>CCA	p.P931P	RERE_uc001apf.2_Silent_p.P931P|RERE_uc010nzx.1_Silent_p.P663P|RERE_uc001apd.2_Silent_p.P377P	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	931	Pro-rich.				multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)														---	---	---	---
CA6	765	broad.mit.edu	37	1	9017324	9017324	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9017324G>A	uc001apm.2	+	3	412	c.388G>A	c.(388-390)GGG>AGG	p.G130R	CA6_uc009vmn.2_Missense_Mutation_p.G70R	NM_001215	NP_001206	P23280	CAH6_HUMAN	carbonic anhydrase VI precursor	130					one-carbon metabolic process	extracellular region	carbonate dehydratase activity|zinc ion binding			ovary(2)	2	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|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;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
TMEM201	199953	broad.mit.edu	37	1	9656943	9656943	+	Silent	SNP	C	T	T	rs143914018		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9656943C>T	uc001apz.2	+	3	273	c.261C>T	c.(259-261)CCC>CCT	p.P87P	TMEM201_uc001apy.2_Silent_p.P87P	NM_001130924	NP_001124396	Q5SNT2	TM201_HUMAN	transmembrane protein 201 isoform 1	87						integral to membrane|nuclear inner membrane					0	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
NMNAT1	64802	broad.mit.edu	37	1	10042553	10042553	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10042553G>A	uc001aqp.2	+	5	778	c.634G>A	c.(634-636)GTG>ATG	p.V212M		NM_022787	NP_073624	Q9HAN9	NMNA1_HUMAN	nicotinamide mononucleotide adenylyltransferase	212					water-soluble vitamin metabolic process	nucleoplasm	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity|protein binding				0		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.31e-08)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(185;0.00028)|BRCA - Breast invasive adenocarcinoma(304;0.00032)|KIRC - Kidney renal clear cell carcinoma(229;0.00101)|STAD - Stomach adenocarcinoma(132;0.00908)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
CASZ1	54897	broad.mit.edu	37	1	10706296	10706296	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10706296C>T	uc001aro.2	-	17	3905	c.3585G>A	c.(3583-3585)ACG>ACA	p.T1195T		NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	1195					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	11168277	11168277	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11168277G>A	uc001asd.2	-	57	7716	c.7595C>T	c.(7594-7596)GCG>GTG	p.A2532V	MTOR_uc001asc.2_Missense_Mutation_p.A737V	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	2532	FATC.				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																		---	---	---	---
KAZ	23254	broad.mit.edu	37	1	15428216	15428216	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15428216G>T	uc001avm.3	+	11	2006	c.1725G>T	c.(1723-1725)CAG>CAT	p.Q575H	KAZ_uc001avs.3_Missense_Mutation_p.Q22H	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E	575	SAM 2.				keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0																		---	---	---	---
RSC1A1	6248	broad.mit.edu	37	1	15987413	15987413	+	Silent	SNP	G	A	A	rs142914242		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15987413G>A	uc010obn.1	+	1	1050	c.1050G>A	c.(1048-1050)CCG>CCA	p.P350P		NM_006511	NP_006502	Q92681	RSCA1_HUMAN	regulatory solute carrier protein, family 1,	350					negative regulation of transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transport	cell junction|Golgi apparatus|nucleus	ion channel inhibitor activity			ovary(1)	1		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00276)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
ARHGEF19	128272	broad.mit.edu	37	1	16525645	16525645	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16525645C>T	uc001ayc.1	-	15	2388	c.2251G>A	c.(2251-2253)GGC>AGC	p.G751S	ARHGEF19_uc009voo.1_Missense_Mutation_p.G104S|ARHGEF19_uc001ayb.1_Missense_Mutation_p.G228S	NM_153213	NP_694945	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	751	SH3.				regulation of actin cytoskeleton organization	intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PADI2	11240	broad.mit.edu	37	1	17431556	17431556	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17431556G>A	uc001baf.2	-	2	175	c.93C>T	c.(91-93)AGC>AGT	p.S31S	PADI2_uc010ocm.1_Silent_p.S31S|PADI2_uc001bag.1_Silent_p.S31S	NM_007365	NP_031391	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	31					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity			ovary(3)|pancreas(1)|central_nervous_system(1)|skin(1)	6		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)													---	---	---	---
PADI1	29943	broad.mit.edu	37	1	17552661	17552661	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17552661G>A	uc001bah.1	+							NM_013358	NP_037490			peptidylarginine deiminase type I						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)													---	---	---	---
PAX7	5081	broad.mit.edu	37	1	19062344	19062344	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19062344C>T	uc001bay.2	+	8	1972	c.1374C>T	c.(1372-1374)GCC>GCT	p.A458A	PAX7_uc001baz.2_Silent_p.A456A|PAX7_uc010oct.1_Silent_p.A458A	NM_002584	NP_002575	P23759	PAX7_HUMAN	paired box 7 isoform 1	458					anti-apoptosis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	p.A458A(1)	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								---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22181934	22181934	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22181934C>T	uc001bfj.2	-	47	5900	c.5860G>A	c.(5860-5862)GGT>AGT	p.G1954S	HSPG2_uc009vqd.2_Missense_Mutation_p.G1955S	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	1954	Ig-like C2-type 4.				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)													---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23208938	23208938	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23208938G>A	uc009vqj.1	+	6	1535	c.1390G>A	c.(1390-1392)GGC>AGC	p.G464S	EPHB2_uc001bge.2_Missense_Mutation_p.G464S|EPHB2_uc001bgf.2_Missense_Mutation_p.G464S|EPHB2_uc010odu.1_Missense_Mutation_p.G464S	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	464	Fibronectin type-III 2.|Extracellular (Potential).				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				---	---	---	---
ASAP3	55616	broad.mit.edu	37	1	23760793	23760793	+	Silent	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23760793G>T	uc001bha.2	-	19	2029	c.1905C>A	c.(1903-1905)CCC>CCA	p.P635P	ASAP3_uc001bgy.1_Silent_p.P139P|ASAP3_uc001bgz.1_RNA|ASAP3_uc010odz.1_Silent_p.P504P|ASAP3_uc010oea.1_Silent_p.P626P|ASAP3_uc001bhb.2_Silent_p.P158P	NM_017707	NP_060177	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH	635	ANK 2.				regulation of ARF GTPase activity	cytoplasm	ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
TMEM57	55219	broad.mit.edu	37	1	25812092	25812092	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25812092A>G	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)														---	---	---	---
EXTL1	2134	broad.mit.edu	37	1	26357744	26357744	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26357744A>G	uc001blf.2	+	5	2090	c.1223A>G	c.(1222-1224)TAC>TGC	p.Y408C		NM_004455	NP_004446	Q92935	EXTL1_HUMAN	exostoses-like 1	408	Lumenal (Potential).				skeletal system development	integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|protein binding			central_nervous_system(1)	1		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;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
ARID1A	8289	broad.mit.edu	37	1	27106862	27106862	+	Missense_Mutation	SNP	G	A	A	rs142069738		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27106862G>A	uc001bmv.1	+	20	6846	c.6473G>A	c.(6472-6474)CGA>CAA	p.R2158Q	ARID1A_uc001bmu.1_Missense_Mutation_p.R1941Q|ARID1A_uc001bmx.1_Missense_Mutation_p.R1004Q|ARID1A_uc009vsm.1_Missense_Mutation_p.R486Q|ARID1A_uc009vsn.1_Missense_Mutation_p.R400Q	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	2158					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	p.R2158*(1)		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								---	---	---	---
MATN1	4146	broad.mit.edu	37	1	31194535	31194535	+	Missense_Mutation	SNP	C	T	T	rs147880584		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31194535C>T	uc001brz.2	-	2	192	c.158G>A	c.(157-159)CGG>CAG	p.R53Q	uc001bsb.1_RNA|MATN1_uc001bsa.1_5'Flank	NM_002379	NP_002370	P21941	MATN1_HUMAN	matrilin 1, cartilage matrix protein precursor	53	VWFA 1.				protein complex assembly	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			central_nervous_system(1)	1		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PUM1	9698	broad.mit.edu	37	1	31452917	31452917	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31452917G>A	uc001bsi.1	-	9	1459	c.1346C>T	c.(1345-1347)GCG>GTG	p.A449V	PUM1_uc001bsf.1_Missense_Mutation_p.A115V|PUM1_uc001bsg.1_Missense_Mutation_p.A262V|PUM1_uc001bsh.1_Missense_Mutation_p.A449V|PUM1_uc001bsj.1_Missense_Mutation_p.A450V|PUM1_uc010oga.1_Missense_Mutation_p.A353V|PUM1_uc001bsk.1_Missense_Mutation_p.A485V|PUM1_uc010ogb.1_Missense_Mutation_p.A390V	NM_014676	NP_055491	Q14671	PUM1_HUMAN	pumilio 1 isoform 2	449	Ala-rich.				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)														---	---	---	---
TMEM39B	55116	broad.mit.edu	37	1	32557419	32557419	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32557419C>T	uc010ogv.1	+	6	880	c.734C>T	c.(733-735)ACG>ATG	p.T245M	TMEM39B_uc010ogt.1_RNA|TMEM39B_uc010ogu.1_Missense_Mutation_p.T118M|TMEM39B_uc001bue.3_Missense_Mutation_p.T246M|TMEM39B_uc001buf.3_Missense_Mutation_p.T46M|TMEM39B_uc010ogw.1_Missense_Mutation_p.T46M	NM_018056	NP_060526	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	245						integral to membrane					0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)																---	---	---	---
IQCC	55721	broad.mit.edu	37	1	32672879	32672879	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32672879G>A	uc001bum.2	+	5	644	c.597G>A	c.(595-597)GCG>GCA	p.A199A	IQCC_uc009vua.2_Silent_p.A279A|IQCC_uc010ogz.1_Silent_p.A99A|DCDC2B_uc001bun.2_5'Flank	NM_018134	NP_060604	Q4KMZ1	IQCC_HUMAN	IQ motif containing C isoform 2	199										ovary(4)	4		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
GJA4	2701	broad.mit.edu	37	1	35260514	35260514	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35260514C>T	uc001bya.2	+	2	788	c.700C>T	c.(700-702)CGC>TGC	p.R234C	GJA4_uc009vul.2_Missense_Mutation_p.R310C|GJA4_uc009vum.1_Missense_Mutation_p.R234C	NM_002060	NP_002051	P35212	CXA4_HUMAN	connexin 37	234	Cytoplasmic (Potential).				cell-cell junction assembly	integral to plasma membrane				central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)																---	---	---	---
NCDN	23154	broad.mit.edu	37	1	36026733	36026733	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36026733G>A	uc001bza.2	+	4	1108	c.981G>A	c.(979-981)ACG>ACA	p.T327T	NCDN_uc001bzb.2_Silent_p.T327T|NCDN_uc001bzc.2_Silent_p.T310T	NM_001014839	NP_001014839	Q9UBB6	NCDN_HUMAN	neurochondrin isoform 1	327					neuron projection development	cytosol|dendrite|neuronal cell body				large_intestine(2)|pancreas(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
THRAP3	9967	broad.mit.edu	37	1	36757051	36757051	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36757051C>T	uc001cae.3	+	6	2046	c.1822C>T	c.(1822-1824)CGT>TGT	p.R608C	THRAP3_uc001caf.3_Missense_Mutation_p.R608C	NM_005119	NP_005110	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	608					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								---	---	---	---
MTF1	4520	broad.mit.edu	37	1	38288328	38288328	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38288328G>A	uc001cce.1	-	9	1373	c.1232C>T	c.(1231-1233)ACA>ATA	p.T411I	MTF1_uc009vvj.1_Missense_Mutation_p.T102I	NM_005955	NP_005946	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	411						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
MTF1	4520	broad.mit.edu	37	1	38305655	38305655	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38305655G>A	uc001cce.1	-	3	725	c.584C>T	c.(583-585)ACG>ATG	p.T195M	MTF1_uc009vvj.1_Translation_Start_Site	NM_005955	NP_005946	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	195						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
KIAA0754	643314	broad.mit.edu	37	1	39879412	39879412	+	Missense_Mutation	SNP	G	A	A	rs55976345	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39879412G>A	uc009vvt.1	+	1	4237	c.3475G>A	c.(3475-3477)GCA>ACA	p.A1159T	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	1023	Ala-rich.|12.										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)															---	---	---	---
NT5C1A	84618	broad.mit.edu	37	1	40131856	40131856	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40131856C>T	uc001cdq.1	-	2	188	c.188G>A	c.(187-189)CGC>CAC	p.R63H		NM_032526	NP_115915	Q9BXI3	5NT1A_HUMAN	5'-nucleotidase, cytosolic IA	63					purine base metabolic process|purine nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			ovary(1)	1	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)															---	---	---	---
MIR30E	407034	broad.mit.edu	37	1	41220094	41220094	+	RNA	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41220094G>A	hsa-mir-30e|MI0000749	+			c.68G>A			NFYC_uc010ojm.1_Intron|NFYC_uc001cfx.3_Intron|NFYC_uc009vwd.2_Intron|NFYC_uc001cfz.2_Intron|NFYC_uc010ojn.1_Intron|NFYC_uc001cfy.3_Intron|NFYC_uc001cgc.2_Intron|NFYC_uc001cgb.2_Intron|NFYC_uc001cgd.3_Intron|NFYC_uc001cge.2_Intron|uc001cgf.1_RNA|uc001cgg.2_5'Flank|MIR30C1_hsa-mir-30c-1|MI0000736_5'Flank																	0																		---	---	---	---
FOXJ3	22887	broad.mit.edu	37	1	42776750	42776750	+	Silent	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42776750T>A	uc001che.2	-	4	327	c.15A>T	c.(13-15)GGA>GGT	p.G5G	FOXJ3_uc001chf.2_Silent_p.G5G|FOXJ3_uc001chg.2_Silent_p.G5G|FOXJ3_uc001chh.1_Silent_p.G5G	NM_014947	NP_055762	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	5					embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
KIAA0467	23334	broad.mit.edu	37	1	43886645	43886645	+	5'Flank	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43886645C>T	uc001cjk.1	+						KIAA0467_uc009vws.1_Missense_Mutation_p.T496M	NM_015284	NP_056099			hypothetical protein LOC23334							peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
PTPRF	5792	broad.mit.edu	37	1	44069662	44069662	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44069662C>T	uc001cjr.2	+	16	3179	c.2839C>T	c.(2839-2841)CGC>TGC	p.R947C	PTPRF_uc001cjs.2_Missense_Mutation_p.R938C|PTPRF_uc001cju.2_Intron|PTPRF_uc009vwt.2_Missense_Mutation_p.R507C|PTPRF_uc001cjv.2_Missense_Mutation_p.R407C|PTPRF_uc001cjw.2_Missense_Mutation_p.R173C	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	947	Fibronectin type-III 7.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
TOE1	114034	broad.mit.edu	37	1	45808744	45808744	+	Intron	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45808744C>A	uc009vxq.2	+						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_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)																	---	---	---	---
TOE1	114034	broad.mit.edu	37	1	45809251	45809251	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45809251T>C	uc009vxq.2	+	8	1993	c.1410T>C	c.(1408-1410)CCT>CCC	p.P470P	TOE1_uc001cnq.3_RNA|TOE1_uc010olm.1_Silent_p.P390P|TOE1_uc001cnr.3_RNA	NM_025077	NP_079353	Q96GM8	TOE1_HUMAN	target of EGR1, member 1 (nuclear)	470						nuclear speck|nucleolus	nucleic acid binding|zinc ion binding			central_nervous_system(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
TESK2	10420	broad.mit.edu	37	1	45813598	45813598	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45813598G>A	uc001cns.1	-	6	1018	c.615C>T	c.(613-615)CCC>CCT	p.P205P	TESK2_uc009vxr.1_Silent_p.P205P|TESK2_uc010olo.1_Silent_p.P122P|TESK2_uc009vxs.1_5'UTR	NM_007170	NP_009101	Q96S53	TESK2_HUMAN	testis-specific protein kinase 2	205	Protein kinase.				actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
CCDC17	149483	broad.mit.edu	37	1	46088681	46088681	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46088681C>T	uc010olt.1	-	4	750	c.602G>A	c.(601-603)CGG>CAG	p.R201Q	CCDC17_uc009vxy.2_Missense_Mutation_p.R169Q|CCDC17_uc010ols.1_Missense_Mutation_p.R192Q|CCDC17_uc001com.3_Missense_Mutation_p.R22Q|CCDC17_uc001con.3_RNA|CCDC17_uc009vxz.2_Intron	NM_001114938	NP_001108410	Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	201	Potential.									ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
GLIS1	148979	broad.mit.edu	37	1	54059810	54059810	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54059810G>A	uc001cvr.1	-	3	1333	c.766C>T	c.(766-768)CAC>TAC	p.H256Y		NM_147193	NP_671726	Q8NBF1	GLIS1_HUMAN	GLIS family zinc finger 1	256	C2H2-type 2; atypical.				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																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62503676	62503676	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62503676C>T	uc001dab.2	+	30	4101	c.3987C>T	c.(3985-3987)GCC>GCT	p.A1329A	INADL_uc009waf.1_Silent_p.A1329A|INADL_uc001daa.2_Silent_p.A1329A|INADL_uc001dad.3_Silent_p.A1026A|INADL_uc001dac.2_RNA|INADL_uc010oot.1_Silent_p.A113A|INADL_uc009wag.2_Silent_p.A113A|INADL_uc010oou.1_Silent_p.A2A	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	1329					intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
MIER1	57708	broad.mit.edu	37	1	67450349	67450349	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67450349A>C	uc001dde.2	+	14	1598	c.1464A>C	c.(1462-1464)AAA>AAC	p.K488N	MIER1_uc010opf.1_Intron|MIER1_uc009way.2_Intron|MIER1_uc001ddc.2_Intron|MIER1_uc001ddh.2_Intron|MIER1_uc001ddf.2_Missense_Mutation_p.K452N|MIER1_uc001ddg.2_Missense_Mutation_p.K408N|MIER1_uc010opg.1_Missense_Mutation_p.K452N|MIER1_uc001ddj.1_Missense_Mutation_p.K435N|MIER1_uc001ddi.2_Intron	NM_001077700	NP_001071168	Q8N108	MIER1_HUMAN	mesoderm induction early response 1 isoform b	459					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																		---	---	---	---
SERBP1	26135	broad.mit.edu	37	1	67880887	67880887	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67880887G>A	uc001ddv.2	-	7	1272	c.1132C>T	c.(1132-1134)CGT>TGT	p.R378C	SERBP1_uc001ddx.2_Missense_Mutation_p.R372C|SERBP1_uc001ddy.2_Missense_Mutation_p.R357C|SERBP1_uc001ddw.2_Missense_Mutation_p.R363C	NM_001018067	NP_001018077	Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1 isoform 1	378					regulation of mRNA stability	nucleus|perinuclear region of cytoplasm	mRNA 3'-UTR binding|protein binding			skin(1)	1																		---	---	---	---
TNNI3K	51086	broad.mit.edu	37	1	74957869	74957869	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74957869G>A	uc001dgf.1	+	23	2321	c.2270G>A	c.(2269-2271)CGG>CAG	p.R757Q	TNNI3K_uc001dge.1_Missense_Mutation_p.R858Q	NM_015978	NP_057062	Q59H18	TNI3K_HUMAN	TNNI3 interacting kinase isoform b	757						cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10																		---	---	---	---
C1orf173	127254	broad.mit.edu	37	1	75037295	75037295	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75037295C>T	uc001dgg.2	-	14	4318	c.4099G>A	c.(4099-4101)GAG>AAG	p.E1367K		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	1367	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5																		---	---	---	---
FUBP1	8880	broad.mit.edu	37	1	78422353	78422353	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78422353A>G	uc001dii.2	-	17	1698	c.1609T>C	c.(1609-1611)TGG>CGG	p.W537R	FUBP1_uc001dih.3_RNA|FUBP1_uc010orm.1_Missense_Mutation_p.W558R	NM_003902	NP_003893	Q96AE4	FUBP1_HUMAN	far upstream element-binding protein	537	Pro-rich.				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																		---	---	---	---
PTGFR	5737	broad.mit.edu	37	1	78959195	78959195	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78959195G>A	uc001din.2	+	2	1033	c.767G>A	c.(766-768)TGT>TAT	p.C256Y	PTGFR_uc001dim.2_Missense_Mutation_p.C256Y	NM_000959	NP_000950	P43088	PF2R_HUMAN	prostaglandin F receptor isoform a precursor	256	Helical; Name=6; (Potential).				parturition	extracellular region|integral to plasma membrane	prostaglandin F receptor activity			ovary(3)|breast(2)|skin(1)	6				Colorectal(170;0.248)	Bimatoprost(DB00905)|Latanoprost(DB00654)|Travoprost(DB00287)													---	---	---	---
LMO4	8543	broad.mit.edu	37	1	87814424	87814424	+	3'UTR	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87814424G>T	uc001dmi.2	+	5					LMO4_uc001dmj.2_3'UTR	NM_006769	NP_006760			LIM domain only 4						neural tube closure|transcription from RNA polymerase II promoter	transcription factor complex	sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding				0		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)														---	---	---	---
PKN2	5586	broad.mit.edu	37	1	89206691	89206691	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89206691G>A	uc001dmn.2	+	2	411	c.69G>A	c.(67-69)CCG>CCA	p.P23P	PKN2_uc001dmm.1_Silent_p.P23P|PKN2_uc010osp.1_Silent_p.P23P|PKN2_uc010osq.1_Intron|PKN2_uc009wcv.2_Silent_p.P23P	NM_006256	NP_006247	Q16513	PKN2_HUMAN	protein kinase N2	23					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)														---	---	---	---
HFM1	164045	broad.mit.edu	37	1	91844741	91844741	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91844741C>T	uc001doa.3	-	9	1137	c.1037G>A	c.(1036-1038)CGT>CAT	p.R346H	HFM1_uc010osu.1_Missense_Mutation_p.R25H|HFM1_uc010osv.1_Missense_Mutation_p.R30H|HFM1_uc001doc.1_Missense_Mutation_p.R346H	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein	346	Helicase ATP-binding.						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)														---	---	---	---
EVI5	7813	broad.mit.edu	37	1	93029202	93029202	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93029202A>G	uc001dox.2	-	17	2125	c.2115T>C	c.(2113-2115)CAT>CAC	p.H705H	EVI5_uc010otf.1_Silent_p.H716H|EVI5_uc001doy.1_RNA	NM_005665	NP_005656	O60447	EVI5_HUMAN	ecotropic viral integration site 5	705	Targeting to the centrosomes.|Potential.|Interaction with AURKB and INCENP.				cell cycle|cell division|cell proliferation|multicellular organismal development	microtubule organizing center|nucleus|spindle	protein binding|Rab GTPase activator activity			ovary(1)|breast(1)	2		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)														---	---	---	---
KCNA2	3737	broad.mit.edu	37	1	111146149	111146149	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111146149C>T	uc001dzu.2	-	2	1752	c.1256G>A	c.(1255-1257)CGG>CAG	p.R419Q	KCNA2_uc009wfv.1_Intron|KCNA2_uc009wfw.2_Missense_Mutation_p.R419Q	NM_004974	NP_004965	P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related	419						juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(1)	1		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)														---	---	---	---
WNT2B	7482	broad.mit.edu	37	1	113033683	113033683	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113033683G>A	uc001eca.2	+	2	225	c.105G>A	c.(103-105)GCG>GCA	p.A35A	WNT2B_uc009wgg.2_Intron	NM_004185	NP_004176	Q93097	WNT2B_HUMAN	wingless-type MMTV integration site family,	Error:Variant_position_missing_in_Q93097_after_alignment					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)														---	---	---	---
WNT2B	7482	broad.mit.edu	37	1	113051942	113051942	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113051942G>A	uc001ecb.2	+	1	573	c.58G>A	c.(58-60)GCC>ACC	p.A20T	WNT2B_uc001eca.2_Intron|WNT2B_uc009wgg.2_Intron	NM_024494	NP_078613	Q93097	WNT2B_HUMAN	wingless-type MMTV integration site family,	20					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)														---	---	---	---
SLC22A15	55356	broad.mit.edu	37	1	116609275	116609275	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116609275G>A	uc001egb.3	+	11	1630	c.1500G>A	c.(1498-1500)TCG>TCA	p.S500S		NM_018420	NP_060890	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	500					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)														---	---	---	---
IGSF3	3321	broad.mit.edu	37	1	117146451	117146451	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117146451C>T	uc001egr.1	-	6	2124	c.1419G>A	c.(1417-1419)TCG>TCA	p.S473S	IGSF3_uc001egq.1_Silent_p.S493S|IGSF3_uc001egs.1_Silent_p.S146S	NM_001007237	NP_001007238	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 2	473	Ig-like C2-type 4.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)														---	---	---	---
TRIM45	80263	broad.mit.edu	37	1	117661189	117661189	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117661189A>G	uc001egz.2	-	2	1277	c.689T>C	c.(688-690)GTC>GCC	p.V230A	TRIM45_uc009whe.2_Missense_Mutation_p.V230A|TRIM45_uc001eha.2_Missense_Mutation_p.V126A	NM_025188	NP_079464	Q9H8W5	TRI45_HUMAN	tripartite motif-containing 45 isoform 1	230						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)	1	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)														---	---	---	---
SPAG17	200162	broad.mit.edu	37	1	118634309	118634309	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118634309T>C	uc001ehk.2	-	10	1347	c.1279A>G	c.(1279-1281)AGA>GGA	p.R427G		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	427						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	118642346	118642346	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118642346C>T	uc001ehk.2	-	6	780	c.712G>A	c.(712-714)GCT>ACT	p.A238T		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	238						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)														---	---	---	---
ADAM30	11085	broad.mit.edu	37	1	120437609	120437609	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120437609G>A	uc001eij.2	-	1	1505	c.1351C>T	c.(1351-1353)CGT>TGT	p.R451C		NM_021794	NP_068566	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30 preproprotein	451	Disintegrin.|Extracellular (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)														---	---	---	---
PPIAL4G	644591	broad.mit.edu	37	1	143767446	143767446	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143767446G>A	uc001ejt.2	-	1	436	c.403C>T	c.(403-405)CGT>TGT	p.R135C		NM_001123068	NP_001116540	A2BFH1	PAL4G_HUMAN	peptidylprolyl isomerase A (cyclophilin A)-like	135	PPIase cyclophilin-type.				protein folding	cytoplasm	peptidyl-prolyl cis-trans isomerase activity				0																		---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144952189	144952189	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144952189G>A	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emg.1_3'UTR|PDE4DIP_uc001emh.2_3'UTR	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								---	---	---	---
POLR3C	10623	broad.mit.edu	37	1	145608566	145608566	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145608566G>A	uc001eoh.2	-	3	402	c.241C>T	c.(241-243)CGG>TGG	p.R81W	NBPF10_uc001emp.3_Intron|RNF115_uc001eoj.2_5'Flank|RNF115_uc001eok.2_5'Flank|RNF115_uc009wiy.2_5'Flank|POLR3C_uc001eog.2_Missense_Mutation_p.R94W|POLR3C_uc001eoi.2_Intron|POLR3C_uc009wix.2_Missense_Mutation_p.R81W	NM_006468	NP_006459	Q9BUI4	RPC3_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	81					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	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity			ovary(1)	1	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		Epithelial(2;7.55e-13)															---	---	---	---
PLEKHO1	51177	broad.mit.edu	37	1	150123100	150123100	+	Splice_Site	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150123100A>G	uc001ett.2	+	2	309	c.31_splice	c.e2-2	p.G11_splice	PLEKHO1_uc001etr.2_Splice_Site|PLEKHO1_uc001ets.2_Splice_Site	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)															---	---	---	---
VPS72	6944	broad.mit.edu	37	1	151149142	151149142	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151149142C>T	uc001exe.1	-	6	1116	c.1073G>A	c.(1072-1074)CGC>CAC	p.R358H	TMOD4_uc001exd.2_5'Flank|TMOD4_uc001exc.3_5'Flank|TMOD4_uc010pct.1_5'Flank	NM_005997	NP_005988	Q15906	VPS72_HUMAN	transcription factor-like 1	358					chromatin modification|negative regulation of transcription from RNA polymerase II promoter	nucleus|protein complex	DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|pancreas(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)															---	---	---	---
ZNF687	57592	broad.mit.edu	37	1	151261166	151261166	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151261166C>T	uc001exq.2	+	3	2376	c.2278C>T	c.(2278-2280)CGC>TGC	p.R760C	ZNF687_uc009wmo.2_Missense_Mutation_p.R760C|ZNF687_uc009wmp.2_Missense_Mutation_p.R760C	NM_020832	NP_065883	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	760					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding			central_nervous_system(3)|ovary(1)	4	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)															---	---	---	---
FLG	2312	broad.mit.edu	37	1	152275642	152275642	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152275642C>T	uc001ezu.1	-	3	11756	c.11720G>A	c.(11719-11721)CGC>CAC	p.R3907H		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	3907	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	152283084	152283084	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152283084G>A	uc001ezu.1	-	3	4314	c.4278C>T	c.(4276-4278)TCC>TCT	p.S1426S	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1426	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	152284397	152284397	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152284397G>A	uc001ezu.1	-	3	3001	c.2965C>T	c.(2965-2967)CAC>TAC	p.H989Y	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	989	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	152284999	152284999	+	Missense_Mutation	SNP	C	T	T	rs142483068	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152284999C>T	uc001ezu.1	-	3	2399	c.2363G>A	c.(2362-2364)CGA>CAA	p.R788Q	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	788	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				---	---	---	---
LCE2C	353140	broad.mit.edu	37	1	152648744	152648744	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152648744C>T	uc001fah.2	+	2	308	c.253C>T	c.(253-255)CGG>TGG	p.R85W		NM_178429	NP_848516	Q5TA81	LCE2C_HUMAN	late cornified envelope 2C	85	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)															---	---	---	---
CREB3L4	148327	broad.mit.edu	37	1	153941400	153941400	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153941400C>T	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)															---	---	---	---
UBAP2L	9898	broad.mit.edu	37	1	154229634	154229634	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154229634T>A	uc001fep.3	+	19	2420	c.2253T>A	c.(2251-2253)AGT>AGA	p.S751R	UBAP2L_uc009wot.2_Missense_Mutation_p.S751R|UBAP2L_uc010pek.1_Missense_Mutation_p.S743R|UBAP2L_uc010pel.1_Missense_Mutation_p.S761R|UBAP2L_uc010pen.1_Missense_Mutation_p.S665R|UBAP2L_uc001feq.2_5'UTR|UBAP2L_uc001fer.2_5'UTR	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a	751					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)															---	---	---	---
ADAR	103	broad.mit.edu	37	1	154557387	154557387	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154557387G>A	uc001ffh.2	-	15	3776	c.3576C>T	c.(3574-3576)TAC>TAT	p.Y1192Y	ADAR_uc001ffj.2_Silent_p.Y1147Y|ADAR_uc001ffi.2_Silent_p.Y1166Y|ADAR_uc001ffk.2_Silent_p.Y897Y	NM_001111	NP_001102	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific isoform a	1192	A to I editase.				adenosine to inosine editing|gene silencing by RNA|mRNA modification|mRNA processing|type I interferon-mediated signaling pathway	cytoplasm|nucleolus|nucleoplasm	DNA binding|double-stranded RNA adenosine deaminase activity|metal ion binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)														---	---	---	---
HCN3	57657	broad.mit.edu	37	1	155252423	155252423	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155252423G>A	uc001fjz.1	+	2	508	c.500G>A	c.(499-501)CGC>CAC	p.R167H	RAG1AP1_uc010pey.1_Intron|HCN3_uc010pfz.1_5'UTR	NM_020897	NP_065948	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic	167	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)|breast(1)	2	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
LMNA	4000	broad.mit.edu	37	1	156108451	156108451	+	Missense_Mutation	SNP	G	A	A	rs13768		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156108451G>A	uc001fni.2	+	11	2120	c.1871G>A	c.(1870-1872)CGC>CAC	p.R624H	LMNA_uc001fnf.1_3'UTR|LMNA_uc001fnh.2_Missense_Mutation_p.R594H|LMNA_uc009wro.1_Intron|LMNA_uc001fnj.2_3'UTR|LMNA_uc001fnk.2_Missense_Mutation_p.R525H|LMNA_uc010pha.1_3'UTR|LMNA_uc010phb.1_RNA	NM_170707	NP_733821	P02545	LMNA_HUMAN	lamin A/C isoform 1 precursor	624	Tail.		R -> H (in EDMD2).		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				---	---	---	---
CCT3	7203	broad.mit.edu	37	1	156303398	156303398	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156303398C>T	uc001fol.1	-	5	464	c.244G>A	c.(244-246)GAA>AAA	p.E82K	CCT3_uc001fom.1_Missense_Mutation_p.E82K|CCT3_uc001fon.1_Missense_Mutation_p.E44K|CCT3_uc010phj.1_Missense_Mutation_p.E36K|CCT3_uc010phk.1_Missense_Mutation_p.E36K|CCT3_uc010phl.1_Missense_Mutation_p.E36K	NM_005998	NP_005989	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 isoform a	82					'de novo' posttranslational protein folding	cytoskeleton|cytosol|plasma membrane	ATP binding|unfolded protein binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)																	---	---	---	---
PEAR1	375033	broad.mit.edu	37	1	156883740	156883740	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156883740G>C	uc001fqj.1	+	22	2926	c.2810G>C	c.(2809-2811)GGC>GCC	p.G937A	PEAR1_uc001fqk.1_Missense_Mutation_p.G562A	NM_001080471	NP_001073940	Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	937	Pro-rich.					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)																	---	---	---	---
OR10T2	128360	broad.mit.edu	37	1	158368816	158368816	+	Silent	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158368816A>C	uc010pih.1	-	1	441	c.441T>G	c.(439-441)TCT>TCG	p.S147S		NM_001004475	NP_001004475	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T,	147	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	all_hematologic(112;0.0378)																	---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158621239	158621239	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158621239G>T	uc001fst.1	-	24	3594	c.3395C>A	c.(3394-3396)CCT>CAT	p.P1132H		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1132	Spectrin 11.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)																	---	---	---	---
SLAMF8	56833	broad.mit.edu	37	1	159799702	159799702	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159799702C>T	uc001fue.3	+	2	297	c.87C>T	c.(85-87)GTC>GTT	p.V29V		NM_020125	NP_064510	Q9P0V8	SLAF8_HUMAN	SLAM family member 8 precursor	29	Extracellular (Potential).					integral to membrane					0	all_hematologic(112;0.0597)																	---	---	---	---
HSD17B7	51478	broad.mit.edu	37	1	162762614	162762614	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162762614G>A	uc001gci.2	+	2	296	c.201G>A	c.(199-201)CTG>CTA	p.L67L	HSD17B7_uc009wuv.2_RNA	NM_016371	NP_057455	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	67	Extracellular (Potential).				cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	3-keto sterol reductase activity|estradiol 17-beta-dehydrogenase activity			ovary(1)	1	all_hematologic(112;0.115)				NADH(DB00157)													---	---	---	---
ATP1B1	481	broad.mit.edu	37	1	169100579	169100579	+	RNA	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169100579G>A	uc001gfs.1	+	6		c.823G>A								Synthetic construct DNA, clone: pF1KB8186, Homo sapiens ATP1B1 gene for ATPase, Na+/K+ transporting, beta 1 polypeptide, without stop codon, in Flexi system.						ATP biosynthetic process|blood coagulation|leukocyte migration	sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	all_hematologic(923;0.208)																	---	---	---	---
SELL	6402	broad.mit.edu	37	1	169677594	169677594	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169677594C>T	uc001ggk.2	-	3	634	c.436G>A	c.(436-438)GCC>ACC	p.A146T	C1orf112_uc001ggj.2_Intron|SELL_uc010pls.1_Missense_Mutation_p.A99T|SELL_uc001ggl.1_Missense_Mutation_p.A159T	NM_000655	NP_000646	P14151	LYAM1_HUMAN	selectin L precursor	146	C-type lectin.|Extracellular (Potential).				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)																	---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173912741	173912741	+	Silent	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173912741T>G	uc001gju.3	-	17	3061	c.2974A>C	c.(2974-2976)AGG>CGG	p.R992R	RC3H1_uc010pms.1_Intron|RC3H1_uc001gjv.2_Intron|RC3H1_uc010pmt.1_Silent_p.R992R	NM_172071	NP_742068	Q5TC82	RC3H1_HUMAN	roquin	992					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																		---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173953746	173953746	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173953746C>T	uc001gju.3	-	2	330	c.243G>A	c.(241-243)CAG>CAA	p.Q81Q	RC3H1_uc010pms.1_Silent_p.Q81Q|RC3H1_uc001gjv.2_Silent_p.Q81Q|RC3H1_uc010pmt.1_Silent_p.Q81Q	NM_172071	NP_742068	Q5TC82	RC3H1_HUMAN	roquin	81					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																		---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180775653	180775653	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180775653C>A	uc001goi.2	+	6	833	c.641C>A	c.(640-642)GCT>GAT	p.A214D	XPR1_uc009wxm.2_Missense_Mutation_p.A214D|XPR1_uc009wxn.2_Missense_Mutation_p.A214D	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor	214	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
ZNF648	127665	broad.mit.edu	37	1	182026636	182026636	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182026636A>G	uc001goz.2	-	2	718	c.510T>C	c.(508-510)AAT>AAC	p.N170N		NM_001009992	NP_001009992	Q5T619	ZN648_HUMAN	zinc finger protein 648	170					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
C1orf21	81563	broad.mit.edu	37	1	184446659	184446659	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184446659G>A	uc001gqv.1	+	2	493	c.16G>A	c.(16-18)GCC>ACC	p.A6T		NM_030806	NP_110433	Q9H246	CA021_HUMAN	chromosome 1 open reading frame 21	6											0		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)														---	---	---	---
TPR	7175	broad.mit.edu	37	1	186313658	186313658	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186313658T>C	uc001grv.2	-	25	3563	c.3266A>G	c.(3265-3267)CAT>CGT	p.H1089R		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	1089	Potential.				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	186645044	186645044	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186645044G>A	uc001gsb.2	-	8	1380	c.1243C>T	c.(1243-1245)CAA>TAA	p.Q415*	PTGS2_uc009wyo.2_Nonsense_Mutation_p.Q262*	NM_000963	NP_000954	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 precursor	415					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)													---	---	---	---
RGS2	5997	broad.mit.edu	37	1	192780201	192780201	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192780201C>A	uc001gsl.2	+	4	398	c.365C>A	c.(364-366)ACC>AAC	p.T122N		NM_002923	NP_002914	P41220	RGS2_HUMAN	regulator of G-protein signaling 2	122	RGS.				cell cycle|negative regulation of cardiac muscle hypertrophy|negative regulation of G-protein coupled receptor protein signaling pathway|negative regulation of MAP kinase activity|negative regulation of phospholipase activity|positive regulation of cardiac muscle contraction|regulation of adrenergic receptor signaling pathway|regulation of translation|relaxation of cardiac muscle	cytosol|internal side of plasma membrane|mitochondrion|nucleolus	calmodulin binding|GTPase activator activity|signal transducer activity				0																		---	---	---	---
TROVE2	6738	broad.mit.edu	37	1	193051307	193051307	+	Intron	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193051307A>T	uc001gss.2	+						TROVE2_uc001gst.1_Intron|TROVE2_uc001gsu.1_Intron|TROVE2_uc001gsv.1_Intron|TROVE2_uc001gsw.2_Intron|TROVE2_uc009wyp.2_Intron|TROVE2_uc009wyq.2_Intron|TROVE2_uc001gsx.1_Intron	NM_004600	NP_004591			TROVE domain family, member 2 isoform 2						transcription from RNA polymerase III promoter	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|RNA binding				0																		---	---	---	---
B3GALT2	8707	broad.mit.edu	37	1	193149443	193149443	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193149443C>T	uc001gtc.3	-	2	1965	c.1250G>A	c.(1249-1251)CGC>CAC	p.R417H	CDC73_uc001gtb.2_Intron	NM_003783	NP_003774	O43825	B3GT2_HUMAN	UDP-Gal:betaGlcNAc beta	417	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)	1																		---	---	---	---
F13B	2165	broad.mit.edu	37	1	197031010	197031010	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197031010C>T	uc001gtt.1	-	3	399	c.355G>A	c.(355-357)GCT>ACT	p.A119T		NM_001994	NP_001985	P05160	F13B_HUMAN	coagulation factor XIII B subunit precursor	119	Sushi 2.				blood coagulation	extracellular region				upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197480898	197480898	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197480898T>A	uc010ppe.1	-	21	2053	c.1715A>T	c.(1714-1716)GAT>GTT	p.D572V	DENND1B_uc010ppf.1_RNA	NM_001142795	NP_001136267	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B isoform 1	Error:Variant_position_missing_in_Q6P3S1_after_alignment						clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0																		---	---	---	---
KIF21B	23046	broad.mit.edu	37	1	200974489	200974489	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200974489C>T	uc001gvs.1	-	5	996	c.679G>A	c.(679-681)GCC>ACC	p.A227T	KIF21B_uc001gvr.1_Missense_Mutation_p.A227T|KIF21B_uc009wzl.1_Missense_Mutation_p.A227T|KIF21B_uc010ppn.1_Missense_Mutation_p.A227T|KIF21B_uc001gvt.1_Missense_Mutation_p.A10T	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	227	Kinesin-motor.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6																		---	---	---	---
PKP1	5317	broad.mit.edu	37	1	201289420	201289420	+	Missense_Mutation	SNP	C	T	T	rs146785756		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201289420C>T	uc001gwd.2	+	8	1572	c.1321C>T	c.(1321-1323)CGC>TGC	p.R441C	PKP1_uc001gwe.2_Missense_Mutation_p.R420C|PKP1_uc009wzm.2_Missense_Mutation_p.R28C	NM_000299	NP_000290	Q13835	PKP1_HUMAN	plakophilin 1 isoform 1b	441	ARM 5.				cell adhesion|cellular component disassembly involved in apoptosis|multicellular organismal development	desmosome|intermediate filament|nucleus	intermediate filament binding|signal transducer activity|structural constituent of epidermis			ovary(2)	2																		---	---	---	---
TNNT2	7139	broad.mit.edu	37	1	201333455	201333455	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201333455G>A	uc001gwf.2	-	11	529	c.460C>T	c.(460-462)CGG>TGG	p.R154W	TNNT2_uc009wzn.2_5'Flank|TNNT2_uc009wzo.2_5'Flank|TNNT2_uc009wzp.2_5'Flank|TNNT2_uc001gwg.2_Missense_Mutation_p.R144W|TNNT2_uc001gwh.2_Missense_Mutation_p.R139W|TNNT2_uc001gwi.2_Missense_Mutation_p.R114W|TNNT2_uc009wzr.2_Missense_Mutation_p.R85W|TNNT2_uc001gwj.1_5'Flank|TNNT2_uc009wzs.1_Missense_Mutation_p.R119W|TNNT2_uc001gwk.1_Missense_Mutation_p.R85W|TNNT2_uc009wzt.1_Missense_Mutation_p.R144W	NM_000364	NP_000355	P45379	TNNT2_HUMAN	troponin T type 2, cardiac isoform 1	154					ATP catabolic process|muscle filament sliding|negative regulation of ATPase activity|positive regulation of ATPase activity|regulation of heart contraction|response to calcium ion|response to calcium ion|ventricular cardiac muscle tissue morphogenesis	cytosol|troponin complex	actin binding|tropomyosin binding|troponin C binding|troponin I binding				0																		---	---	---	---
PPFIA4	8497	broad.mit.edu	37	1	203040880	203040880	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203040880C>T	uc001gyz.2	+	15	2460	c.1867C>T	c.(1867-1869)CTG>TTG	p.L623L	PPFIA4_uc009xaj.2_Silent_p.L1254L|PPFIA4_uc010pqf.1_Silent_p.L836L|PPFIA4_uc001gza.2_Silent_p.L614L|PPFIA4_uc001gzb.1_Silent_p.L309L|PPFIA4_uc001gzc.1_Silent_p.L165L	NM_015053	NP_055868	O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f	623					cell communication	cell surface|cytoplasm	protein binding			ovary(4)|skin(1)	5																		---	---	---	---
ADORA1	134	broad.mit.edu	37	1	203098074	203098074	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203098074G>T	uc001gze.1	+	3	538	c.105G>T	c.(103-105)AAG>AAT	p.K35N	ADORA1_uc001gzf.1_Missense_Mutation_p.K35N|ADORA1_uc010pqg.1_Translation_Start_Site|ADORA1_uc009xak.1_Translation_Start_Site|ADORA1_uc010pqh.1_Missense_Mutation_p.K68N	NM_000674	NP_000665	P30542	AA1R_HUMAN	adenosine A1 receptor	35	Cytoplasmic (Potential).				induction of apoptosis by extracellular signals|inflammatory response|nervous system development|phagocytosis	integral to plasma membrane				large_intestine(1)	1					Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Gabapentin(DB00996)|Imipramine(DB00458)|Pegademase bovine(DB00061)|Theophylline(DB00277)													---	---	---	---
LAMB3	3914	broad.mit.edu	37	1	209811925	209811925	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209811925A>G	uc001hhg.2	-	3	642	c.252T>C	c.(250-252)AAT>AAC	p.N84N	LAMB3_uc009xco.2_Silent_p.N84N|LAMB3_uc001hhh.2_Silent_p.N84N|LAMB3_uc010psl.1_RNA|LAMB3_uc009xcp.1_Silent_p.N84N	NM_001017402	NP_001017402	Q13751	LAMB3_HUMAN	laminin, beta 3 precursor	84	Laminin N-terminal.				cell adhesion|epidermis development|hemidesmosome assembly		structural molecule activity			central_nervous_system(2)|skin(2)|large_intestine(1)|ovary(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0519)														---	---	---	---
SERTAD4	56256	broad.mit.edu	37	1	210415509	210415509	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210415509G>A	uc001hhy.2	+	4	1077	c.898G>A	c.(898-900)GAA>AAA	p.E300K	SERTAD4_uc009xcw.2_Missense_Mutation_p.E300K	NM_019605	NP_062551	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	300							protein binding			ovary(1)|pancreas(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)														---	---	---	---
GPATCH2	55105	broad.mit.edu	37	1	217793680	217793680	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217793680C>T	uc001hlf.1	-	2	314	c.218G>A	c.(217-219)CGG>CAG	p.R73Q	GPATCH2_uc001hlg.3_Missense_Mutation_p.R73Q	NM_018040	NP_060510	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	73						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)														---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220369638	220369638	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220369638A>G	uc010puk.1	-	10	1078	c.914T>C	c.(913-915)ATC>ACC	p.I305T	RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_5'UTR	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	305					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
LBR	3930	broad.mit.edu	37	1	225594521	225594521	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225594521G>A	uc001hoy.2	-	11	1471	c.1328C>T	c.(1327-1329)ACG>ATG	p.T443M	LBR_uc001hoz.2_Missense_Mutation_p.T443M|LBR_uc001hpa.1_Missense_Mutation_p.T443M	NM_002296	NP_002287	Q14739	LBR_HUMAN	lamin B receptor	443					cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)														---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228402783	228402783	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228402783G>A	uc009xez.1	+	5	1856	c.1812G>A	c.(1810-1812)CCG>CCA	p.P604P	OBSCN_uc001hsn.2_Silent_p.P604P|uc001hsm.1_5'Flank	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	604	Fibronectin type-III 1.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
RAB4A	5867	broad.mit.edu	37	1	229422273	229422273	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229422273T>C	uc001hth.2	+	2	280	c.72T>C	c.(70-72)ACT>ACC	p.T24T	RAB4A_uc001hti.2_RNA|RAB4A_uc001htj.2_Intron	NM_004578	NP_004569	P20338	RAB4A_HUMAN	RAB4A, member RAS oncogene family	19	GTP.						GDP binding|GTP binding|GTPase activity			ovary(1)	1	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)																---	---	---	---
ACTA1	58	broad.mit.edu	37	1	229568185	229568185	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229568185G>A	uc001htm.2	-							NM_001100	NP_001091			actin, alpha 1, skeletal muscle						muscle filament sliding|skeletal muscle fiber development|skeletal muscle thin filament assembly	actin filament|cytosol|stress fiber|striated muscle thin filament	ADP binding|ATP binding|myosin binding|structural constituent of cytoskeleton				0	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)			Dornase Alfa(DB00003)													---	---	---	---
ABCB10	23456	broad.mit.edu	37	1	229667403	229667403	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229667403T>G	uc001htp.3	-	7	1458	c.1415A>C	c.(1414-1416)GAG>GCG	p.E472A		NM_012089	NP_036221	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B, member 10	472	Mitochondrial intermembrane (Potential).|Mitochondrial matrix (Potential).					integral to mitochondrial membrane|mitochondrial inner membrane	ATP binding|oligopeptide-transporting ATPase activity			breast(2)	2	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)																---	---	---	---
URB2	9816	broad.mit.edu	37	1	229772399	229772399	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229772399A>C	uc001hts.1	+	4	2175	c.2039A>C	c.(2038-2040)CAG>CCG	p.Q680P	URB2_uc009xfd.1_Missense_Mutation_p.Q680P	NM_014777	NP_055592	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog	680						nucleolus				central_nervous_system(2)|ovary(1)	3																		---	---	---	---
NID1	4811	broad.mit.edu	37	1	236142400	236142400	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236142400C>T	uc001hxo.2	-	19	3619	c.3517G>A	c.(3517-3519)GTG>ATG	p.V1173M	NID1_uc009xgd.2_Missense_Mutation_p.V1040M|NID1_uc009xgc.2_Missense_Mutation_p.V254M	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor	1173					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)													---	---	---	---
NID1	4811	broad.mit.edu	37	1	236154336	236154336	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236154336C>T	uc001hxo.2	-	14	2880	c.2778G>A	c.(2776-2778)CCG>CCA	p.P926P	NID1_uc009xgd.2_Silent_p.P793P|NID1_uc009xgc.2_Silent_p.P12P	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor	926					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)													---	---	---	---
ZP4	57829	broad.mit.edu	37	1	238048857	238048857	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238048857C>T	uc001hym.2	-	8	994	c.994G>A	c.(994-996)GGT>AGT	p.G332S	LOC100130331_uc010pyc.1_Intron	NM_021186	NP_067009	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4 preproprotein	332	ZP.|Extracellular (Potential).				acrosomal vesicle exocytosis|negative regulation of binding of sperm to zona pellucida|positive regulation of acrosome reaction|positive regulation of humoral immune response|positive regulation of protein kinase activity|positive regulation of T cell proliferation|protein kinase A signaling cascade|protein kinase C signaling cascade	integral to membrane|intracellular|plasma membrane|proteinaceous extracellular matrix	acrosin binding|receptor activity			ovary(2)|skin(1)	3	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245849621	245849621	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245849621C>T	uc001ibf.1	+	12	3776	c.3336C>T	c.(3334-3336)GGC>GGT	p.G1112G	KIF26B_uc001ibg.1_Silent_p.G730G|KIF26B_uc001ibh.1_Silent_p.G354G	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1112					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)															---	---	---	---
OR13G1	441933	broad.mit.edu	37	1	247836183	247836183	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247836183G>A	uc001idi.1	-	1	161	c.161C>T	c.(160-162)ACG>ATG	p.T54M		NM_001005487	NP_001005487	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G,	54	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)															---	---	---	---
OR2T8	343172	broad.mit.edu	37	1	248084867	248084867	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248084867T>C	uc010pzc.1	+	1	548	c.548T>C	c.(547-549)GTG>GCG	p.V183A		NM_001005522	NP_001005522	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T,	183	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)															---	---	---	---
OR14I1	401994	broad.mit.edu	37	1	248845531	248845531	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248845531G>A	uc001ieu.1	-	1	75	c.75C>T	c.(73-75)CAC>CAT	p.H25H		NM_001004734	NP_001004734	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I,	25	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
ZNF692	55657	broad.mit.edu	37	1	249149812	249149812	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249149812C>T	uc001ifc.1	-	8	1071	c.904G>A	c.(904-906)GCT>ACT	p.A302T	ZNF692_uc001iez.1_Missense_Mutation_p.A24T|ZNF692_uc001ifa.1_Missense_Mutation_p.A24T|ZNF692_uc001ifb.1_Missense_Mutation_p.A98T|ZNF692_uc001ifd.1_Missense_Mutation_p.A301T|ZNF692_uc001ife.1_RNA|ZNF692_uc001iff.1_Missense_Mutation_p.A257T|ZNF692_uc010pzr.1_Missense_Mutation_p.A307T	NM_017865	NP_060335	Q9BU19	ZN692_HUMAN	zinc finger protein 692 isoform 2	302					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)															---	---	---	---
TPO	7173	broad.mit.edu	37	2	1459959	1459959	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1459959G>A	uc002qww.2	+	7	815	c.724G>A	c.(724-726)GCG>ACG	p.A242T	TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Missense_Mutation_p.A242T|TPO_uc002qwr.2_Missense_Mutation_p.A242T|TPO_uc002qwx.2_Missense_Mutation_p.A242T|TPO_uc010yio.1_Missense_Mutation_p.A242T|TPO_uc010yip.1_Missense_Mutation_p.A242T	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a	242	Extracellular (Potential).				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	p.A242A(1)		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)													---	---	---	---
MBOAT2	129642	broad.mit.edu	37	2	9017344	9017344	+	Splice_Site	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9017344C>A	uc002qzg.1	-	7	640	c.507_splice	c.e7-1	p.R169_splice	MBOAT2_uc010yix.1_Splice_Site_p.R169_splice	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)																	---	---	---	---
HPCAL1	3241	broad.mit.edu	37	2	10560003	10560003	+	Silent	SNP	C	T	T	rs143370055	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10560003C>T	uc002raj.2	+	3	494	c.120C>T	c.(118-120)ACC>ACT	p.T40T	HPCAL1_uc002rak.2_Silent_p.T40T|HPCAL1_uc002ral.2_Silent_p.T40T|HPCAL1_uc010exe.2_RNA|HPCAL1_uc010exf.2_Silent_p.T40T	NM_002149	NP_002140	P37235	HPCL1_HUMAN	hippocalcin-like 1	40	EF-hand 1.						calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)														---	---	---	---
GREB1	9687	broad.mit.edu	37	2	11756801	11756801	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11756801C>T	uc002rbk.1	+	21	3667	c.3367C>T	c.(3367-3369)CGC>TGC	p.R1123C	GREB1_uc002rbp.1_Missense_Mutation_p.R121C	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1123	Ser-rich.					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)														---	---	---	---
KCNS3	3790	broad.mit.edu	37	2	18112315	18112315	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18112315G>A	uc002rcv.2	+	3	491	c.40G>A	c.(40-42)GAG>AAG	p.E14K	KCNS3_uc002rcw.2_Missense_Mutation_p.E14K	NM_002252	NP_002243	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel	14	Cytoplasmic (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)																	---	---	---	---
SDC1	6382	broad.mit.edu	37	2	20402951	20402951	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20402951C>T	uc002rdo.1	-	4	959	c.660G>A	c.(658-660)ACG>ACA	p.T220T	SDC1_uc002rdp.1_Silent_p.T220T|SDC1_uc010exv.2_Intron	NM_002997	NP_002988	P18827	SDC1_HUMAN	syndecan 1 precursor	220	Extracellular (Potential).				lipid metabolic process|lipoprotein metabolic process|myoblast development|striated muscle cell development	cytoplasm|extracellular region|focal adhesion|integral to plasma membrane	cytoskeletal protein binding|protein C-terminus binding			ovary(4)|skin(1)	5	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			OV - Ovarian serous cystadenocarcinoma(76;0.221)														---	---	---	---
KIF3C	3797	broad.mit.edu	37	2	26203351	26203351	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26203351C>T	uc002rgu.2	-	1	2093	c.1436G>A	c.(1435-1437)CGC>CAC	p.R479H	KIF3C_uc010eyj.1_RNA|KIF3C_uc010ykr.1_Missense_Mutation_p.R479H	NM_002254	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	479	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)																	---	---	---	---
EPT1	85465	broad.mit.edu	37	2	26606214	26606214	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26606214A>G	uc010ykz.1	+	7	877	c.730A>G	c.(730-732)AGA>GGA	p.R244G	EPT1_uc010eyl.1_RNA	NM_033505	NP_277040	Q9C0D9	EPT1_HUMAN	selenoprotein I	244					phospholipid biosynthetic process	integral to membrane	ethanolaminephosphotransferase activity|metal ion binding				0																		---	---	---	---
OTOF	9381	broad.mit.edu	37	2	26693574	26693574	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26693574C>T	uc002rhk.2	-	32	4037	c.3910G>A	c.(3910-3912)GAG>AAG	p.E1304K	OTOF_uc010yla.1_Missense_Mutation_p.E34K|OTOF_uc002rhh.2_Missense_Mutation_p.E537K|OTOF_uc002rhi.2_Missense_Mutation_p.E614K|OTOF_uc002rhj.2_Missense_Mutation_p.E537K	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	1304	Cytoplasmic (Potential).|Poly-Lys.				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)																	---	---	---	---
CIB4	130106	broad.mit.edu	37	2	26818194	26818194	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26818194G>A	uc002rhm.2	-							NM_001029881	NP_001025052			calcium and integrin binding family member 4								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
KCNK3	3777	broad.mit.edu	37	2	26950703	26950703	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26950703G>A	uc002rhn.2	+	2	615	c.452G>A	c.(451-453)CGC>CAC	p.R151H		NM_002246	NP_002237	O14649	KCNK3_HUMAN	potassium channel, subfamily K, member 3	151	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
DPYSL5	56896	broad.mit.edu	37	2	27150265	27150265	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27150265C>T	uc002rhu.3	+	4	723	c.565C>T	c.(565-567)CGC>TGC	p.R189C	DPYSL5_uc002rhv.3_Missense_Mutation_p.R189C	NM_020134	NP_064519	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	189					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)																	---	---	---	---
AGBL5	60509	broad.mit.edu	37	2	27278613	27278613	+	Silent	SNP	G	A	A	rs140050281		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27278613G>A	uc002rie.2	+	7	1189	c.972G>A	c.(970-972)CCG>CCA	p.P324P	AGBL5_uc002ric.2_Silent_p.P324P|AGBL5_uc002rid.2_Silent_p.P324P|AGBL5_uc002rif.2_RNA	NM_021831	NP_068603	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5 isoform 1	324					protein branching point deglutamylation|proteolysis	cytosol|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
AGBL5	60509	broad.mit.edu	37	2	27282079	27282079	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27282079C>T	uc002rie.2	+	11	2113	c.1896C>T	c.(1894-1896)TCC>TCT	p.S632S	AGBL5_uc002rid.2_Silent_p.S632S|AGBL5_uc002rif.2_RNA	NM_021831	NP_068603	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5 isoform 1	632					protein branching point deglutamylation|proteolysis	cytosol|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
IFT172	26160	broad.mit.edu	37	2	27679392	27679392	+	Silent	SNP	G	A	A	rs76787560	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27679392G>A	uc002rku.2	-	30	3408	c.3357C>T	c.(3355-3357)CAC>CAT	p.H1119H	IFT172_uc010ezb.2_5'Flank	NM_015662	NP_056477	Q9UG01	IF172_HUMAN	selective LIM binding factor homolog	1119					cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
PLB1	151056	broad.mit.edu	37	2	28825712	28825712	+	Missense_Mutation	SNP	G	A	A	rs142314104	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28825712G>A	uc002rmb.1	+	39	2698	c.2698G>A	c.(2698-2700)GTG>ATG	p.V900M	PLB1_uc010ezj.1_Missense_Mutation_p.V889M|PLB1_uc002rme.1_Translation_Start_Site|PLB1_uc002rmf.1_5'Flank	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor	900	4 X 308-326 AA approximate repeats.|Extracellular (Potential).|3.				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	29011679	29011679	+	Intron	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29011679T>C	uc002rmg.2	+						PPP1CB_uc010ymj.1_Intron|PPP1CB_uc010yml.1_Intron|PPP1CB_uc002rmh.2_Intron|SPDYA_uc002rmi.2_Intron	NM_206876	NP_996759			protein phosphatase 1, catalytic subunit, beta						cell cycle|cell division|glycogen metabolic process|triglyceride catabolic process	MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|myosin phosphatase activity|myosin-light-chain-phosphatase activity|protein binding			skin(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
C2orf71	388939	broad.mit.edu	37	2	29295029	29295029	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29295029C>A	uc002rmt.1	-	1	2099	c.2099G>T	c.(2098-2100)GGG>GTG	p.G700V		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	700					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1																		---	---	---	---
TMEM178	130733	broad.mit.edu	37	2	39931305	39931305	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39931305C>T	uc002rrt.2	+	2	510	c.485C>T	c.(484-486)ACC>ATC	p.T162I	TMEM178_uc010fam.1_Missense_Mutation_p.T162I	NM_152390	NP_689603	Q8NBL3	TM178_HUMAN	transmembrane protein 178 precursor	162	Extracellular (Potential).					integral to membrane					0		all_hematologic(82;0.248)																---	---	---	---
ABCG8	64241	broad.mit.edu	37	2	44079930	44079930	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44079930C>T	uc002rtq.2	+	6	977	c.887C>T	c.(886-888)GCG>GTG	p.A296V	ABCG8_uc010yoa.1_Missense_Mutation_p.A296V	NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8	296	ABC transporter.|Cytoplasmic (Potential).				cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45778340	45778340	+	Silent	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45778340A>C	uc002rus.2	-	12	1675	c.1599T>G	c.(1597-1599)CCT>CCG	p.P533P	SRBD1_uc010yoc.1_Silent_p.P52P	NM_018079	NP_060549	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	533					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)															---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45800478	45800478	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45800478G>A	uc002rus.2	-	9	1249	c.1173C>T	c.(1171-1173)TGC>TGT	p.C391C		NM_018079	NP_060549	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	391					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)															---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49210115	49210115	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49210115C>T	uc002rww.2	-	8	678	c.604G>A	c.(604-606)GAT>AAT	p.D202N	FSHR_uc002rwx.2_Missense_Mutation_p.D202N|FSHR_uc010fbn.2_Missense_Mutation_p.D176N	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	202	LRR 7.|Extracellular (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50318469	50318469	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50318469T>C	uc010fbp.2	-	3	1412	c.605A>G	c.(604-606)TAC>TGC	p.Y202C	NRXN1_uc002rxb.3_Missense_Mutation_p.Y909C|NRXN1_uc010fbq.2_Missense_Mutation_p.Y1277C|NRXN1_uc002rxe.3_Missense_Mutation_p.Y1237C	NM_138735	NP_620072	P58400	NRX1B_HUMAN	neurexin 1 isoform beta precursor	202	Extracellular (Potential).|Laminin G-like.				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	50573961	50573961	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50573961C>T	uc010fbp.2	-	1	934	c.127G>A	c.(127-129)GGC>AGC	p.G43S	NRXN1_uc002rxb.3_Intron|NRXN1_uc010fbq.2_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxc.1_Intron	NM_138735	NP_620072	P58400	NRX1B_HUMAN	neurexin 1 isoform beta precursor	43					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)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61441428	61441428	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61441428G>A	uc002sbe.2	-	68	8471	c.8449C>T	c.(8449-8451)CGC>TGC	p.R2817C		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	2817					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)															---	---	---	---
B3GNT2	10678	broad.mit.edu	37	2	62450427	62450427	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62450427A>G	uc002sbs.2	+	2	1310	c.1072A>G	c.(1072-1074)ATC>GTC	p.I358V		NM_006577	NP_006568	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal	358	Lumenal (Potential).					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)															---	---	---	---
ANTXR1	84168	broad.mit.edu	37	2	69409628	69409628	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69409628C>T	uc002sfg.2	+	16	1545	c.1189C>T	c.(1189-1191)CGT>TGT	p.R397C		NM_032208	NP_115584	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1 isoform 1 precursor	397	Cytoplasmic (Potential).				actin cytoskeleton reorganization|substrate adhesion-dependent cell spreading	filopodium membrane|integral to membrane|lamellipodium membrane	actin filament binding|collagen binding|metal ion binding|protein binding|transmembrane receptor activity			ovary(2)|skin(2)	4														Familial_Infantile_Hemangioma				---	---	---	---
ANXA4	307	broad.mit.edu	37	2	70039823	70039823	+	Silent	SNP	C	T	T	rs141776547		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70039823C>T	uc002sfr.3	+	8	743	c.516C>T	c.(514-516)CTC>CTT	p.L172L	ANXA4_uc010yqn.1_RNA|ANXA4_uc002sfs.3_Silent_p.L150L|ANXA4_uc010yqo.1_Silent_p.L88L	NM_001153	NP_001144	P09525	ANXA4_HUMAN	annexin IV	170					anti-apoptosis|signal transduction	cytoplasm	calcium ion binding|calcium-dependent phospholipid binding|phospholipase inhibitor activity				0																		---	---	---	---
CLEC4F	165530	broad.mit.edu	37	2	71043196	71043196	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71043196C>A	uc002shf.2	-	4	1394	c.1317G>T	c.(1315-1317)CAG>CAT	p.Q439H	CLEC4F_uc010yqv.1_Missense_Mutation_p.Q439H	NM_173535	NP_775806	Q8N1N0	CLC4F_HUMAN	C-type lectin, superfamily member 13	439	Extracellular (Potential).				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(5)	5																		---	---	---	---
VAX2	25806	broad.mit.edu	37	2	71148370	71148370	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71148370C>T	uc002shh.2	+	2	422	c.390C>T	c.(388-390)CGC>CGT	p.R130R		NM_012476	NP_036608	Q9UIW0	VAX2_HUMAN	ventral anterior homeobox 2	130	Homeobox.				ectoderm development|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
ZNF638	27332	broad.mit.edu	37	2	71591248	71591248	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71591248G>A	uc002shx.2	+	5	1902	c.1583G>A	c.(1582-1584)CGT>CAT	p.R528H	ZNF638_uc010fec.2_Missense_Mutation_p.R634H|ZNF638_uc010yqw.1_Missense_Mutation_p.R107H|ZNF638_uc002shw.2_Missense_Mutation_p.R528H|ZNF638_uc002shy.2_Missense_Mutation_p.R528H|ZNF638_uc002shz.2_Missense_Mutation_p.R528H|ZNF638_uc002sia.2_Missense_Mutation_p.R528H|ZNF638_uc002sib.1_Missense_Mutation_p.R528H|ZNF638_uc010fed.2_5'Flank	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638	528	Arg-rich.				RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4																		---	---	---	---
SLC4A5	57835	broad.mit.edu	37	2	74454683	74454683	+	Silent	SNP	G	A	A	rs142137764	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74454683G>A	uc002sko.1	-	22	2927	c.2925C>T	c.(2923-2925)ACC>ACT	p.T975T	SLC4A5_uc002skl.2_RNA|SLC4A5_uc002skn.2_Intron|SLC4A5_uc010ffc.1_Intron|SLC4A5_uc002skp.1_Intron|SLC4A5_uc002sks.1_Intron	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a	975	Cytoplasmic (Potential).					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																		---	---	---	---
LRRTM1	347730	broad.mit.edu	37	2	80529936	80529936	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80529936C>T	uc002sok.1	-	2	1279	c.1009G>A	c.(1009-1011)GAT>AAT	p.D337N	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	337	LRRCT.|Lumenal (Potential).					axon|endoplasmic reticulum membrane|growth cone|integral to membrane				ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5															HNSCC(69;0.2)			---	---	---	---
PTCD3	55037	broad.mit.edu	37	2	86355071	86355071	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86355071G>A	uc002sqw.2	+	14	1170	c.1104G>A	c.(1102-1104)TCG>TCA	p.S368S	PTCD3_uc002sqx.1_5'UTR	NM_017952	NP_060422	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3 precursor	368	PPR 6.					mitochondrion	protein binding			ovary(1)	1																		---	---	---	---
ZAP70	7535	broad.mit.edu	37	2	98351851	98351851	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98351851C>T	uc002syd.1	+	10	1428	c.1221C>T	c.(1219-1221)GCC>GCT	p.A407A	ZAP70_uc010yvf.1_3'UTR|ZAP70_uc002sye.1_Silent_p.A297A|ZAP70_uc002syf.1_Silent_p.A100A	NM_001079	NP_001070	P43403	ZAP70_HUMAN	zeta-chain associated protein kinase 70kDa	407	Protein kinase.				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																		---	---	---	---
CNGA3	1261	broad.mit.edu	37	2	99008387	99008387	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99008387G>A	uc002syt.2	+	7	1044	c.627G>A	c.(625-627)TCG>TCA	p.S209S	CNGA3_uc002syu.2_Silent_p.S191S|CNGA3_uc010fij.2_Silent_p.S213S	NM_001298	NP_001289	Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3 isoform	209					signal transduction|visual perception	integral to membrane	cGMP binding			ovary(5)|upper_aerodigestive_tract(1)	6																		---	---	---	---
LIPT1	51601	broad.mit.edu	37	2	99779031	99779031	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99779031C>T	uc002szm.3	+	4	951	c.611C>T	c.(610-612)GCC>GTC	p.A204V	MRPL30_uc002szl.1_Intron|LIPT1_uc002szn.3_Missense_Mutation_p.A204V|LIPT1_uc002szo.3_Missense_Mutation_p.A204V|LIPT1_uc002szp.3_Missense_Mutation_p.A204V|LIPT1_uc002szq.3_Missense_Mutation_p.A204V|MRPL30_uc002szr.2_Intron	NM_145198	NP_660199	Q9Y234	LIPT_HUMAN	lipoyltransferase 1 precursor	204					lipid metabolic process|protein lipoylation	mitochondrion	acyltransferase activity				0					Lipoic Acid(DB00166)													---	---	---	---
EIF5B	9669	broad.mit.edu	37	2	100013282	100013282	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100013282G>A	uc002tab.2	+	22	3498	c.3314G>A	c.(3313-3315)CGA>CAA	p.R1105Q	EIF5B_uc010yvq.1_Missense_Mutation_p.R87Q	NM_015904	NP_056988	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	1105					regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
PDCL3	79031	broad.mit.edu	37	2	101188062	101188062	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101188062T>C	uc002tao.2	+	5	491	c.379T>C	c.(379-381)TGT>CGT	p.C127R		NM_024065	NP_076970	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	127					apoptosis|interspecies interaction between organisms	cytoplasm	protein binding				0																		---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112614259	112614259	+	Intron	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112614259A>T	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	112614266	112614266	+	Intron	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112614266C>A	uc002thi.2	-							NM_022662	NP_073153			anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2																		---	---	---	---
INSIG2	51141	broad.mit.edu	37	2	118860775	118860775	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118860775G>A	uc002tlk.2	+	3	453	c.247G>A	c.(247-249)GTG>ATG	p.V83M	INSIG2_uc010yye.1_Translation_Start_Site|INSIG2_uc002tll.2_Translation_Start_Site	NM_016133	NP_057217	Q9Y5U4	INSI2_HUMAN	insulin induced protein 2	83	Helical; (Potential).				ER-nuclear sterol response pathway	SREBP-SCAP-Insig complex				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
STEAP3	55240	broad.mit.edu	37	2	120020821	120020821	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120020821C>T	uc002tlp.2	+	6	1531	c.1374C>T	c.(1372-1374)CTC>CTT	p.L458L	STEAP3_uc002tlq.2_Silent_p.L468L|STEAP3_uc002tlr.2_Silent_p.L458L|STEAP3_uc010fle.2_3'UTR	NM_018234	NP_060704	Q658P3	STEA3_HUMAN	dudulin 2 isoform b	458	Cytoplasmic (Potential).				apoptosis|cell cycle|cellular iron ion homeostasis|protein secretion|transferrin transport|transmembrane transport	endosome membrane|integral to membrane|multivesicular body	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			central_nervous_system(2)|skin(1)	3																		---	---	---	---
TMEM37	140738	broad.mit.edu	37	2	120195018	120195018	+	3'UTR	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120195018C>T	uc002tly.2	+	2						NM_183240	NP_899063			transmembrane protein 37							integral to membrane	calcium channel activity|voltage-gated ion channel activity			breast(1)	1																		---	---	---	---
INHBB	3625	broad.mit.edu	37	2	121107076	121107076	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121107076G>A	uc002tmn.2	+	2	896	c.850G>A	c.(850-852)GAC>AAC	p.D284N		NM_002193	NP_002184	P09529	INHBB_HUMAN	inhibin beta B subunit preproprotein	284					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)																---	---	---	---
CYP27C1	339761	broad.mit.edu	37	2	127958688	127958688	+	Intron	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127958688C>A	uc002tod.2	-							NM_001001665	NP_001001665			cytochrome P450, family 27, subfamily C,							membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)														---	---	---	---
IWS1	55677	broad.mit.edu	37	2	128281353	128281353	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128281353T>C	uc002ton.2	-	2	352	c.49A>G	c.(49-51)ACC>GCC	p.T17A	IWS1_uc010yzl.1_RNA|IWS1_uc010fma.2_Intron	NM_017969	NP_060439	Q96ST2	IWS1_HUMAN	IWS1 homolog	17					transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)														---	---	---	---
TUBA3E	112714	broad.mit.edu	37	2	130951399	130951399	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130951399C>T	uc002tqv.2	-	4	1117	c.1016G>A	c.(1015-1017)CGC>CAC	p.R339H		NM_207312	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	339					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	131103825	131103825	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131103825C>T	uc002tra.1	+	8	758	c.741C>T	c.(739-741)GTC>GTT	p.V247V		NM_033416	NP_219484	Q96G21	IMP4_HUMAN	IMP4, U3 small nucleolar ribonucleoprotein,	247	Brix.				rRNA processing|translation	nucleolus|ribonucleoprotein complex	aminoacyl-tRNA ligase activity|ATP binding|protein binding			central_nervous_system(2)	2	Colorectal(110;0.1)																	---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137852592	137852592	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137852592A>T	uc002tva.1	+	3	1007	c.1007A>T	c.(1006-1008)AAC>ATC	p.N336I	THSD7B_uc010zbj.1_RNA|THSD7B_uc002tvb.2_Missense_Mutation_p.N226I	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
SPOPL	339745	broad.mit.edu	37	2	139326628	139326628	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139326628G>A	uc002tvh.2	+	11	1557	c.1157G>A	c.(1156-1158)CGC>CAC	p.R386H		NM_001001664	NP_001001664	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like	386						nucleus				skin(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0296)														---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	144710386	144710386	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144710386A>C	uc002tvp.2	-	10	1434	c.1155T>G	c.(1153-1155)TGT>TGG	p.C385W	GTDC1_uc002tvo.2_Missense_Mutation_p.V337G|GTDC1_uc002tvq.2_Missense_Mutation_p.C267W|GTDC1_uc002tvr.2_Missense_Mutation_p.C300W|GTDC1_uc010fnn.2_Missense_Mutation_p.C385W|GTDC1_uc002tvs.2_Missense_Mutation_p.C353W|GTDC1_uc010fno.2_Missense_Mutation_p.C256W	NM_001006636	NP_001006637	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	385					biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)														---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148674946	148674946	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148674946G>A	uc002twg.2	+	7	1036	c.767G>A	c.(766-768)GGC>GAC	p.G256D	ACVR2A_uc010zbn.1_Missense_Mutation_p.G148D|ACVR2A_uc002twh.2_Missense_Mutation_p.G256D	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	256	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)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152521924	152521924	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152521924C>T	uc010fnx.2	-	42	5352	c.5161G>A	c.(5161-5163)GAG>AAG	p.E1721K		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	1721	Nebulin 44.				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)														---	---	---	---
FAP	2191	broad.mit.edu	37	2	163072486	163072486	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163072486C>T	uc002ucd.2	-	10	996	c.788G>A	c.(787-789)CGG>CAG	p.R263Q	FAP_uc010zct.1_Missense_Mutation_p.R238Q|FAP_uc010fpd.2_Intron|FAP_uc010fpe.1_Missense_Mutation_p.R230Q	NM_004460	NP_004451	Q12884	SEPR_HUMAN	fibroblast activation protein, alpha subunit	263	Extracellular (Potential).				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																		---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170099985	170099985	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170099985G>A	uc002ues.2	-	23	3691	c.3478C>T	c.(3478-3480)CGA>TGA	p.R1160*	LRP2_uc010zdf.1_Nonsense_Mutation_p.R1023*	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	1160	LDL-receptor class A 11.|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)													---	---	---	---
METTL8	79828	broad.mit.edu	37	2	172188335	172188335	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172188335A>G	uc010zdo.1	-	6	840	c.699T>C	c.(697-699)TCT>TCC	p.S233S	METTL8_uc002ugu.3_Silent_p.S233S|METTL8_uc002ugv.3_Silent_p.S233S|METTL8_uc002ugt.3_Silent_p.S233S|METTL8_uc002ugs.3_Silent_p.S183S|METTL8_uc010zdp.1_Silent_p.S188S	NM_024770	NP_079046	B3KW44	B3KW44_HUMAN	methyltransferase like 8	233							methyltransferase activity			ovary(1)	1																		---	---	---	---
HOXD4	3233	broad.mit.edu	37	2	177017383	177017383	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177017383T>C	uc002uks.2	+	2	730	c.481T>C	c.(481-483)TAC>CAC	p.Y161H		NM_014621	NP_055436	P09016	HXD4_HUMAN	homeobox D4	161	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)														---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179248910	179248910	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179248910G>A	uc002ulx.2	+						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)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179397385	179397385	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179397385G>A	uc010zfg.1	-	307	96477	c.96253C>T	c.(96253-96255)CGT>TGT	p.R32085C	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R25780C|TTN_uc010zfi.1_Missense_Mutation_p.R25713C|TTN_uc010zfj.1_Missense_Mutation_p.R25588C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	33012							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	179435651	179435651	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179435651C>A	uc010zfg.1	-	275	67728	c.67504G>T	c.(67504-67506)GGC>TGC	p.G22502C	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.G16197C|TTN_uc010zfi.1_Missense_Mutation_p.G16130C|TTN_uc010zfj.1_Missense_Mutation_p.G16005C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	23429							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	179499546	179499546	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179499546G>A	uc010zfg.1	-	178	34575	c.34351C>T	c.(34351-34353)CGC>TGC	p.R11451C	TTN_uc010zfh.1_Missense_Mutation_p.R5146C|TTN_uc010zfi.1_Missense_Mutation_p.R5079C|TTN_uc010zfj.1_Missense_Mutation_p.R4954C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	12378							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	179599052	179599052	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179599052A>G	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.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)															---	---	---	---
NCKAP1	10787	broad.mit.edu	37	2	183867725	183867725	+	Missense_Mutation	SNP	C	T	T	rs142669044	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183867725C>T	uc002upc.2	-	4	748	c.346G>A	c.(346-348)GTT>ATT	p.V116I	NCKAP1_uc002upb.2_Missense_Mutation_p.V122I	NM_013436	NP_038464	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1 isoform 1	116					apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)															---	---	---	---
ZSWIM2	151112	broad.mit.edu	37	2	187698688	187698688	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187698688C>T	uc002upu.1	-	6	853	c.813G>A	c.(811-813)ACG>ACA	p.T271T		NM_182521	NP_872327	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM domain containing 2	271	ZZ-type.				apoptosis		zinc ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)															---	---	---	---
PMS1	5378	broad.mit.edu	37	2	190656532	190656532	+	5'UTR	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190656532G>A	uc002urh.3	+	2					PMS1_uc010zga.1_5'UTR|PMS1_uc010zgb.1_5'UTR|PMS1_uc002urk.3_5'UTR|PMS1_uc002uri.3_5'UTR|PMS1_uc010zgc.1_5'UTR|PMS1_uc010zgd.1_5'UTR|PMS1_uc002urj.2_RNA|PMS1_uc010fry.1_5'UTR|PMS1_uc010frz.2_5'UTR|PMS1_uc010zfz.1_5'UTR	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					---	---	---	---
MFSD6	54842	broad.mit.edu	37	2	191301046	191301046	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191301046A>G	uc002urz.2	+	3	615	c.291A>G	c.(289-291)GGA>GGG	p.G97G		NM_017694	NP_060164	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing	97					transmembrane transport	integral to membrane				ovary(2)	2																		---	---	---	---
STAT1	6772	broad.mit.edu	37	2	191850352	191850352	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191850352G>A	uc002usj.2	-	15	1644	c.1256C>T	c.(1255-1257)ACG>ATG	p.T419M	STAT1_uc010fse.1_Missense_Mutation_p.T419M|STAT1_uc002usk.2_Missense_Mutation_p.T419M|STAT1_uc002usl.2_Missense_Mutation_p.T421M|STAT1_uc010fsf.1_Missense_Mutation_p.T231M	NM_007315	NP_009330	P42224	STAT1_HUMAN	signal transducer and activator of transcription	419					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)													---	---	---	---
PLCL1	5334	broad.mit.edu	37	2	198950564	198950564	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198950564A>G	uc010fsp.2	+	2	2614	c.2323A>G	c.(2323-2325)AAT>GAT	p.N775D	PLCL1_uc002uuv.3_Missense_Mutation_p.N696D	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	775	C2.				intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)													---	---	---	---
PLCL1	5334	broad.mit.edu	37	2	198950794	198950794	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198950794T>C	uc010fsp.2	+	2	2844	c.2553T>C	c.(2551-2553)AGT>AGC	p.S851S	PLCL1_uc002uuv.3_Silent_p.S772S	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	851					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)													---	---	---	---
PLCL1	5334	broad.mit.edu	37	2	199011601	199011601	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199011601C>A	uc010fsp.2	+	6	3494	c.3203C>A	c.(3202-3204)CCC>CAC	p.P1068H	PLCL1_uc002uuv.3_Missense_Mutation_p.P989H	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	1068					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)													---	---	---	---
ALS2	57679	broad.mit.edu	37	2	202625614	202625614	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202625614A>G	uc002uyo.2	-	4	1459	c.1103T>C	c.(1102-1104)GTG>GCG	p.V368A	ALS2_uc002uyp.3_Missense_Mutation_p.V368A|ALS2_uc002uyq.2_Missense_Mutation_p.V368A|ALS2_uc002uyr.2_Missense_Mutation_p.V368A	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1	368					cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7																		---	---	---	---
CREB1	1385	broad.mit.edu	37	2	208424959	208424959	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208424959C>T	uc002vcc.2	+	3	375	c.124C>T	c.(124-126)CCA>TCA	p.P42S	CREB1_uc010ziz.1_Missense_Mutation_p.P40S|CREB1_uc002vcd.2_Missense_Mutation_p.P42S|CREB1_uc010zja.1_RNA	NM_134442	NP_604391	P16220	CREB1_HUMAN	cAMP responsive element binding protein 1	42					activation of phospholipase C activity|axon guidance|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|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		protein dimerization activity|transcription cofactor activity		EWSR1/CREB1(42)	soft_tissue(42)|breast(1)|central_nervous_system(1)	44				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Bromocriptine(DB01200)|Naloxone(DB01183)			T	EWSR1	clear cell sarcoma|angiomatoid fibrous histiocytoma								---	---	---	---
IKZF2	22807	broad.mit.edu	37	2	213872376	213872376	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213872376C>A	uc002vem.2	-	8	1458	c.1289G>T	c.(1288-1290)AGG>ATG	p.R430M	IKZF2_uc010fuu.2_Missense_Mutation_p.R285M|IKZF2_uc002vej.2_Missense_Mutation_p.R377M|IKZF2_uc002vek.2_RNA|IKZF2_uc010fuv.2_Missense_Mutation_p.R356M|IKZF2_uc002vel.2_Missense_Mutation_p.R351M|IKZF2_uc010fuw.2_Missense_Mutation_p.R204M|IKZF2_uc010fux.2_Missense_Mutation_p.R204M|IKZF2_uc010fuy.2_Missense_Mutation_p.R358M|IKZF2_uc002ven.2_Missense_Mutation_p.R404M|IKZF2_uc002vei.2_Missense_Mutation_p.R208M	NM_016260	NP_057344	Q9UKS7	IKZF2_HUMAN	helios isoform 1	430					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)														---	---	---	---
SMARCAL1	50485	broad.mit.edu	37	2	217315720	217315720	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217315720G>A	uc002vgc.3	+	12	2333	c.2003G>A	c.(2002-2004)CGG>CAG	p.R668Q	SMARCAL1_uc010fvf.2_RNA|SMARCAL1_uc002vgd.3_Missense_Mutation_p.R668Q|SMARCAL1_uc010fvg.2_Missense_Mutation_p.R646Q	NM_014140	NP_054859	Q9NZC9	SMAL1_HUMAN	SWI/SNF-related matrix-associated	668					chromatin modification|DNA metabolic process|regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity			ovary(3)|breast(3)|skin(1)	7		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)										Schimke_Immuno-Osseous_Dysplasia				---	---	---	---
TNS1	7145	broad.mit.edu	37	2	218678471	218678471	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218678471C>T	uc002vgt.2	-	26	4884	c.4486G>A	c.(4486-4488)GCG>ACG	p.A1496T	TNS1_uc002vgr.2_Missense_Mutation_p.A1483T|TNS1_uc002vgs.2_Missense_Mutation_p.A1475T|TNS1_uc002vgq.2_5'UTR	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin	1496	SH2.					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)														---	---	---	---
C2orf62	375307	broad.mit.edu	37	2	219229425	219229425	+	Silent	SNP	C	T	T	rs142758364		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219229425C>T	uc002vhr.2	+	7	734	c.705C>T	c.(703-705)CAC>CAT	p.H235H	C2orf62_uc002vhs.2_Intron	NM_198559	NP_940961	Q7Z7H3	CB062_HUMAN	hypothetical protein LOC375307	235											0		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
STK36	27148	broad.mit.edu	37	2	219561885	219561885	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219561885C>A	uc002viu.2	+	23	2976	c.2710C>A	c.(2710-2712)CTA>ATA	p.L904I	STK36_uc002viv.2_Missense_Mutation_p.L883I|STK36_uc002viw.2_Missense_Mutation_p.L82I|STK36_uc002vix.2_5'UTR	NM_015690	NP_056505	Q9NRP7	STK36_HUMAN	serine/threonine kinase 36	904					cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	11		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)														---	---	---	---
CCDC108	255101	broad.mit.edu	37	2	219893021	219893021	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219893021G>A	uc002vjl.1	-	12	1837	c.1753C>T	c.(1753-1755)CGG>TGG	p.R585W	CCDC108_uc010fwa.1_Missense_Mutation_p.R28W|CCDC108_uc010zkp.1_Missense_Mutation_p.R574W|CCDC108_uc010zkq.1_Missense_Mutation_p.R520W	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	585						integral to membrane	structural molecule activity			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
ACSL3	2181	broad.mit.edu	37	2	223791754	223791754	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223791754C>T	uc002vni.2	+	12	1763	c.1312C>T	c.(1312-1314)CGA>TGA	p.R438*	ACSL3_uc002vnj.2_Nonsense_Mutation_p.R438*	NM_004457	NP_004448	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	438	Cytoplasmic (Potential).				long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|fatty-acyl-CoA synthase activity|long-chain fatty acid-CoA ligase activity|protein binding			ovary(2)	2		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)			T	ETV1	prostate								---	---	---	---
KIAA1486	57624	broad.mit.edu	37	2	226447629	226447629	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226447629C>T	uc002voe.2	+	4	1671	c.1496C>T	c.(1495-1497)CCG>CTG	p.P499L	KIAA1486_uc010fxa.1_Intron|KIAA1486_uc002vof.1_Missense_Mutation_p.P269L	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624	499										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)														---	---	---	---
ALPI	248	broad.mit.edu	37	2	233322044	233322044	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233322044G>A	uc002vst.3	+						ALPI_uc002vsu.3_Intron	NM_001631	NP_001622			intestinal alkaline phosphatase precursor						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)														---	---	---	---
ALPI	248	broad.mit.edu	37	2	233323610	233323610	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233323610G>A	uc002vst.3	+	11	1418	c.1341G>A	c.(1339-1341)TCG>TCA	p.S447S	ALPI_uc002vsu.3_Silent_p.S358S	NM_001631	NP_001622	P09923	PPBI_HUMAN	intestinal alkaline phosphatase precursor	447					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)														---	---	---	---
CHRND	1144	broad.mit.edu	37	2	233393281	233393281	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233393281C>T	uc002vsw.2	+	5	428	c.424C>T	c.(424-426)CTG>TTG	p.L142L	CHRND_uc010zmg.1_Silent_p.L127L|CHRND_uc010fyc.2_Silent_p.G51G|CHRND_uc010zmh.1_Silent_p.G51G	NM_000751	NP_000742	Q07001	ACHD_HUMAN	nicotinic acetylcholine receptor delta	142	Extracellular (Potential).				muscle contraction|musculoskeletal movement|neuromuscular process|skeletal muscle tissue growth|synaptic transmission	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	nicotinic acetylcholine-activated cation-selective channel activity|receptor activity			ovary(1)|breast(1)|skin(1)	3		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;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238233452	238233452	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238233452C>T	uc002vwl.2	-	44	9784	c.9499G>A	c.(9499-9501)GCC>ACC	p.A3167T	COL6A3_uc002vwo.2_Missense_Mutation_p.A2961T|COL6A3_uc010znj.1_Missense_Mutation_p.A2560T|COL6A3_uc002vwj.2_Missense_Mutation_p.A548T	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	3167	Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238253700	238253700	+	Splice_Site	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238253700C>T	uc002vwl.2	-	34	7447	c.7162_splice	c.e34+1	p.P2388_splice	COL6A3_uc002vwo.2_Splice_Site_p.P2182_splice|COL6A3_uc010znj.1_Splice_Site_p.P1781_splice|COL6A3_uc002vwj.2_5'Flank|COL6A3_uc002vwp.1_Splice_Site_p.P209_splice	NM_004369	NP_004360			alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238277739	238277739	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238277739C>T	uc002vwl.2	-	10	4652	c.4367G>A	c.(4366-4368)CGA>CAA	p.R1456Q	COL6A3_uc002vwo.2_Missense_Mutation_p.R1250Q|COL6A3_uc010znj.1_Missense_Mutation_p.R849Q	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1456	VWFA 8.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
MYEOV2	150678	broad.mit.edu	37	2	241066179	241066179	+	Missense_Mutation	SNP	C	T	T	rs140948790		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241066179C>T	uc002vyu.1	-	5	560	c.560G>A	c.(559-561)CGG>CAG	p.R187Q		NM_138336	NP_612209	Q8WXC6	MYOV2_HUMAN	hypothetical protein LOC150678 isoform 1	Error:Variant_position_missing_in_Q8WXC6_after_alignment											0		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)														---	---	---	---
ANKMY1	51281	broad.mit.edu	37	2	241492466	241492466	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241492466A>G	uc002vyz.1	-	3	307	c.78T>C	c.(76-78)CAT>CAC	p.H26H	ANKMY1_uc002vza.1_Silent_p.H115H|ANKMY1_uc010fzd.1_Silent_p.H115H|ANKMY1_uc002vzb.1_Silent_p.H115H|ANKMY1_uc002vzc.1_Silent_p.H115H|ANKMY1_uc002vzd.1_Silent_p.H115H|ANKMY1_uc010fze.1_Intron|ANKMY1_uc002vze.2_Silent_p.H17H|ANKMY1_uc002vzf.2_Silent_p.H17H	NM_016552	NP_057636	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	26	MORN 2.						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)														---	---	---	---
GPR35	2859	broad.mit.edu	37	2	241569453	241569453	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241569453C>T	uc002vzs.1	+	1	659	c.84C>T	c.(82-84)GGC>GGT	p.G28G	GPR35_uc010fzh.1_Silent_p.G59G|GPR35_uc010fzi.1_Silent_p.G59G	NM_005301	NP_005292	Q9HC97	GPR35_HUMAN	G protein-coupled receptor 35	28	Helical; Name=1; (Potential).					integral to plasma membrane	G-protein coupled receptor activity			skin(2)|pancreas(1)	3		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;5.29e-32)|all cancers(36;1.38e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.02e-06)|Lung(119;0.00163)|Colorectal(34;0.00463)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.031)														---	---	---	---
C2orf54	79919	broad.mit.edu	37	2	241831149	241831149	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241831149C>T	uc002wae.3	-	2	705	c.546G>A	c.(544-546)GAG>GAA	p.E182E	C2orf54_uc002wac.2_Silent_p.E14E|C2orf54_uc002wad.2_Silent_p.E33E	NM_001085437	NP_001078906	Q08AI8	CB054_HUMAN	hypothetical protein LOC79919 isoform 1	182											0		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)														---	---	---	---
STK25	10494	broad.mit.edu	37	2	242439681	242439681	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242439681G>T	uc002wbm.2	-	4	605	c.334C>A	c.(334-336)CTG>ATG	p.L112M	STK25_uc002wbk.2_5'Flank|STK25_uc002wbl.2_5'Flank|STK25_uc002wbn.2_Missense_Mutation_p.L112M|STK25_uc002wbo.2_Missense_Mutation_p.L35M|STK25_uc010zos.1_Missense_Mutation_p.L18M|STK25_uc010zot.1_Missense_Mutation_p.L38M|STK25_uc002wbp.2_Missense_Mutation_p.L112M|STK25_uc010fzo.2_Missense_Mutation_p.L35M|STK25_uc010zou.1_Missense_Mutation_p.L18M|STK25_uc010zov.1_Missense_Mutation_p.L18M|STK25_uc010zow.1_Missense_Mutation_p.L112M	NM_006374	NP_006365	O00506	STK25_HUMAN	serine/threonine kinase 25	112	Protein kinase.				response to oxidative stress|signal transduction	Golgi apparatus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity				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;8.24e-34)|all cancers(36;3.46e-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;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)														---	---	---	---
C2orf85	285093	broad.mit.edu	37	2	242815105	242815105	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242815105G>A	uc010fzu.1	+	2	1421	c.1398G>A	c.(1396-1398)ACG>ACA	p.T466T		NM_173821	NP_776182	Q14D33	CB085_HUMAN	hypothetical protein LOC285093	466						integral to membrane				ovary(1)	1																		---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7503408	7503408	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7503408A>T	uc003bqm.2	+	7	1788	c.1514A>T	c.(1513-1515)AAT>ATT	p.N505I	GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Missense_Mutation_p.N505I|GRM7_uc003bql.2_Missense_Mutation_p.N505I|GRM7_uc003bqn.1_Missense_Mutation_p.N88I|GRM7_uc010hch.1_5'UTR	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a	505	Extracellular (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16358730	16358730	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16358730G>A	uc003cay.2	-	10	1624	c.1342C>T	c.(1342-1344)CGA>TGA	p.R448*	RFTN1_uc010hes.2_Nonsense_Mutation_p.R412*|OXNAD1_uc003cax.2_Intron|OXNAD1_uc011awb.1_Intron	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein	448						plasma membrane		p.R448*(1)		ovary(3)|central_nervous_system(1)	4																		---	---	---	---
PLCL2	23228	broad.mit.edu	37	3	17051544	17051544	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17051544G>A	uc011awc.1	+	5	787	c.682G>A	c.(682-684)GCA>ACA	p.A228T	PLCL2_uc010het.1_Missense_Mutation_p.A110T|PLCL2_uc011awd.1_Missense_Mutation_p.A110T	NM_001144382	NP_001137854	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2 isoform 1	236	PH.				intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
RAB5A	5868	broad.mit.edu	37	3	20025266	20025266	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20025266A>G	uc003cbn.2	+	6	1134	c.599A>G	c.(598-600)GAC>GGC	p.D200G	RAB5A_uc010hey.2_RNA|RAB5A_uc011awg.1_Missense_Mutation_p.D186G|C3orf48_uc010hez.2_Intron	NM_004162	NP_004153	P20339	RAB5A_HUMAN	RAB5A, member RAS oncogene family	200					blood coagulation|protein transport|receptor internalization|regulation of filopodium assembly|small GTPase mediated signal transduction	early endosome membrane|melanosome|plasma membrane	GDP binding|GTP binding|GTPase activity				0																		---	---	---	---
KAT2B	8850	broad.mit.edu	37	3	20153198	20153198	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20153198G>A	uc003cbq.2	+	6	1408	c.962G>A	c.(961-963)CGA>CAA	p.R321Q		NM_003884	NP_003875	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	321					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																		---	---	---	---
SGOL1	151648	broad.mit.edu	37	3	20225413	20225413	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20225413C>T	uc003cbs.2	-	2	294	c.107G>A	c.(106-108)CGC>CAC	p.R36H	SGOL1_uc003cbr.2_Missense_Mutation_p.R36H|SGOL1_uc010hfa.2_Missense_Mutation_p.R36H|SGOL1_uc003cbt.2_Missense_Mutation_p.R36H|SGOL1_uc003cbu.2_Missense_Mutation_p.R36H|SGOL1_uc003cbv.2_Missense_Mutation_p.R36H|SGOL1_uc003cbw.2_Missense_Mutation_p.R36H|SGOL1_uc003cbx.2_Missense_Mutation_p.R36H|SGOL1_uc003cby.2_Missense_Mutation_p.R36H|SGOL1_uc003cbz.2_Missense_Mutation_p.R36H|SGOL1_uc003cca.2_Missense_Mutation_p.R36H|SGOL1_uc003ccb.2_Missense_Mutation_p.R36H|SGOL1_uc003ccc.2_Missense_Mutation_p.R36H	NM_001012410	NP_001012410	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 isoform A2	36	Potential.|Necessary for interaction with PPP2CA and PPP2R1A.				attachment of spindle microtubules to kinetochore|cell division|centriole-centriole cohesion|meiotic chromosome segregation|mitotic prometaphase	centrosome|condensed chromosome kinetochore|cytosol|mitotic cohesin complex|spindle pole	protein binding				0																		---	---	---	---
PDCD6IP	10015	broad.mit.edu	37	3	33877588	33877588	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33877588A>T	uc003cfx.2	+	8	1042	c.887A>T	c.(886-888)AAT>ATT	p.N296I	PDCD6IP_uc003cfy.2_Missense_Mutation_p.N301I|PDCD6IP_uc011axw.1_Missense_Mutation_p.N77I	NM_013374	NP_037506	Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	296	Interaction with EIAV p9.|Interaction with CHMP4A, CHMP4B and CHMP4C.|BRO1.				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																		---	---	---	---
LRRFIP2	9209	broad.mit.edu	37	3	37170567	37170567	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37170567C>T	uc003cgp.2	-	4	587	c.164G>A	c.(163-165)CGA>CAA	p.R55Q	LRRFIP2_uc011ayf.1_Missense_Mutation_p.R55Q|LRRFIP2_uc003cgr.2_Missense_Mutation_p.R55Q|LRRFIP2_uc003cgs.3_Missense_Mutation_p.R55Q|LRRFIP2_uc003cgt.3_Missense_Mutation_p.R55Q	NM_006309	NP_006300	Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting	55	DVL3-binding.				Wnt receptor signaling pathway		LRR domain binding			ovary(1)	1																		---	---	---	---
XYLB	9942	broad.mit.edu	37	3	38414150	38414150	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38414150C>T	uc003cic.2	+	10	879	c.770C>T	c.(769-771)GCC>GTC	p.A257V	XYLB_uc011ayp.1_Missense_Mutation_p.A120V|XYLB_uc003cid.1_Missense_Mutation_p.A179V	NM_005108	NP_005099	O75191	XYLB_HUMAN	xylulokinase	257					D-xylose metabolic process|generation of precursor metabolites and energy|xylulose catabolic process		ATP binding|xylulokinase activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)														---	---	---	---
RPSA	3921	broad.mit.edu	37	3	39453213	39453213	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39453213G>A	uc003cjp.2	+	5	657	c.572G>A	c.(571-573)CGT>CAT	p.R191H	RPSA_uc003cjq.2_Missense_Mutation_p.R196H|RPSA_uc003cjr.2_Missense_Mutation_p.R191H|RPSA_uc003cjt.2_RNA	NM_002295	NP_002286	P08865	RSSA_HUMAN	ribosomal protein SA	191					cell adhesion|endocrine pancreas development|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 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|ribosomal small subunit assembly|rRNA export from nucleus|translational elongation|translational termination|viral transcription	90S preribosome|cytosolic small ribosomal subunit|nucleus|plasma membrane	protein binding|receptor activity|ribosome binding|structural constituent of ribosome			lung(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0509)|Kidney(284;0.064)														---	---	---	---
ANO10	55129	broad.mit.edu	37	3	43616359	43616359	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43616359A>G	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																		---	---	---	---
ZNF167	55888	broad.mit.edu	37	3	44612793	44612793	+	Missense_Mutation	SNP	C	T	T	rs148767433		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44612793C>T	uc010hin.2	+	6	2579	c.2191C>T	c.(2191-2193)CGT>TGT	p.R731C	ZNF167_uc003cni.2_Intron|ZNF167_uc010hio.2_Intron|ZNF167_uc003cnj.2_Missense_Mutation_p.R731C|ZNF167_uc003cnk.2_Intron	NM_018651	NP_061121	Q9P0L1	ZN167_HUMAN	zinc finger protein 167 isoform 1	731	C2H2-type 13.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(197;0.0486)|Kidney(197;0.0609)														---	---	---	---
PTH1R	5745	broad.mit.edu	37	3	46943318	46943318	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46943318C>T	uc003cqm.2	+	13	1382	c.1179C>T	c.(1177-1179)AAC>AAT	p.N393N	PTH1R_uc003cqn.2_Silent_p.N393N	NM_000316	NP_000307	Q03431	PTH1R_HUMAN	parathyroid hormone receptor 1 precursor	393	Cytoplasmic (Potential).					cytoplasm|integral to plasma membrane|nucleus	parathyroid hormone receptor activity|peptide hormone binding|protein self-association			breast(1)	1														Ollier_disease_/_Maffuci_syndrome				---	---	---	---
NBEAL2	23218	broad.mit.edu	37	3	47050494	47050494	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47050494G>A	uc003cqp.2	+	53	8222	c.8043G>A	c.(8041-8043)GCG>GCA	p.A2681A	NRADDP_uc011bas.1_5'Flank|NBEAL2_uc010hjm.1_Silent_p.A2058A|NBEAL2_uc010hjn.1_Silent_p.A1047A|NBEAL2_uc010hjo.1_Silent_p.A241A	NM_015175	NP_055990	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2681							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)														---	---	---	---
ARIH2	10425	broad.mit.edu	37	3	49004710	49004710	+	Splice_Site	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49004710T>C	uc003cvb.2	+	6	850	c.538_splice	c.e6+2	p.G180_splice	ARIH2_uc003cvc.2_Splice_Site_p.G180_splice|ARIH2_uc003cvf.2_Splice_Site_p.G98_splice|ARIH2_uc010hkl.2_Splice_Site_p.G180_splice	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)														---	---	---	---
LAMB2	3913	broad.mit.edu	37	3	49159606	49159606	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49159606G>A	uc003cwe.2	-	28	5070	c.4771C>T	c.(4771-4773)CGG>TGG	p.R1591W	USP19_uc003cvz.3_5'Flank|USP19_uc011bcg.1_5'Flank|USP19_uc003cwb.2_5'Flank|USP19_uc003cwd.1_5'Flank|USP19_uc011bch.1_5'Flank|USP19_uc011bci.1_5'Flank	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	1591	Potential.|Domain I.				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)														---	---	---	---
CCDC36	339834	broad.mit.edu	37	3	49292817	49292817	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49292817A>G	uc003cwk.2	+						CCDC36_uc011bck.1_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)														---	---	---	---
AMIGO3	386724	broad.mit.edu	37	3	49756307	49756307	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49756307T>C	uc003cxj.2	-	1	932	c.592A>G	c.(592-594)ATC>GTC	p.I198V	RNF123_uc003cxh.2_Intron|RNF123_uc003cxi.2_Intron	NM_198722	NP_942015	Q86WK7	AMGO3_HUMAN	adhesion molecule with Ig-like domain 3	198	Extracellular (Potential).|LRR 6.				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)	---	---	---	---
CAMKV	79012	broad.mit.edu	37	3	49897038	49897038	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49897038C>T	uc003cxt.1	-	11	1412	c.1219G>A	c.(1219-1221)GAT>AAT	p.D407N	CAMKV_uc011bcy.1_Missense_Mutation_p.D332N|CAMKV_uc003cxv.1_Missense_Mutation_p.D379N|CAMKV_uc003cxw.1_Missense_Mutation_p.D239N|CAMKV_uc003cxx.1_Missense_Mutation_p.D239N|CAMKV_uc003cxu.2_Missense_Mutation_p.D376N|CAMKV_uc011bcz.1_Missense_Mutation_p.D339N|CAMKV_uc011bda.1_Missense_Mutation_p.D333N	NM_024046	NP_076951	Q8NCB2	CAMKV_HUMAN	CaM kinase-like vesicle-associated	407	Ala-rich.					cytoplasmic vesicle membrane|plasma membrane	ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|large_intestine(2)|central_nervous_system(1)	7				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)														---	---	---	---
RBM6	10180	broad.mit.edu	37	3	50099537	50099537	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50099537C>T	uc003cyc.2	+	15	2715	c.2582C>T	c.(2581-2583)ACG>ATG	p.T861M	RBM6_uc010hlc.1_Missense_Mutation_p.T380M|RBM6_uc003cyd.2_Missense_Mutation_p.T339M|RBM6_uc003cye.2_Missense_Mutation_p.T339M|RBM6_uc011bdi.1_Missense_Mutation_p.T203M|RBM6_uc010hld.1_RNA|RBM6_uc010hle.1_RNA|RBM6_uc010hlf.1_RNA	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6	861					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)														---	---	---	---
SEMA3F	6405	broad.mit.edu	37	3	50211341	50211341	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50211341C>T	uc003cyj.2	+	3	426	c.228C>T	c.(226-228)TAC>TAT	p.Y76Y	SEMA3F_uc003cyk.2_Silent_p.Y76Y	NM_004186	NP_004177	Q13275	SEM3F_HUMAN	semaphorin 3F precursor	76	Sema.				axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)														---	---	---	---
RASSF1	11186	broad.mit.edu	37	3	50369011	50369011	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50369011G>A	uc003dad.1	-	4	882	c.751C>T	c.(751-753)CGC>TGC	p.R251C	RASSF1_uc003daa.1_Missense_Mutation_p.R96C|RASSF1_uc003dab.1_Missense_Mutation_p.R177C|RASSF1_uc003dac.2_Missense_Mutation_p.R96C|RASSF1_uc003dae.1_Missense_Mutation_p.R247C|RASSF1_uc010hlk.1_RNA|RASSF1_uc003daf.1_Missense_Mutation_p.R96C	NM_170714	NP_733832	Q9NS23	RASF1_HUMAN	Ras association domain family 1 isoform D	251	Ras-associating.				cell cycle arrest|negative regulation of cell cycle arrest|positive regulation of protein ubiquitination|protein stabilization|Ras protein signal transduction|response to DNA damage stimulus	microtubule|microtubule cytoskeleton|microtubule organizing center|nucleus|spindle pole	identical protein binding|protein binding|protein N-terminus binding|zinc ion binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000278)|OV - Ovarian serous cystadenocarcinoma(275;0.0015)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)														---	---	---	---
NISCH	11188	broad.mit.edu	37	3	52522196	52522196	+	Silent	SNP	G	A	A	rs113789685		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52522196G>A	uc011beg.1	+	17	2760	c.2688G>A	c.(2686-2688)GCG>GCA	p.A896A	NISCH_uc003ded.3_Silent_p.A896A|NISCH_uc003dee.3_Silent_p.A385A|NISCH_uc003deg.1_RNA|NISCH_uc003deh.3_5'Flank	NM_007184	NP_009115	Q9Y2I1	NISCH_HUMAN	nischarin	896					apoptosis|cell communication	cytosol|early endosome|plasma membrane|recycling endosome	phosphatidylinositol binding|receptor activity			ovary(3)|central_nervous_system(1)	4				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)														---	---	---	---
STAB1	23166	broad.mit.edu	37	3	52557277	52557277	+	Missense_Mutation	SNP	G	A	A	rs137992546		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52557277G>A	uc003dej.2	+	64	7134	c.7060G>A	c.(7060-7062)GAC>AAC	p.D2354N	STAB1_uc003dek.1_Missense_Mutation_p.D369N|STAB1_uc003del.2_Missense_Mutation_p.D241N	NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	2354	Extracellular (Potential).|FAS1 7.				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52595936	52595936	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52595936G>A	uc003des.2	-	25	4147	c.4135C>T	c.(4135-4137)CGG>TGG	p.R1379W	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.R1379W|PBRM1_uc003der.2_Missense_Mutation_p.R1347W|PBRM1_uc003det.2_Missense_Mutation_p.R1394W|PBRM1_uc003deu.2_Missense_Mutation_p.R1394W|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.R1379W|PBRM1_uc010hmk.1_Missense_Mutation_p.R1354W|PBRM1_uc003dey.2_Missense_Mutation_p.R1327W|PBRM1_uc003dez.1_Missense_Mutation_p.R1378W	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1379	HMG box.				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								---	---	---	---
SFMBT1	51460	broad.mit.edu	37	3	52941285	52941285	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52941285C>A	uc003dgf.2	-	20	2700	c.2131G>T	c.(2131-2133)GAT>TAT	p.D711Y	SFMBT1_uc010hmr.2_Missense_Mutation_p.D658Y|SFMBT1_uc003dgg.2_Missense_Mutation_p.D711Y|SFMBT1_uc003dgh.2_Missense_Mutation_p.D711Y	NM_001005159	NP_001005159	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1	711					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)														---	---	---	---
CADPS	8618	broad.mit.edu	37	3	62477973	62477973	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62477973C>T	uc003dll.2	-	20	3236	c.2876G>A	c.(2875-2877)CGT>CAT	p.R959H	CADPS_uc003dlk.1_Missense_Mutation_p.R456H|CADPS_uc003dlm.2_Missense_Mutation_p.R969H|CADPS_uc003dln.2_Missense_Mutation_p.R929H	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1	959	MHD1.|Interaction with DRD2.				exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)														---	---	---	---
PDZRN3	23024	broad.mit.edu	37	3	73432742	73432742	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73432742C>T	uc003dpl.1	-	10	3071	c.2975G>A	c.(2974-2976)CGC>CAC	p.R992H	PDZRN3_uc011bgh.1_Missense_Mutation_p.R649H|PDZRN3_uc010hoe.1_Missense_Mutation_p.R690H|PDZRN3_uc011bgf.1_Missense_Mutation_p.R709H|PDZRN3_uc011bgg.1_Missense_Mutation_p.R712H	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	992	Potential.						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	73432975	73432975	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73432975C>T	uc003dpl.1	-	10	2838	c.2742G>A	c.(2740-2742)CCG>CCA	p.P914P	PDZRN3_uc011bgh.1_Silent_p.P571P|PDZRN3_uc010hoe.1_Silent_p.P612P|PDZRN3_uc011bgf.1_Silent_p.P631P|PDZRN3_uc011bgg.1_Silent_p.P634P	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	914							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)														---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	78685077	78685077	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78685077G>A	uc003dqe.2	-	23	3427	c.3219C>T	c.(3217-3219)TAC>TAT	p.Y1073Y	ROBO1_uc003dqb.2_Silent_p.Y1034Y|ROBO1_uc003dqc.2_Silent_p.Y973Y|ROBO1_uc003dqd.2_Silent_p.Y1028Y|ROBO1_uc010hoh.2_Silent_p.Y265Y|ROBO1_uc011bgl.1_Silent_p.Y645Y	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	1073	Cytoplasmic (Potential).				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)														---	---	---	---
C3orf26	84319	broad.mit.edu	37	3	99890707	99890707	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99890707C>T	uc003dtl.2	+	7	686	c.543C>T	c.(541-543)GAC>GAT	p.D181D		NM_032359	NP_115735	Q9BQ75	CC026_HUMAN	hypothetical protein LOC84319	181							ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(1)	1																		---	---	---	---
DPPA4	55211	broad.mit.edu	37	3	109050737	109050737	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109050737T>C	uc003dxq.3	-	3	375	c.320A>G	c.(319-321)AAG>AGG	p.K107R	DPPA4_uc011bho.1_Missense_Mutation_p.K107R|DPPA4_uc011bhp.1_Missense_Mutation_p.K107R	NM_018189	NP_060659	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	107						nucleus	protein binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
GSK3B	2932	broad.mit.edu	37	3	119631658	119631658	+	Splice_Site	SNP	C	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119631658C>G	uc003edo.2	-	6	1592	c.609_splice	c.e6-1	p.S203_splice	GSK3B_uc003edn.2_Splice_Site_p.S203_splice	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)													---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	120760631	120760631	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120760631A>G	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	121206524	121206524	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121206524T>A	uc003eee.3	-	16	5383	c.5254A>T	c.(5254-5256)ATT>TTT	p.I1752F	POLQ_uc003eed.2_Missense_Mutation_p.I924F	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	1752					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)					---	---	---	---
POLQ	10721	broad.mit.edu	37	3	121230875	121230875	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121230875G>A	uc003eee.3	-	10	1599	c.1470C>T	c.(1468-1470)GGC>GGT	p.G490G		NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	490	Helicase C-terminal.				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)					---	---	---	---
ADCY5	111	broad.mit.edu	37	3	123051470	123051470	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123051470C>T	uc003egh.1	-	4	1459	c.1459G>A	c.(1459-1461)GCA>ACA	p.A487T	ADCY5_uc003egg.1_Missense_Mutation_p.A120T|ADCY5_uc003egi.1_Missense_Mutation_p.A46T	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5	487	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)														---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123427553	123427553	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123427553G>A	uc003ego.2	-	15	2414	c.2132C>T	c.(2131-2133)ACG>ATG	p.T711M	MYLK_uc011bjw.1_Missense_Mutation_p.T711M|MYLK_uc003egp.2_Missense_Mutation_p.T642M|MYLK_uc003egq.2_Missense_Mutation_p.T711M|MYLK_uc003egr.2_Missense_Mutation_p.T642M|MYLK_uc003egs.2_Missense_Mutation_p.T535M	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	711	Ig-like C2-type 5.				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)														---	---	---	---
ITGB5	3693	broad.mit.edu	37	3	124485139	124485139	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124485139C>T	uc003eho.2	-	13	2368	c.2071G>A	c.(2071-2073)GTC>ATC	p.V691I	ITGB5_uc010hrx.2_RNA	NM_002213	NP_002204	P18084	ITB5_HUMAN	integrin, beta 5 precursor	691	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)														---	---	---	---
KLF15	28999	broad.mit.edu	37	3	126062587	126062587	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126062587C>T	uc011bkk.1	-	3	1416	c.1234G>A	c.(1234-1236)GTG>ATG	p.V412M		NM_014079	NP_054798	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	412						nucleus	DNA binding|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(114;0.147)														---	---	---	---
XRN1	54464	broad.mit.edu	37	3	142122802	142122802	+	Missense_Mutation	SNP	C	T	T	rs138660782		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142122802C>T	uc003eus.2	-	17	1980	c.1913G>A	c.(1912-1914)CGT>CAT	p.R638H	XRN1_uc010huu.2_Missense_Mutation_p.R104H|XRN1_uc003eut.2_Missense_Mutation_p.R638H|XRN1_uc003euu.2_Missense_Mutation_p.R638H|XRN1_uc003euv.1_Missense_Mutation_p.R499H	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1 isoform a	638					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																		---	---	---	---
PAQR9	344838	broad.mit.edu	37	3	142681763	142681763	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142681763G>A	uc003evg.2	-	1	416	c.416C>T	c.(415-417)GCG>GTG	p.A139V	PAQR9_uc003evf.1_5'Flank	NM_198504	NP_940906	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	139	Cytoplasmic (Potential).					integral to membrane	receptor activity				0																		---	---	---	---
PLSCR1	5359	broad.mit.edu	37	3	146254325	146254325	+	Splice_Site	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146254325A>C	uc003evx.3	-	2	401	c.13_splice	c.e2+1	p.N5_splice	PLSCR1_uc003evy.3_Intron|PLSCR1_uc011bnn.1_Splice_Site|PLSCR1_uc003evz.3_Splice_Site|PLSCR1_uc003ewa.2_Splice_Site_p.N5_splice	NM_021105	NP_066928			phospholipid scramblase 1						phospholipid scrambling|platelet activation|response to virus	integral to membrane|plasma membrane	calcium ion binding|phospholipid scramblase activity|SH3 domain binding			ovary(2)	2																		---	---	---	---
AADACL2	344752	broad.mit.edu	37	3	151458608	151458608	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151458608C>T	uc003ezc.2	+	2	433	c.313C>T	c.(313-315)CGA>TGA	p.R105*	AADACL2_uc010hvn.2_Intron	NM_207365	NP_997248	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2 precursor	105						extracellular region|integral to membrane	carboxylesterase activity				0			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)															---	---	---	---
DHX36	170506	broad.mit.edu	37	3	154007599	154007599	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154007599A>T	uc003ezy.3	-	16	1912	c.1831T>A	c.(1831-1833)TGC>AGC	p.C611S	DHX36_uc010hvq.2_Missense_Mutation_p.C597S|DHX36_uc003ezz.3_Missense_Mutation_p.C611S	NM_020865	NP_065916	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	611	Helicase C-terminal.					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	155301426	155301426	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155301426G>A	uc011bok.1	-	5	847	c.570C>T	c.(568-570)GCC>GCT	p.A190A	PLCH1_uc011boj.1_Silent_p.A190A|PLCH1_uc011bol.1_Silent_p.A172A	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	190	EF-hand 2.				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)															---	---	---	---
LEKR1	389170	broad.mit.edu	37	3	156763551	156763551	+	3'UTR	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156763551G>T	uc003fba.1	+	14						NM_001004316	NP_001004316			leucine, glutamate and lysine rich 1												0			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
RARRES1	5918	broad.mit.edu	37	3	158428614	158428614	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158428614C>T	uc003fci.2	-	3	519	c.448G>A	c.(448-450)GAG>AAG	p.E150K	RARRES1_uc003fcj.2_Missense_Mutation_p.E150K	NM_206963	NP_996846	P49788	TIG1_HUMAN	retinoic acid receptor responder (tazarotene	150	Extracellular (Potential).				negative regulation of cell proliferation	integral to membrane					0			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)													---	---	---	---
ZBBX	79740	broad.mit.edu	37	3	167077712	167077712	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167077712T>G	uc003fep.2	-	8	701	c.378A>C	c.(376-378)AAA>AAC	p.K126N	ZBBX_uc011bpc.1_Missense_Mutation_p.K126N|ZBBX_uc003feq.2_Missense_Mutation_p.K97N	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	126						intracellular	zinc ion binding			ovary(2)	2																		---	---	---	---
SLC7A14	57709	broad.mit.edu	37	3	170204127	170204127	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170204127C>T	uc003fgz.2	-	5	1106	c.790G>A	c.(790-792)GCT>ACT	p.A264T	CLDN11_uc011bpt.1_Intron|uc003fha.1_Intron	NM_020949	NP_066000	Q8TBB6	S7A14_HUMAN	solute carrier family 7 (cationic amino acid	264	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)															---	---	---	---
SLC7A14	57709	broad.mit.edu	37	3	170218991	170218991	+	Missense_Mutation	SNP	C	T	T	rs146405741		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170218991C>T	uc003fgz.2	-	3	764	c.448G>A	c.(448-450)GGA>AGA	p.G150R	CLDN11_uc011bpt.1_Intron|uc003fha.1_Intron	NM_020949	NP_066000	Q8TBB6	S7A14_HUMAN	solute carrier family 7 (cationic amino acid	150						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)															---	---	---	---
MCCC1	56922	broad.mit.edu	37	3	182743546	182743546	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182743546C>T	uc003fle.2	-	15	1865	c.1728G>A	c.(1726-1728)ATG>ATA	p.M576I	MCCC1_uc010hxi.2_RNA|MCCC1_uc011bqo.1_Intron|MCCC1_uc003flf.2_Missense_Mutation_p.M459I|MCCC1_uc003flg.2_Missense_Mutation_p.M467I|MCCC1_uc011bqp.1_Missense_Mutation_p.M529I	NM_020166	NP_064551	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	576					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)													---	---	---	---
EIF2B5	8893	broad.mit.edu	37	3	183860016	183860016	+	Intron	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183860016T>C	uc003fmp.2	+						EIF2B5_uc003fmq.2_Intron|EIF2B5_uc003fmr.2_5'Flank	NM_003907	NP_003898			eukaryotic translation initiation factor 2B,						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)															---	---	---	---
AP2M1	1173	broad.mit.edu	37	3	183896808	183896808	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183896808G>A	uc011bqx.1	+	3	395	c.238G>A	c.(238-240)GAA>AAA	p.E80K	AP2M1_uc003fmw.2_Missense_Mutation_p.E80K|AP2M1_uc003fmx.2_Missense_Mutation_p.E80K|AP2M1_uc003fmy.2_Missense_Mutation_p.E80K|AP2M1_uc011bqy.1_5'Flank|AP2M1_uc011bqz.1_5'Flank	NM_004068	NP_004059	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	80					axon guidance|cellular membrane organization|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|clathrin coat of coated pit|cytosol|endocytic vesicle membrane|peroxisomal membrane	lipid binding|protein binding|transporter activity				0	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
THPO	7066	broad.mit.edu	37	3	184090371	184090371	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184090371G>A	uc003fol.1	-	6	1207	c.992C>T	c.(991-993)ACG>ATG	p.T331M	THPO_uc003fom.1_Missense_Mutation_p.T327M|THPO_uc003fon.2_3'UTR|THPO_uc011bro.1_Missense_Mutation_p.T207M|THPO_uc003fop.2_3'UTR|THPO_uc011brp.1_Missense_Mutation_p.T144M	NM_000460	NP_000451	P40225	TPO_HUMAN	thrombopoietin precursor	331	Pro-rich.				cell proliferation|platelet activation	extracellular space	cytokine activity|growth factor activity|hormone activity			ovary(1)	1	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
IGF2BP2	10644	broad.mit.edu	37	3	185375140	185375140	+	Silent	SNP	G	A	A	rs142081639		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185375140G>A	uc003fpo.2	-	12	1399	c.1320C>T	c.(1318-1320)GGC>GGT	p.G440G	IGF2BP2_uc010hyi.2_Silent_p.G383G|IGF2BP2_uc010hyj.2_Silent_p.G377G|IGF2BP2_uc010hyk.2_Silent_p.G304G|IGF2BP2_uc010hyl.2_Silent_p.G334G|IGF2BP2_uc003fpp.2_Silent_p.G397G|IGF2BP2_uc003fpq.2_Silent_p.G445G	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding	440	KH 3.				anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)															---	---	---	---
HRG	3273	broad.mit.edu	37	3	186395437	186395437	+	Missense_Mutation	SNP	G	A	A	rs149578094		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186395437G>A	uc003fqq.2	+	7	1366	c.1343G>A	c.(1342-1344)CGT>CAT	p.R448H		NM_000412	NP_000403	P04196	HRG_HUMAN	histidine-rich glycoprotein precursor	448	His/Pro-rich (HRR).				fibrinolysis|platelet activation|platelet degranulation	extracellular region|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding			ovary(1)|central_nervous_system(1)	2	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)														---	---	---	---
LPP	4026	broad.mit.edu	37	3	188123957	188123957	+	Missense_Mutation	SNP	G	A	A	rs139718801	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188123957G>A	uc003frs.1	+	3	295	c.49G>A	c.(49-51)GGC>AGC	p.G17S	LPP_uc011bsg.1_Missense_Mutation_p.G17S|LPP_uc011bsi.1_Missense_Mutation_p.G17S|LPP_uc003frt.2_Missense_Mutation_p.G17S	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation	17					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								---	---	---	---
GP5	2814	broad.mit.edu	37	3	194118379	194118379	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194118379C>T	uc003ftv.1	-	2	664	c.633G>A	c.(631-633)TCG>TCA	p.S211S		NM_004488	NP_004479	P40197	GPV_HUMAN	glycoprotein V (platelet) precursor	211	Extracellular (Potential).|LRR 6.				blood coagulation, intrinsic pathway|cell adhesion|platelet activation	integral to plasma membrane				skin(2)|breast(1)	3	all_cancers(143;6.64e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;7.38e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.06e-05)														---	---	---	---
TNK2	10188	broad.mit.edu	37	3	195594978	195594978	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195594978T>C	uc003fvu.1	-	12	2689	c.2146A>G	c.(2146-2148)AGG>GGG	p.R716G	TNK2_uc003fvq.1_Missense_Mutation_p.R123G|TNK2_uc003fvr.1_Missense_Mutation_p.R241G|TNK2_uc003fvs.1_Missense_Mutation_p.R748G|TNK2_uc003fvt.1_Missense_Mutation_p.R794G|TNK2_uc010hzw.1_RNA	NM_005781	NP_005772	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2 isoform 1	716	Pro-rich.			Missing (in Ref. 4; AAH08884).	positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction	adherens junction|cytoplasmic vesicle membrane|endosome|nucleus	ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1)	10	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)													---	---	---	---
OSTalpha	200931	broad.mit.edu	37	3	195944785	195944785	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195944785C>T	uc003fwd.2	+	2	312	c.111C>T	c.(109-111)CCC>CCT	p.P37P	OSTalpha_uc011btu.1_Silent_p.P37P	NM_152672	NP_689885	Q86UW1	OSTA_HUMAN	organic solute transporter alpha	37						integral to membrane|plasma membrane	transporter activity			ovary(1)	1	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;8.83e-25)|all cancers(36;8.38e-23)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;7.51e-07)|Lung(62;1.06e-06)	GBM - Glioblastoma multiforme(46;0.00202)														---	---	---	---
MFI2	4241	broad.mit.edu	37	3	196749822	196749822	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196749822G>A	uc003fxk.3	-						MFI2_uc003fxl.3_Intron|MFI2_uc011bua.1_Intron	NM_005929	NP_005920			melanoma-associated antigen p97 isoform 1						cellular iron ion homeostasis|iron ion transport	anchored to membrane|extracellular region|integral to plasma membrane	ferric iron binding|protein binding				0	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-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;0.00536)														---	---	---	---
KIAA1530	57654	broad.mit.edu	37	4	1348916	1348916	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1348916C>T	uc003gde.3	+	7	1506	c.1059C>T	c.(1057-1059)CGC>CGT	p.R353R		NM_020894	NP_065945	Q2YD98	K1530_HUMAN	hypothetical protein LOC57654	353											0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)															---	---	---	---
TACC3	10460	broad.mit.edu	37	4	1742700	1742700	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1742700A>T	uc003gdo.2	+	13	2318	c.2210A>T	c.(2209-2211)GAG>GTG	p.E737V	TACC3_uc003gdp.2_Missense_Mutation_p.E377V|TACC3_uc010ica.2_Missense_Mutation_p.E158V	NM_006342	NP_006333	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing	737	Potential.					centrosome				ovary(1)|central_nervous_system(1)	2		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)															---	---	---	---
ZFYVE28	57732	broad.mit.edu	37	4	2306791	2306791	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2306791C>T	uc003gex.1	-	8	1595	c.1276G>A	c.(1276-1278)GCA>ACA	p.A426T	ZFYVE28_uc011bvk.1_Missense_Mutation_p.A356T|ZFYVE28_uc011bvl.1_Missense_Mutation_p.A396T|ZFYVE28_uc003gew.1_Missense_Mutation_p.A312T	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	426					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																		---	---	---	---
TNIP2	79155	broad.mit.edu	37	4	2746454	2746454	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2746454C>T	uc003gfg.2	-	4	963	c.876G>A	c.(874-876)GCG>GCA	p.A292A	TNIP2_uc003gff.2_Silent_p.A185A|TNIP2_uc003gfh.2_Intron	NM_024309	NP_077285	Q8NFZ5	TNIP2_HUMAN	A20-binding inhibitor of NF-kappaB activation 2	292	Potential.					cytosol	protein binding			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
NOP14	8602	broad.mit.edu	37	4	2948228	2948228	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2948228C>T	uc003ggj.1	-	11	1618	c.1546G>A	c.(1546-1548)GCT>ACT	p.A516T	C4orf10_uc003gge.1_Intron|C4orf10_uc003ggh.2_Intron|C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_Missense_Mutation_p.A262T|NOP14_uc003ggk.3_Missense_Mutation_p.A516T|NOP14_uc003ggl.2_Missense_Mutation_p.A516T	NM_003703	NP_003694	P78316	NOP14_HUMAN	probable nucleolar complex protein 14	516					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1																		---	---	---	---
EVC2	132884	broad.mit.edu	37	4	5664926	5664926	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5664926A>G	uc003gij.2	-	9	1107	c.1053T>C	c.(1051-1053)GCT>GCC	p.A351A	EVC2_uc011bwb.1_5'UTR|EVC2_uc003gik.2_Silent_p.A271A	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	limbin	351						integral to membrane				large_intestine(3)|ovary(2)	5																		---	---	---	---
EVC	2121	broad.mit.edu	37	4	5733277	5733277	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5733277C>T	uc003gil.1	+	4	694	c.510C>T	c.(508-510)GAC>GAT	p.D170D	EVC_uc003gim.1_RNA	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein	170					muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)																---	---	---	---
CRMP1	1400	broad.mit.edu	37	4	5862758	5862758	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5862758A>G	uc003gip.2	-	4	409	c.308T>C	c.(307-309)ATG>ACG	p.M103T	CRMP1_uc003gin.1_Intron|CRMP1_uc003giq.2_Missense_Mutation_p.M103T|CRMP1_uc003gir.2_Missense_Mutation_p.M98T|CRMP1_uc003gis.2_Missense_Mutation_p.M217T	NM_001313	NP_001304	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1 isoform 2	103					axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)														---	---	---	---
CCDC96	257236	broad.mit.edu	37	4	7043508	7043508	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7043508C>A	uc003gjv.2	-	1	1221	c.1158G>T	c.(1156-1158)CTG>CTT	p.L386L	TADA2B_uc003gjw.3_5'Flank|TADA2B_uc010idi.2_5'Flank	NM_153376	NP_699207	Q2M329	CCD96_HUMAN	coiled-coil domain containing 96	386	Potential.										0																		---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7736111	7736111	+	Intron	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7736111T>G	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																		---	---	---	---
DRD5	1816	broad.mit.edu	37	4	9784659	9784659	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9784659G>A	uc003gmb.3	+	1	1402	c.1006G>A	c.(1006-1008)GTC>ATC	p.V336I		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	336	Extracellular (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane				skin(1)	1					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)													---	---	---	---
SLC2A9	56606	broad.mit.edu	37	4	9987317	9987317	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9987317G>A	uc003gmc.2	-	4	572	c.511C>T	c.(511-513)CGC>TGC	p.R171C	SLC2A9_uc003gmd.2_Missense_Mutation_p.R142C	NM_020041	NP_064425	Q9NRM0	GTR9_HUMAN	solute carrier family 2, member 9 protein	171	Extracellular (Potential).				glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			ovary(3)	3																		---	---	---	---
C1QTNF7	114905	broad.mit.edu	37	4	15444178	15444178	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15444178G>A	uc011bxb.1	+	3	852	c.625G>A	c.(625-627)GGA>AGA	p.G209R	C1QTNF7_uc003gno.2_Missense_Mutation_p.G216R|C1QTNF7_uc003gnp.2_Missense_Mutation_p.G209R	NM_001135171	NP_001128643	Q9BXJ2	C1QT7_HUMAN	C1q and tumor necrosis factor related protein 7	209	C1q.					collagen					0																		---	---	---	---
GPR125	166647	broad.mit.edu	37	4	22425982	22425982	+	Intron	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22425982G>T	uc003gqm.1	-						GPR125_uc010ieo.1_Intron|GPR125_uc003gqn.1_Intron|GPR125_uc003gqo.2_Intron	NM_145290	NP_660333			G protein-coupled receptor 125 precursor						neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)																---	---	---	---
LGI2	55203	broad.mit.edu	37	4	25014047	25014047	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25014047C>T	uc003grf.2	-	7	829	c.730G>A	c.(730-732)GTG>ATG	p.V244M		NM_018176	NP_060646	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	244	EAR 1.					extracellular region					0		Breast(46;0.173)																---	---	---	---
ZCCHC4	29063	broad.mit.edu	37	4	25334863	25334863	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25334863C>T	uc003grl.3	+	4	424	c.388C>T	c.(388-390)CAG>TAG	p.Q130*	ZCCHC4_uc003grm.1_RNA|ZCCHC4_uc003grn.3_5'UTR	NM_024936	NP_079212	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	130							methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(2)	2		Breast(46;0.0503)																---	---	---	---
SLC34A2	10568	broad.mit.edu	37	4	25665888	25665888	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25665888C>T	uc003grr.2	+	4	396	c.315C>T	c.(313-315)CTC>CTT	p.L105L	SLC34A2_uc003grs.2_Silent_p.L104L|SLC34A2_uc010iev.2_Silent_p.L104L	NM_006424	NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (sodium phosphate),	105	Helical; Name=M1; (Potential).				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)																---	---	---	---
LIAS	11019	broad.mit.edu	37	4	39460787	39460787	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39460787G>A	uc003guf.2	+						RPL9_uc003gub.2_5'Flank|RPL9_uc003guc.2_5'Flank|RPL9_uc011byk.1_5'Flank|RPL9_uc011byl.1_5'Flank|RPL9_uc003gud.1_5'Flank|LIAS_uc003gue.3_Intron|LIAS_uc011bym.1_Intron|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)													---	---	---	---
CHRNA9	55584	broad.mit.edu	37	4	40356371	40356371	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40356371C>T	uc003gva.1	+	5	1290	c.1274C>T	c.(1273-1275)ACG>ATG	p.T425M		NM_017581	NP_060051	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9	425	Cytoplasmic (Potential).				elevation of cytosolic calcium ion concentration|synaptic transmission	cell junction|postsynaptic membrane	calcium channel activity|receptor activity			breast(3)|skin(3)|central_nervous_system(1)	7					Nicotine(DB00184)													---	---	---	---
UCHL1	7345	broad.mit.edu	37	4	41259153	41259153	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41259153G>A	uc003gvo.2	+						UCHL1_uc003gvp.2_5'UTR|UCHL1_uc003gvq.2_Intron|UCHL1_uc003gvr.2_5'UTR	NM_004181	NP_004172			ubiquitin carboxyl-terminal esterase L1						cell death|negative regulation of MAP kinase activity|protein deubiquitination|ubiquitin-dependent protein catabolic process	nucleus|plasma membrane	alpha-2A adrenergic receptor binding|cysteine-type endopeptidase activity|ligase activity|omega peptidase activity|ubiquitin binding|ubiquitin thiolesterase activity			central_nervous_system(1)|skin(1)	2																		---	---	---	---
BEND4	389206	broad.mit.edu	37	4	42119703	42119703	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42119703C>T	uc003gwn.2	-	6	2017	c.1437G>A	c.(1435-1437)TCG>TCA	p.S479S	BEND4_uc003gwm.2_3'UTR	NM_207406	NP_997289	Q6ZU67	BEND4_HUMAN	BEN domain containing 4 isoform a	479	BEN.										0																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48569288	48569288	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48569288G>A	uc003gyh.1	-	28	3751	c.3146C>T	c.(3145-3147)GCG>GTG	p.A1049V	FRYL_uc003gyk.2_Missense_Mutation_p.A1049V|FRYL_uc003gyi.1_5'Flank	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	1049					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
LRRC66	339977	broad.mit.edu	37	4	52861190	52861190	+	Silent	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52861190T>G	uc003gzi.2	-	4	2011	c.1998A>C	c.(1996-1998)CCA>CCC	p.P666P		NM_001024611	NP_001019782	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	666						integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
GSX2	170825	broad.mit.edu	37	4	54966533	54966533	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54966533G>A	uc010igp.1	+	1	286	c.22G>A	c.(22-24)GAC>AAC	p.D8N	PDGFRA_uc003haa.2_Intron	NM_133267	NP_573574	Q9BZM3	GSX2_HUMAN	GS homeobox 2	8						nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(7;0.00671)|Lung NSC(11;0.0154)|all_neural(26;0.0209)|Glioma(25;0.08)|all_epithelial(27;0.147)		LUSC - Lung squamous cell carcinoma(32;0.00216)															---	---	---	---
KIAA1211	57482	broad.mit.edu	37	4	57181853	57181853	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57181853T>C	uc003hbk.2	+	8	2576	c.2185T>C	c.(2185-2187)TCC>CCC	p.S729P	KIAA1211_uc010iha.2_Missense_Mutation_p.S722P|KIAA1211_uc011bzz.1_Missense_Mutation_p.S639P|KIAA1211_uc003hbm.1_Missense_Mutation_p.S615P	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	729								p.S729S(1)		ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
CSN3	1448	broad.mit.edu	37	4	71114781	71114781	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71114781C>T	uc003hfe.3	+	4	212	c.154C>T	c.(154-156)CCA>TCA	p.P52S		NM_005212	NP_005203	P07498	CASK_HUMAN	casein kappa precursor	52						extracellular region	protein binding	p.P52A(1)		ovary(2)|kidney(1)|central_nervous_system(1)	4																		---	---	---	---
C4orf35	85438	broad.mit.edu	37	4	71201047	71201047	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71201047C>A	uc003hff.2	+	1	377	c.291C>A	c.(289-291)ACC>ACA	p.T97T		NM_033122	NP_149113	Q96KC9	CABS1_HUMAN	testis development protein NYD-SP26	97						flagellum	calcium ion binding				0		all_hematologic(202;0.196)																---	---	---	---
NAAA	27163	broad.mit.edu	37	4	76842177	76842177	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76842177G>A	uc003hjb.2	-	6	830	c.766C>T	c.(766-768)CGG>TGG	p.R256W	NAAA_uc003hja.2_Missense_Mutation_p.R256W|NAAA_uc003hjc.3_Missense_Mutation_p.R256W|NAAA_uc003hjd.3_RNA|NAAA_uc011cbq.1_Missense_Mutation_p.R155W	NM_014435	NP_055250	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase isoform 1	256					lipid metabolic process	lysosome	hydrolase activity			skin(1)	1																		---	---	---	---
ANKRD56	345079	broad.mit.edu	37	4	77817102	77817102	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77817102G>A	uc003hki.2	-	1	1901	c.1901C>T	c.(1900-1902)GCG>GTG	p.A634V		NM_001029870	NP_001025041	A6NEL2	ANR56_HUMAN	ankyrin repeat domain 56	634	ANK 1.										0																		---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79371314	79371314	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79371314C>T	uc003hlb.2	+	45	6724	c.6284C>T	c.(6283-6285)GCA>GTA	p.A2095V		NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	2094	CSPG 9.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5																		---	---	---	---
PRDM8	56978	broad.mit.edu	37	4	81122567	81122567	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81122567C>T	uc010ijo.2	+	7	1182	c.343C>T	c.(343-345)CGC>TGC	p.R115C	PRDM8_uc003hmb.3_Missense_Mutation_p.R115C|PRDM8_uc003hmc.3_Missense_Mutation_p.R115C	NM_020226	NP_064611	Q9NQV8	PRDM8_HUMAN	PR domain containing 8	115	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
BMP3	651	broad.mit.edu	37	4	81952623	81952623	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81952623G>A	uc003hmg.3	+	1	505	c.185G>A	c.(184-186)CGG>CAG	p.R62Q		NM_001201	NP_001192	P12645	BMP3_HUMAN	bone morphogenetic protein 3 preproprotein	62					cartilage development|cell differentiation|cell-cell signaling|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity			ovary(4)|central_nervous_system(1)	5																		---	---	---	---
RASGEF1B	153020	broad.mit.edu	37	4	82355785	82355785	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82355785A>G	uc003hmi.1	-						RASGEF1B_uc003hmj.1_Intron|RASGEF1B_uc010ijq.1_Intron	NM_152545	NP_689758			RasGEF domain family, member 1B						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0																		---	---	---	---
AGPAT9	84803	broad.mit.edu	37	4	84516122	84516122	+	Intron	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84516122T>C	uc003how.2	+						AGPAT9_uc003hox.2_Intron|AGPAT9_uc003hoy.2_Intron	NM_032717	NP_116106			1-acylglycerol-3-phosphate O-acyltransferase 9						phospholipid biosynthetic process|regulation of TOR signaling cascade|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	glycerol-3-phosphate O-acyltransferase activity			skin(1)	1		Hepatocellular(203;0.114)																---	---	---	---
SLC10A6	345274	broad.mit.edu	37	4	87754575	87754575	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87754575A>G	uc003hqd.2	-	2	528	c.380T>C	c.(379-381)ATC>ACC	p.I127T		NM_197965	NP_932069	Q3KNW5	SOAT_HUMAN	sodium-dependent organic anion transporter	127	Cytoplasmic (Potential).					integral to membrane|plasma membrane	bile acid:sodium symporter activity				0		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.00099)														---	---	---	---
KLHL8	57563	broad.mit.edu	37	4	88091757	88091757	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88091757C>T	uc011cdb.1	-	7	1604	c.1219G>A	c.(1219-1221)GCC>ACC	p.A407T	KLHL8_uc003hql.1_Missense_Mutation_p.A407T|KLHL8_uc003hqm.1_Missense_Mutation_p.A331T|KLHL8_uc003hqn.1_Missense_Mutation_p.A224T|KLHL8_uc010ikj.1_Missense_Mutation_p.A56T	NM_020803	NP_065854	Q9P2G9	KLHL8_HUMAN	kelch-like 8	407	Kelch 2.										0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
HERC5	51191	broad.mit.edu	37	4	89388315	89388315	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89388315G>A	uc003hrt.2	+	7	1170	c.1017G>A	c.(1015-1017)CCG>CCA	p.P339P	HERC5_uc011cdm.1_5'Flank	NM_016323	NP_057407	Q9UII4	HERC5_HUMAN	hect domain and RLD 5	339	RCC1 5.				innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)														---	---	---	---
PDHA2	5161	broad.mit.edu	37	4	96761964	96761964	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96761964G>T	uc003htr.3	+	1	726	c.663G>T	c.(661-663)GAG>GAT	p.E221D		NM_005390	NP_005381	P29803	ODPAT_HUMAN	pyruvate dehydrogenase E1 alpha 2 precursor	221					glycolysis	mitochondrial matrix	pyruvate dehydrogenase (acetyl-transferring) activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)	NADH(DB00157)													---	---	---	---
TSPAN5	10098	broad.mit.edu	37	4	99397385	99397385	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99397385A>T	uc003hub.2	-	7	1046	c.696T>A	c.(694-696)AAT>AAA	p.N232K	TSPAN5_uc011cdz.1_Missense_Mutation_p.N161K	NM_005723	NP_005714	P62079	TSN5_HUMAN	transmembrane 4 superfamily member 9	232	Extracellular (Potential).					integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)														---	---	---	---
CASP6	839	broad.mit.edu	37	4	110618908	110618908	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110618908C>T	uc003hzn.1	-	3	178	c.100G>A	c.(100-102)GCA>ACA	p.A34T	CASP6_uc003hzo.1_Intron	NM_001226	NP_001217	P55212	CASP6_HUMAN	caspase 6 isoform alpha preproprotein	34					cellular component disassembly involved in apoptosis|induction of apoptosis|proteolysis	cytosol|nucleoplasm	cysteine-type endopeptidase activity|protein binding			ovary(1)|breast(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000171)														---	---	---	---
RRH	10692	broad.mit.edu	37	4	110757242	110757242	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110757242T>C	uc003hzv.2	+	4	511	c.477T>C	c.(475-477)CCT>CCC	p.P159P		NM_006583	NP_006574	O14718	OPSX_HUMAN	peropsin	159	Helical; Name=4; (Potential).				phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00109)														---	---	---	---
AP1AR	55435	broad.mit.edu	37	4	113189356	113189356	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113189356C>T	uc003iaj.3	+	10	1053	c.700C>T	c.(700-702)CGG>TGG	p.R234W	AP1AR_uc003iak.3_Missense_Mutation_p.R201W	NM_018569	NP_061039	Q63HQ0	AP1AR_HUMAN	adaptor-related protein complex 1 associated	234					protein transport	early endosome|Golgi apparatus|late endosome|transport vesicle					0																		---	---	---	---
C4orf21	55345	broad.mit.edu	37	4	113462250	113462250	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113462250G>C	uc003iau.2	-	25	5984	c.5773C>G	c.(5773-5775)CAG>GAG	p.Q1925E	C4orf21_uc003iav.2_RNA|C4orf21_uc003iat.2_Missense_Mutation_p.Q383E	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	747						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114290968	114290968	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114290968C>T	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)														---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123120560	123120560	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123120560T>C	uc003ieh.2	+	12	1380	c.1335T>C	c.(1333-1335)ACT>ACC	p.T445T	KIAA1109_uc003iei.1_Silent_p.T199T|KIAA1109_uc010ins.1_5'UTR	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	445					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126238642	126238642	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126238642C>T	uc003ifj.3	+	1	1076	c.1076C>T	c.(1075-1077)CCG>CTG	p.P359L		NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	359	Cadherin 4.|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)	---	---	---	---
KLHL2	11275	broad.mit.edu	37	4	166238981	166238981	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166238981T>G	uc003irb.2	+	14	1872	c.1613T>G	c.(1612-1614)GTT>GGT	p.V538G	KLHL2_uc011cjm.1_Missense_Mutation_p.V542G|KLHL2_uc003irc.2_Missense_Mutation_p.V450G|KLHL2_uc010ira.2_Missense_Mutation_p.V191G	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1	538	Kelch 5.				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)														---	---	---	---
SPOCK3	50859	broad.mit.edu	37	4	167675677	167675677	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167675677A>C	uc003iri.1	-	9	1063	c.922T>G	c.(922-924)TGC>GGC	p.C308G	SPOCK3_uc011cjp.1_Missense_Mutation_p.C265G|SPOCK3_uc011cjq.1_Missense_Mutation_p.C317G|SPOCK3_uc011cjr.1_Missense_Mutation_p.C188G|SPOCK3_uc003irj.1_Missense_Mutation_p.C305G|SPOCK3_uc011cjs.1_Missense_Mutation_p.C257G|SPOCK3_uc011cjt.1_Missense_Mutation_p.C216G|SPOCK3_uc011cju.1_Missense_Mutation_p.C201G|SPOCK3_uc011cjv.1_Missense_Mutation_p.C210G|SPOCK3_uc003irk.3_Missense_Mutation_p.C305G	NM_016950	NP_058646	Q9BQ16	TICN3_HUMAN	testican 3 isoform 2	308					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)														---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169190007	169190007	+	Silent	SNP	G	A	A	rs145361158		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169190007G>A	uc003irp.2	-	20	3076	c.2784C>T	c.(2782-2784)ACC>ACT	p.T928T		NM_017631	NP_060101	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	928	Helicase ATP-binding.						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	169812119	169812119	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169812119G>T	uc011cjx.1	+	11	2222	c.2011G>T	c.(2011-2013)GAG>TAG	p.E671*	CBR4_uc011cjy.1_Intron|PALLD_uc003iru.2_Nonsense_Mutation_p.E671*|PALLD_uc003irv.2_Nonsense_Mutation_p.E289*|PALLD_uc003irw.2_Nonsense_Mutation_p.E173*	NM_016081	NP_057165	Q8WX93	PALLD_HUMAN	palladin isoform 2	895					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				---	---	---	---
NEK1	4750	broad.mit.edu	37	4	170345785	170345785	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170345785C>T	uc003isb.1	-	29	3549	c.3057G>A	c.(3055-3057)TCG>TCA	p.S1019S	NEK1_uc003isc.1_Silent_p.S975S|NEK1_uc003isd.1_Silent_p.S1047S|NEK1_uc003ise.1_Silent_p.S1003S|NEK1_uc003isf.1_Silent_p.S950S	NM_012224	NP_036356	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	1019					cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)														---	---	---	---
FBXO8	26269	broad.mit.edu	37	4	175183955	175183955	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175183955C>T	uc003itp.2	-	2	1139	c.289G>A	c.(289-291)GTT>ATT	p.V97I	FBXO8_uc003itq.2_Intron	NM_012180	NP_036312	Q9NRD0	FBX8_HUMAN	F-box only protein 8	97	F-box.				regulation of ARF protein signal transduction|ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ARF guanyl-nucleotide exchange factor activity			breast(2)	2		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)														---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183600990	183600990	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183600990A>G	uc003ivd.1	+	7	1535	c.1498A>G	c.(1498-1500)AAA>GAA	p.K500E	ODZ3_uc003ive.1_5'Flank	NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	500	Extracellular (Potential).				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)														---	---	---	---
IRF2	3660	broad.mit.edu	37	4	185339687	185339687	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185339687T>C	uc003iwf.3	-	4	563	c.363A>G	c.(361-363)AAA>AAG	p.K121K		NM_002199	NP_002190	P14316	IRF2_HUMAN	interferon regulatory factor 2	121					blood coagulation|cell proliferation|interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	focal adhesion|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)														---	---	---	---
SNX25	83891	broad.mit.edu	37	4	186272770	186272770	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186272770C>T	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)														---	---	---	---
MTNR1A	4543	broad.mit.edu	37	4	187455100	187455100	+	Missense_Mutation	SNP	C	T	T	rs148793802		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187455100C>T	uc003izd.1	-	2	814	c.796G>A	c.(796-798)GCC>ACC	p.A266T		NM_005958	NP_005949	P48039	MTR1A_HUMAN	melatonin receptor 1A	266	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)													---	---	---	---
SLC9A3	6550	broad.mit.edu	37	5	488455	488455	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:488455C>T	uc003jbe.2	-	3	763	c.651G>A	c.(649-651)TCG>TCA	p.S217S	SLC9A3_uc011clx.1_Silent_p.S217S	NM_004174	NP_004165	P48764	SL9A3_HUMAN	solute carrier family 9 (sodium/hydrogen	217	Helical; Name=G/M5B; (Potential).					cell surface|integral to membrane	sodium:hydrogen antiporter activity				0			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)															---	---	---	---
LPCAT1	79888	broad.mit.edu	37	5	1466903	1466903	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1466903G>A	uc003jcm.2	-	13	1498	c.1381C>T	c.(1381-1383)CGA>TGA	p.R461*	LPCAT1_uc003jcl.2_Nonsense_Mutation_p.R35*	NM_024830	NP_079106	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	461	Lumenal (Potential).|EF-hand 2.				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)														---	---	---	---
IRX4	50805	broad.mit.edu	37	5	1878859	1878859	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1878859C>T	uc003jcz.2	-	5	903	c.784G>A	c.(784-786)GAC>AAC	p.D262N	IRX4_uc011cmf.1_Missense_Mutation_p.D123N	NM_016358	NP_057442	P78413	IRX4_HUMAN	iroquois homeobox 4	262					heart development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				GBM - Glioblastoma multiforme(108;0.242)														---	---	---	---
C5orf38	153571	broad.mit.edu	37	5	2752844	2752844	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2752844G>A	uc003jdc.2	+	2	426	c.309G>A	c.(307-309)GCG>GCA	p.A103A	C5orf38_uc011cmg.1_Silent_p.A103A|C5orf38_uc011cmh.1_RNA|C5orf38_uc011cmi.1_RNA|C5orf38_uc011cmj.1_Intron	NM_178569	NP_848664	Q86SI9	CEI_HUMAN	hypothetical protein LOC153571 precursor	103						extracellular region					0				GBM - Glioblastoma multiforme(108;0.205)														---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7709334	7709334	+	Missense_Mutation	SNP	G	A	A	rs141886153	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7709334G>A	uc003jdz.1	+	10	1479	c.1412G>A	c.(1411-1413)CGG>CAG	p.R471Q	ADCY2_uc011cmo.1_Missense_Mutation_p.R291Q	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	471	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																		---	---	---	---
FAM105A	54491	broad.mit.edu	37	5	14610394	14610394	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14610394G>A	uc003jfj.2	+	8	1155	c.1042G>A	c.(1042-1044)GAC>AAC	p.D348N		NM_019018	NP_061891	Q9NUU6	F105A_HUMAN	hypothetical protein LOC54491	348										ovary(1)	1	Lung NSC(4;0.00592)																	---	---	---	---
ANKH	56172	broad.mit.edu	37	5	14769138	14769138	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14769138C>T	uc003jfm.3	-	2	590	c.259G>A	c.(259-261)GTC>ATC	p.V87I		NM_054027	NP_473368	Q9HCJ1	ANKH_HUMAN	progressive ankylosis protein	87	Helical; (Potential).				locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32230244	32230244	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32230244T>C	uc003jhq.2	-	16	2054	c.1884A>G	c.(1882-1884)TTA>TTG	p.L628L	MTMR12_uc010iuk.2_Silent_p.L574L|MTMR12_uc010iul.2_Silent_p.L518L	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	628	Myotubularin phosphatase.					cytoplasm	phosphatase activity			ovary(1)	1																		---	---	---	---
ZFR	51663	broad.mit.edu	37	5	32404048	32404048	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32404048G>A	uc003jhr.1	-	7	1267	c.1187C>T	c.(1186-1188)GCG>GTG	p.A396V		NM_016107	NP_057191	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	396					multicellular organismal development	chromosome|cytoplasm|nucleus	DNA binding|RNA binding|zinc ion binding				0				STAD - Stomach adenocarcinoma(35;0.19)														---	---	---	---
RAI14	26064	broad.mit.edu	37	5	34824014	34824014	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34824014C>T	uc003jir.2	+	15	2263	c.2067C>T	c.(2065-2067)AAC>AAT	p.N689N	RAI14_uc010iur.2_Silent_p.N660N|RAI14_uc011coj.1_Silent_p.N689N|RAI14_uc003jis.2_Silent_p.N692N|RAI14_uc003jit.2_Silent_p.N689N|RAI14_uc011cok.1_Silent_p.N681N	NM_015577	NP_056392	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14 isoform a	689	Potential.					cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)																	---	---	---	---
HEATR7B2	133558	broad.mit.edu	37	5	41009422	41009422	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41009422G>A	uc003jmj.3	-	32	3870	c.3380C>T	c.(3379-3381)ACT>ATT	p.T1127I	HEATR7B2_uc003jmi.3_Missense_Mutation_p.T682I	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	1127	HEAT 12.						binding			ovary(6)|central_nervous_system(2)	8																		---	---	---	---
C6	729	broad.mit.edu	37	5	41203323	41203323	+	Missense_Mutation	SNP	G	A	A	rs150931891	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41203323G>A	uc003jmk.2	-	2	220	c.10C>T	c.(10-12)CGC>TGC	p.R4C	C6_uc003jml.1_Missense_Mutation_p.R4C	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	4					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)																---	---	---	---
MGC42105	167359	broad.mit.edu	37	5	43280635	43280635	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43280635G>A	uc003jno.2	+	4	1996	c.1115G>A	c.(1114-1116)CGA>CAA	p.R372Q		NM_153361	NP_699192	Q8IY84	NIM1_HUMAN	serine/threonine-protein kinase NIM1	372							ATP binding|magnesium ion binding|protein serine/threonine kinase activity	p.R372*(2)		lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9																		---	---	---	---
PELO	53918	broad.mit.edu	37	5	52096812	52096812	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52096812G>A	uc003jos.2	+	2	1569	c.584G>A	c.(583-585)CGC>CAC	p.R195H	ITGA1_uc003jov.2_Intron|ITGA1_uc003jou.2_Intron|PELO_uc003jot.1_Intron	NM_015946	NP_057030	Q9BRX2	PELO_HUMAN	pelota homolog	195					cell cycle|cell division|translation	cytoplasm|nucleus	endonuclease activity|metal ion binding|protein binding				0		Lung NSC(810;4.94e-05)|Breast(144;0.0848)																---	---	---	---
HTR1A	3350	broad.mit.edu	37	5	63256991	63256991	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63256991C>T	uc011cqt.1	-	1	556	c.556G>A	c.(556-558)GCA>ACA	p.A186T		NM_000524	NP_000515	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A	186	Extracellular (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)													---	---	---	---
SFRS12	140890	broad.mit.edu	37	5	65473381	65473381	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65473381C>T	uc003juo.2	+	12	1932	c.1272C>T	c.(1270-1272)GAC>GAT	p.D424D	SFRS12_uc003jun.2_Silent_p.D540D|SFRS12_uc010iwy.2_Silent_p.D423D	NM_139168	NP_631907	Q8WXA9	SREK1_HUMAN	splicing factor, arginine/serine-rich 12 isoform	424	Arg/Glu/Lys/Ser-rich.				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)														---	---	---	---
ZNF366	167465	broad.mit.edu	37	5	71756348	71756348	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71756348G>A	uc003kce.1	-	2	1162	c.976C>T	c.(976-978)CGC>TGC	p.R326C		NM_152625	NP_689838	Q8N895	ZN366_HUMAN	zinc finger protein 366	326	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)														---	---	---	---
FCHO2	115548	broad.mit.edu	37	5	72377779	72377779	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72377779C>T	uc003kcl.2	+	23	2266	c.2150C>T	c.(2149-2151)ACG>ATG	p.T717M	FCHO2_uc011csl.1_Missense_Mutation_p.T684M|FCHO2_uc010izb.2_Missense_Mutation_p.T145M|FCHO2_uc011csn.1_Missense_Mutation_p.T145M	NM_138782	NP_620137	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2 isoform a	717										ovary(1)	1		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)														---	---	---	---
UTP15	84135	broad.mit.edu	37	5	72868406	72868406	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72868406C>T	uc003kcw.1	+	7	989	c.766C>T	c.(766-768)CTA>TTA	p.L256L	UTP15_uc011cso.1_Silent_p.L237L|UTP15_uc011csp.1_Silent_p.L66L|UTP15_uc010ize.1_Silent_p.L256L	NM_032175	NP_115551	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein,	256	WD 6.				rRNA processing	cytoplasm|nucleolus					0		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)														---	---	---	---
HOMER1	9456	broad.mit.edu	37	5	78697766	78697766	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78697766G>A	uc003kfy.2	-	6	1743	c.640C>T	c.(640-642)CAA>TAA	p.Q214*	HOMER1_uc010jab.2_Intron|HOMER1_uc010jac.2_Intron|HOMER1_uc010jad.2_Nonsense_Mutation_p.Q40*	NM_004272	NP_004263	Q86YM7	HOME1_HUMAN	homer 1	214	Potential.				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic density|postsynaptic membrane					0		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)														---	---	---	---
ACOT12	134526	broad.mit.edu	37	5	80667576	80667576	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80667576C>T	uc003khl.3	-	3	306	c.251G>A	c.(250-252)AGC>AAC	p.S84N	RNU5E_uc011cto.1_Intron|ACOT12_uc003khm.2_Missense_Mutation_p.S84N	NM_130767	NP_570123	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	84	Coenzyme A binding.|Acyl coenzyme A hydrolase 1.				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)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	89923028	89923028	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89923028G>A	uc003kju.2	+	7	769	c.673G>A	c.(673-675)GTA>ATA	p.V225I	GPR98_uc003kjt.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	225	Calx-beta 2.|Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90015894	90015894	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90015894G>A	uc003kju.2	+	44	9573	c.9477G>A	c.(9475-9477)ACG>ACA	p.T3159T	GPR98_uc003kjt.2_Silent_p.T865T|GPR98_uc003kjv.2_Silent_p.T759T	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	3159	Extracellular (Potential).|Calx-beta 22.				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	92923762	92923762	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92923762G>A	uc003kkj.2	+	2	2290	c.603G>A	c.(601-603)TCG>TCA	p.S201S		NM_005654	NP_005645	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	201					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)														---	---	---	---
AQPEP	206338	broad.mit.edu	37	5	115299005	115299005	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115299005C>T	uc003kro.2	+	1	855	c.691C>T	c.(691-693)CGC>TGC	p.R231C	AQPEP_uc003krp.2_RNA|uc003krn.1_5'Flank	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	231	Lumenal (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0																		---	---	---	---
SNCAIP	9627	broad.mit.edu	37	5	121776408	121776408	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121776408G>A	uc003ksw.1	+	7	1587	c.1381G>A	c.(1381-1383)GTT>ATT	p.V461I	SNCAIP_uc011cwl.1_Missense_Mutation_p.V19I|SNCAIP_uc010jct.2_Missense_Mutation_p.V461I|SNCAIP_uc003ksx.1_Missense_Mutation_p.V508I|SNCAIP_uc003ksy.1_Missense_Mutation_p.V95I|SNCAIP_uc003ksz.1_Missense_Mutation_p.V95I|SNCAIP_uc010jcu.2_Missense_Mutation_p.V57I|SNCAIP_uc011cwm.1_Missense_Mutation_p.V95I|SNCAIP_uc003kta.1_Missense_Mutation_p.V93I|SNCAIP_uc010jcv.1_RNA|SNCAIP_uc010jcw.1_Missense_Mutation_p.V155I|SNCAIP_uc010jcx.1_Missense_Mutation_p.V401I|uc003ktb.1_Intron	NM_005460	NP_005451	Q9Y6H5	SNCAP_HUMAN	synuclein alpha interacting protein	461	ANK 4.				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)														---	---	---	---
CSNK1G3	1456	broad.mit.edu	37	5	122941058	122941058	+	Intron	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122941058T>C	uc003ktm.2	+						CSNK1G3_uc003ktl.2_Splice_Site_p.W438_splice|CSNK1G3_uc003ktn.2_Splice_Site_p.W406_splice|CSNK1G3_uc003kto.2_Intron|CSNK1G3_uc011cwr.1_Splice_Site_p.W331_splice|CSNK1G3_uc011cws.1_Splice_Site_p.W294_splice|CSNK1G3_uc010jda.2_Splice_Site_p.W407_splice	NM_004384	NP_004375			casein kinase 1, gamma 3 isoform 1						Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)														---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	123983851	123983851	+	Silent	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123983851T>A	uc003ktq.1	-	4	2349	c.2226A>T	c.(2224-2226)CCA>CCT	p.P742P	ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Silent_p.P742P|ZNF608_uc003ktt.1_Silent_p.P742P	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	742						intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)														---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	123984642	123984642	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123984642G>A	uc003ktq.1	-	4	1558	c.1435C>T	c.(1435-1437)CGA>TGA	p.R479*	ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Nonsense_Mutation_p.R479*|ZNF608_uc003ktt.1_Nonsense_Mutation_p.R479*	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	479						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)														---	---	---	---
PRRC1	133619	broad.mit.edu	37	5	126874760	126874760	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126874760G>A	uc003kuk.2	+	7	1130	c.950G>A	c.(949-951)CGT>CAT	p.R317H	PRRC1_uc003kuj.3_Missense_Mutation_p.R317H	NM_130809	NP_570721	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1	317						Golgi apparatus					0		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)														---	---	---	---
P4HA2	8974	broad.mit.edu	37	5	131543466	131543466	+	Missense_Mutation	SNP	C	T	T	rs148040234		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131543466C>T	uc003kwh.2	-	8	1579	c.1015G>A	c.(1015-1017)GTC>ATC	p.V339I	P4HA2_uc003kwg.2_Missense_Mutation_p.V339I|P4HA2_uc003kwi.2_Missense_Mutation_p.V339I|P4HA2_uc003kwk.2_Missense_Mutation_p.V339I|P4HA2_uc003kwl.2_Missense_Mutation_p.V339I|P4HA2_uc003kwj.2_Missense_Mutation_p.V339I	NM_004199	NP_004190	O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha II subunit isoform 1	339						endoplasmic reticulum lumen	electron carrier activity|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|protein binding				0		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)													---	---	---	---
PDLIM4	8572	broad.mit.edu	37	5	131606656	131606656	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131606656C>T	uc003kwn.2	+	4	453	c.376C>T	c.(376-378)CCA>TCA	p.P126S	uc003kwm.3_Intron|PDLIM4_uc003kwp.2_Missense_Mutation_p.P126S|PDLIM4_uc003kwo.2_Missense_Mutation_p.P126S	NM_003687	NP_003678	P50479	PDLI4_HUMAN	PDZ and LIM domain 4 isoform 1	126							protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
RAD50	10111	broad.mit.edu	37	5	131953826	131953826	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131953826C>T	uc003kxi.2	+	21	3616	c.3229C>T	c.(3229-3231)CGA>TGA	p.R1077*	RAD50_uc003kxh.2_Nonsense_Mutation_p.R938*	NM_005732	NP_005723	Q92878	RAD50_HUMAN	RAD50 homolog isoform 1	1077	Potential.				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					---	---	---	---
TRPC7	57113	broad.mit.edu	37	5	135692750	135692750	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135692750G>A	uc003lbn.1	-	1	326	c.323C>T	c.(322-324)GCG>GTG	p.A108V	TRPC7_uc010jef.1_Missense_Mutation_p.A100V|TRPC7_uc010jeg.1_RNA|TRPC7_uc010jeh.1_Missense_Mutation_p.A100V|TRPC7_uc010jei.1_Missense_Mutation_p.A100V|TRPC7_uc010jej.1_5'UTR	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,	109	Cytoplasmic (Potential).|ANK 3.				axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
FAM13B	51306	broad.mit.edu	37	5	137278577	137278577	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137278577G>A	uc003lbz.2	-	21	3043	c.2509C>T	c.(2509-2511)CGA>TGA	p.R837*	FAM13B_uc003lcb.2_Nonsense_Mutation_p.R713*|FAM13B_uc003lca.2_Nonsense_Mutation_p.R809*	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN	hypothetical protein LOC51306 isoform 1	837					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
FAM13B	51306	broad.mit.edu	37	5	137289904	137289904	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137289904G>A	uc003lbz.2	-	14	2137	c.1603C>T	c.(1603-1605)CAT>TAT	p.H535Y	FAM13B_uc003lcb.2_Missense_Mutation_p.H439Y|FAM13B_uc003lca.2_Missense_Mutation_p.H535Y	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN	hypothetical protein LOC51306 isoform 1	535					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
WNT8A	7478	broad.mit.edu	37	5	137420203	137420203	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137420203C>T	uc003lcd.1	+	3	124	c.119C>T	c.(118-120)ACG>ATG	p.T40M	BRD8_uc003lcc.1_Intron|WNT8A_uc011cyj.1_Missense_Mutation_p.T58M|WNT8A_uc011cyk.1_Missense_Mutation_p.T58M	NM_058244	NP_490645	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family,	40					brain segmentation|canonical Wnt receptor signaling pathway involved in neural crest cell differentiation|cell migration involved in gastrulation|dorsal/ventral pattern formation|ectoderm development|endoderm development|eye development|hindbrain development|mesodermal cell fate commitment|negative regulation of Wnt receptor signaling pathway|neural crest cell fate commitment|neural plate pattern specification|notochord development|palate development|polarity specification of anterior/posterior axis|polarity specification of proximal/distal axis|positive regulation of fibroblast growth factor receptor signaling pathway|regulation of transcription involved in anterior/posterior axis specification|response to retinoic acid|somitogenesis|spinal cord anterior/posterior patterning|tail morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled binding|signal transducer activity			ovary(1)|lung(1)|breast(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
NRG2	9542	broad.mit.edu	37	5	139251390	139251390	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139251390C>T	uc003lex.1	-	4	1253	c.1028G>A	c.(1027-1029)CGG>CAG	p.R343Q	NRG2_uc003lev.1_Missense_Mutation_p.R343Q|NRG2_uc003lew.1_Missense_Mutation_p.R343Q|NRG2_uc003ley.1_Missense_Mutation_p.R343Q	NM_004883	NP_004874	O14511	NRG2_HUMAN	neuregulin 2 isoform 1	343	EGF-like.|Extracellular (Potential).				embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139905920	139905920	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139905920G>C	uc003lfs.1	+	26	4956	c.4832G>C	c.(4831-4833)AGC>ACC	p.S1611T	ANKHD1_uc003lfr.2_Missense_Mutation_p.S1611T|ANKHD1_uc003lfu.1_Missense_Mutation_p.S1091T|ANKHD1-EIF4EBP3_uc011czh.1_Missense_Mutation_p.S350T|ANKHD1_uc003lfw.2_Missense_Mutation_p.S249T|ANKHD1_uc010jfl.2_Missense_Mutation_p.S46T|ANKHD1-EIF4EBP3_uc003lfx.1_5'Flank	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein	1611						cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA1	56147	broad.mit.edu	37	5	140166534	140166534	+	Missense_Mutation	SNP	C	T	T	rs149577981	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140166534C>T	uc003lhb.2	+	1	659	c.659C>T	c.(658-660)CCG>CTG	p.P220L	PCDHA1_uc003lha.2_Missense_Mutation_p.P220L|PCDHA1_uc003lgz.2_Missense_Mutation_p.P220L	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	220	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA1	56147	broad.mit.edu	37	5	140167731	140167731	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140167731G>A	uc003lhb.2	+	1	1856	c.1856G>A	c.(1855-1857)CGC>CAC	p.R619H	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lgz.2_Missense_Mutation_p.R619H	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	619	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA3	56145	broad.mit.edu	37	5	140182842	140182842	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140182842C>T	uc003lhf.2	+	1	2060	c.2060C>T	c.(2059-2061)ACG>ATG	p.T687M	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.T687M	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	687	Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA5	56143	broad.mit.edu	37	5	140202765	140202765	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140202765C>A	uc003lhl.2	+	1	1405	c.1405C>A	c.(1405-1407)CCA>ACA	p.P469T	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.P469T|PCDHA5_uc003lhj.1_Missense_Mutation_p.P469T	NM_018908	NP_061731	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5 isoform 1 precursor	469	Extracellular (Potential).|Cadherin 5.				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	140209889	140209889	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140209889C>T	uc003lho.2	+	1	2240	c.2213C>T	c.(2212-2214)ACG>ATG	p.T738M	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.T738M	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	738	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	140215576	140215576	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140215576C>T	uc003lhq.2	+	1	1608	c.1608C>T	c.(1606-1608)AGC>AGT	p.S536S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc011dac.1_Silent_p.S536S	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	536	Cadherin 5.|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)															---	---	---	---
PCDHA13	56136	broad.mit.edu	37	5	140263515	140263515	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140263515C>T	uc003lif.2	+	1	1662	c.1662C>T	c.(1660-1662)TTC>TTT	p.F554F	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.F554F|PCDHA13_uc003lid.2_Silent_p.F554F	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	554	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA13	56136	broad.mit.edu	37	5	140264043	140264043	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140264043C>T	uc003lif.2	+	1	2190	c.2190C>T	c.(2188-2190)GGC>GGT	p.G730G	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.G730G|PCDHA13_uc003lid.2_Silent_p.G730G	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	730	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)															---	---	---	---
PCDHAC1	56135	broad.mit.edu	37	5	140306840	140306840	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140306840A>G	uc003lih.2	+	1	539	c.363A>G	c.(361-363)TCA>TCG	p.S121S	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_uc003lig.1_Silent_p.S121S	NM_018898	NP_061721	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1 isoform 1	121	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHB7	56129	broad.mit.edu	37	5	140553146	140553146	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140553146C>T	uc003lit.2	+	1	904	c.730C>T	c.(730-732)CGG>TGG	p.R244W		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	244	Extracellular (Potential).				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)															---	---	---	---
PCDHB7	56129	broad.mit.edu	37	5	140554034	140554034	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140554034G>A	uc003lit.2	+	1	1792	c.1618G>A	c.(1618-1620)GCG>ACG	p.A540T		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	540	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)															---	---	---	---
PCDHB16	57717	broad.mit.edu	37	5	140564007	140564007	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140564007C>T	uc003liv.2	+	1	3028	c.1873C>T	c.(1873-1875)CGC>TGC	p.R625C	PCDHB9_uc003liw.1_5'Flank	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	625	Cadherin 6.|Extracellular (Potential).				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)															---	---	---	---
PCDHB9	56127	broad.mit.edu	37	5	140568534	140568534	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140568534G>A	uc003liw.1	+	3	1643	c.1643G>A	c.(1642-1644)CGC>CAC	p.R548H		NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	548	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHGA2	56113	broad.mit.edu	37	5	140719254	140719254	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140719254C>T	uc003ljk.1	+	1	901	c.716C>T	c.(715-717)GCG>GTG	p.A239V	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Missense_Mutation_p.A239V	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	239	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGB4	8641	broad.mit.edu	37	5	140768432	140768432	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140768432G>A	uc003lkc.1	+	1	981	c.981G>A	c.(979-981)GCG>GCA	p.A327A	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_uc011dav.1_Silent_p.A327A	NM_003736	NP_003727	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4 isoform 1	327	Cadherin 3.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|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)															---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142437258	142437258	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142437258G>A	uc011dbj.1	+	17	1519	c.1484G>A	c.(1483-1485)CGG>CAG	p.R495Q	ARHGAP26_uc003lmt.2_Missense_Mutation_p.R495Q|ARHGAP26_uc003lmw.2_Missense_Mutation_p.R495Q	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal	495	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)															---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142513670	142513670	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142513670C>T	uc011dbj.1	+	19	1872	c.1837C>T	c.(1837-1839)CAG>TAG	p.Q613*	ARHGAP26_uc003lmt.2_Nonsense_Mutation_p.Q613*|ARHGAP26_uc003lmw.2_Nonsense_Mutation_p.Q613*	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal	613	Ser-rich.				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)															---	---	---	---
SH3RF2	153769	broad.mit.edu	37	5	145393517	145393517	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145393517C>T	uc003lnt.2	+	5	1190	c.952C>T	c.(952-954)CGC>TGC	p.R318C	SH3RF2_uc011dbl.1_Missense_Mutation_p.R318C	NM_152550	NP_689763	Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	318							ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
DPYSL3	1809	broad.mit.edu	37	5	146778698	146778698	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146778698C>T	uc003lon.1	-	11	1338	c.1228G>A	c.(1228-1230)GTC>ATC	p.V410I	DPYSL3_uc003loo.2_Missense_Mutation_p.V524I	NM_001387	NP_001378	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	410					axon guidance|pyrimidine base catabolic process|signal transduction	cytosol|growth cone	dihydropyrimidinase activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ABLIM3	22885	broad.mit.edu	37	5	148577904	148577904	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148577904G>A	uc003lpy.2	+	4	525	c.274G>A	c.(274-276)GAA>AAA	p.E92K	ABLIM3_uc003lpz.1_Missense_Mutation_p.E92K|ABLIM3_uc003lqa.1_Silent_p.A73A|ABLIM3_uc003lqb.2_Missense_Mutation_p.E92K|ABLIM3_uc003lqc.1_Missense_Mutation_p.E92K|ABLIM3_uc003lqd.1_Missense_Mutation_p.E92K|ABLIM3_uc003lqf.2_Missense_Mutation_p.E92K|ABLIM3_uc003lqe.1_Missense_Mutation_p.E92K	NM_014945	NP_055760	O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	92	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)															---	---	---	---
PDE6A	5145	broad.mit.edu	37	5	149263008	149263008	+	Missense_Mutation	SNP	G	A	A	rs142092713		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149263008G>A	uc003lrg.3	-	17	2239	c.2119C>T	c.(2119-2121)CGG>TGG	p.R707W		NM_000440	NP_000431	P16499	PDE6A_HUMAN	phosphodiesterase 6A	707					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)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150948236	150948236	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150948236T>G	uc003lue.3	-	1	270	c.257A>C	c.(256-258)GAG>GCG	p.E86A	GM2A_uc011dcs.1_Intron|FAT2_uc010jhx.1_Missense_Mutation_p.E86A	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	86	Extracellular (Potential).|Cadherin 1.				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)															---	---	---	---
ADRA1B	147	broad.mit.edu	37	5	159399008	159399008	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159399008G>A	uc003lxt.1	+	2	1245	c.1072G>A	c.(1072-1074)GCT>ACT	p.A358T		NM_000679	NP_000670	P35368	ADA1B_HUMAN	alpha-1B-adrenergic receptor	358	Cytoplasmic (By similarity).				cell proliferation|cell-cell signaling|G-protein signaling, coupled to cAMP nucleotide second messenger|intracellular protein kinase cascade	integral to plasma membrane	alpha1-adrenergic receptor activity			lung(1)	1	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Alfuzosin(DB00346)|Bethanidine(DB00217)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Guanfacine(DB01018)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Modafinil(DB00745)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Olanzapine(DB00334)|Phendimetrazine(DB01579)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Trazodone(DB00656)													---	---	---	---
FBLL1	345630	broad.mit.edu	37	5	167957486	167957486	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167957486G>A	uc011dep.1	+	1	905	c.692G>A	c.(691-693)CGA>CAA	p.R231Q		NR_024356				RecName: Full=rRNA/tRNA 2'-O-methyltransferase fibrillarin-like protein 1;          EC=2.1.1.-;												0																		---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169129410	169129410	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169129410G>A	uc003maf.2	+	14	1442	c.1362G>A	c.(1360-1362)GCG>GCA	p.A454A	DOCK2_uc011der.1_RNA|DOCK2_uc010jjm.2_5'Flank|DOCK2_uc010jjl.1_Silent_p.A5A	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	454	DHR-1.				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)													OREG0017017	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GABRP	2568	broad.mit.edu	37	5	170236617	170236617	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170236617G>A	uc003mau.2	+	9	1076	c.878G>A	c.(877-879)CGC>CAC	p.R293H	GABRP_uc011dev.1_Intron	NM_014211	NP_055026	O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	293						cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			breast(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)													OREG0017032	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
STK10	6793	broad.mit.edu	37	5	171614943	171614943	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171614943A>G	uc003mbo.1	-	1	404	c.104T>C	c.(103-105)GTG>GCG	p.V35A		NM_005990	NP_005981	O94804	STK10_HUMAN	serine/threonine kinase 10	35							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)															---	---	---	---
C5orf41	153222	broad.mit.edu	37	5	172513563	172513563	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172513563G>A	uc003mch.2	+	3	373	c.69G>A	c.(67-69)TCG>TCA	p.S23S	C5orf41_uc003mcg.2_Silent_p.S23S|C5orf41_uc003mcf.2_Silent_p.S23S|C5orf41_uc011dfd.1_Silent_p.S23S	NM_153607	NP_705835	Q8IUR6	CE041_HUMAN	luman-recruiting factor	23							protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
HMP19	51617	broad.mit.edu	37	5	173491266	173491266	+	Missense_Mutation	SNP	C	T	T	rs142224266		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173491266C>T	uc003mcx.2	+	3	306	c.161C>T	c.(160-162)CCG>CTG	p.P54L		NM_015980	NP_057064	Q9Y328	NSG2_HUMAN	HMP19 protein	54	Cytoplasmic (Potential).				dopamine receptor signaling pathway	cytoplasmic vesicle membrane|Golgi cisterna membrane|integral to membrane|multivesicular body membrane	dopamine receptor binding			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00925)|all_lung(126;0.0148)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
HK3	3101	broad.mit.edu	37	5	176310832	176310832	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176310832C>T	uc003mfa.2	-	15	2084	c.1992G>A	c.(1990-1992)ACG>ACA	p.T664T	HK3_uc003mez.2_Silent_p.T220T	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3	664	Catalytic.				glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	7	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
RUFY1	80230	broad.mit.edu	37	5	179021923	179021923	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179021923A>T	uc003mka.1	+	12	1470	c.1470A>T	c.(1468-1470)AAA>AAT	p.K490N	RUFY1_uc003mkb.1_Missense_Mutation_p.K382N|RUFY1_uc003mkc.1_Missense_Mutation_p.K382N|RUFY1_uc003mkd.1_Missense_Mutation_p.K92N	NM_025158	NP_079434	Q96T51	RUFY1_HUMAN	RUN and FYVE domain-containing 1 isoform a	490	Potential.				endocytosis|protein transport	early endosome membrane	lipid binding|zinc ion binding			ovary(4)|breast(1)	5	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)												HNSCC(44;0.11)			---	---	---	---
MGAT4B	11282	broad.mit.edu	37	5	179225978	179225978	+	Silent	SNP	G	A	A	rs41285561		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179225978G>A	uc003mks.2	-	11	1662	c.1293C>T	c.(1291-1293)GCC>GCT	p.A431A	MGAT4B_uc003mkp.2_Silent_p.A285A|MGAT4B_uc003mkq.2_Missense_Mutation_p.R207C|MGAT4B_uc003mkr.2_Silent_p.A446A|MIR1229_hsa-mir-1229|MI0006319_5'Flank	NM_014275	NP_055090	Q9UQ53	MGT4B_HUMAN	alpha-1,3-mannosyl-glycoprotein	431	Lumenal (Potential).				N-glycan processing|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				0	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
MGAT4B	11282	broad.mit.edu	37	5	179229020	179229020	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179229020C>T	uc003mks.2	-						MGAT4B_uc003mkp.2_5'Flank|MGAT4B_uc003mkq.2_5'Flank|MGAT4B_uc003mkr.2_Missense_Mutation_p.R31H	NM_014275	NP_055090			alpha-1,3-mannosyl-glycoprotein						N-glycan processing|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				0	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)													OREG0017110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DUSP22	56940	broad.mit.edu	37	6	348155	348155	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:348155G>A	uc003msx.2	+	6	755	c.316G>A	c.(316-318)GTC>ATC	p.V106I	DUSP22_uc011dhn.1_Missense_Mutation_p.V106I|DUSP22_uc003msy.1_Missense_Mutation_p.V63I	NM_020185	NP_064570	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	106	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	p.V106I(1)		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	637806	637806	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:637806G>A	uc003mtd.2	-	2	147	c.13C>T	c.(13-15)CGA>TGA	p.R5*	EXOC2_uc003mte.2_Nonsense_Mutation_p.R5*|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein	5					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)														---	---	---	---
BPHL	670	broad.mit.edu	37	6	3127615	3127615	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3127615T>C	uc003mva.2	+	3	400	c.351T>C	c.(349-351)GAT>GAC	p.D117D	BPHL_uc003muz.2_RNA|BPHL_uc011dht.1_RNA|BPHL_uc003muy.2_Silent_p.D100D	NM_004332	NP_004323	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like precursor	117					cellular amino acid metabolic process|response to toxin	mitochondrion	hydrolase activity				0	Ovarian(93;0.0386)	all_hematologic(90;0.108)																---	---	---	---
TUBB2A	7280	broad.mit.edu	37	6	3154798	3154798	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3154798G>A	uc003mvc.2	-	4	723	c.637C>T	c.(637-639)CGC>TGC	p.R213C	TUBB2A_uc003mvb.2_Missense_Mutation_p.R206C|TUBB2A_uc003mvd.2_Missense_Mutation_p.R176C	NM_001069	NP_001060	Q13885	TBB2A_HUMAN	tubulin, beta 2	213					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			skin(1)	1	Ovarian(93;0.0386)	all_hematologic(90;0.0895)																---	---	---	---
BMP6	654	broad.mit.edu	37	6	7862635	7862635	+	Missense_Mutation	SNP	G	A	A	rs144134653		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7862635G>A	uc003mxu.3	+	4	1286	c.1108G>A	c.(1108-1110)GTG>ATG	p.V370M		NM_001718	NP_001709	P22004	BMP6_HUMAN	bone morphogenetic protein 6 preproprotein	370					BMP signaling pathway|cartilage development|growth|immune response|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|SMAD protein signal transduction	extracellular space	BMP receptor binding|cytokine activity|growth factor activity|protein heterodimerization activity			large_intestine(2)|ovary(1)	3	Ovarian(93;0.0721)																	---	---	---	---
ALDH5A1	7915	broad.mit.edu	37	6	24503644	24503644	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24503644G>T	uc003neg.2	+	3	620	c.592G>T	c.(592-594)GCT>TCT	p.A198S	ALDH5A1_uc003nef.2_Missense_Mutation_p.A198S	NM_001080	NP_001071	P51649	SSDH_HUMAN	aldehyde dehydrogenase 5A1 isoform 2 precursor	198					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)													---	---	---	---
SLC17A3	10786	broad.mit.edu	37	6	25862609	25862609	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25862609G>A	uc003nfi.3	-	3	265	c.155C>T	c.(154-156)ACG>ATG	p.T52M	SLC17A3_uc003nfk.3_Missense_Mutation_p.T52M|SLC17A3_uc011djz.1_Missense_Mutation_p.T52M|SLC17A3_uc011dka.1_Missense_Mutation_p.T52M	NM_006632	NP_006623	O00476	NPT4_HUMAN	solute carrier family 17 (sodium phosphate),	52					glucose-6-phosphate transport|urate metabolic process	apical plasma membrane|brush border membrane|endoplasmic reticulum membrane|integral to plasma membrane|perinuclear region of cytoplasm	drug transmembrane transporter activity|efflux transmembrane transporter activity|organic anion transmembrane transporter activity|sodium:phosphate symporter activity|toxin transporter activity|urate transmembrane transporter activity|voltage-gated anion channel activity				0																		---	---	---	---
BTN3A1	11119	broad.mit.edu	37	6	26406130	26406130	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26406130C>T	uc003nhv.2	+						BTN3A1_uc011dkj.1_Intron|BTN3A1_uc011dkk.1_Intron|BTN3A1_uc010jqj.2_Intron	NM_007048	NP_008979			butyrophilin, subfamily 3, member A1 isoform a						lipid metabolic process	integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
ABT1	29777	broad.mit.edu	37	6	26598515	26598515	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26598515C>T	uc003nii.2	+	3	492	c.461C>T	c.(460-462)TCC>TTC	p.S154F		NM_013375	NP_037507	Q9ULW3	ABT1_HUMAN	activator of basal transcription 1	154					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleolus	DNA binding|nucleotide binding|protein binding|RNA binding|transcription coactivator activity			ovary(1)	1																		---	---	---	---
ZNF184	7738	broad.mit.edu	37	6	27419587	27419587	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27419587C>T	uc003njj.2	-	5	2562	c.1751G>A	c.(1750-1752)CGA>CAA	p.R584Q	ZNF184_uc010jqv.2_Missense_Mutation_p.R584Q|ZNF184_uc003nji.2_Missense_Mutation_p.R584Q	NM_007149	NP_009080	Q99676	ZN184_HUMAN	zinc finger protein 184	584					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
HIST1H3I	8354	broad.mit.edu	37	6	27839989	27839989	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27839989G>A	uc003njy.2	-	1	111	c.105C>T	c.(103-105)GGC>GGT	p.G35G		NM_003533	NP_003524	P68431	H31_HUMAN	histone cluster 1, H3i	35					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)	1																		---	---	---	---
PGBD1	84547	broad.mit.edu	37	6	28251732	28251732	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28251732C>T	uc003nky.2	+	2	512	c.142C>T	c.(142-144)CGG>TGG	p.R48W	PGBD1_uc003nkz.2_Missense_Mutation_p.R48W	NM_032507	NP_115896	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	48	SCAN box.				viral reproduction	membrane|nucleus	scavenger receptor activity|sequence-specific DNA binding transcription factor activity			ovary(4)	4																		---	---	---	---
TRIM26	7726	broad.mit.edu	37	6	30154048	30154048	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30154048C>T	uc003npr.2	-	9	1434	c.1225G>A	c.(1225-1227)GAC>AAC	p.D409N	TRIM26_uc003nps.2_Missense_Mutation_p.D409N|TRIM26_uc010jry.2_Missense_Mutation_p.D139N|TRIM26_uc003npt.2_Missense_Mutation_p.D409N	NM_003449	NP_003440	Q12899	TRI26_HUMAN	tripartite motif-containing 26	409	B30.2/SPRY.						DNA binding|zinc ion binding			ovary(2)|lung(1)	3																		---	---	---	---
ABCF1	23	broad.mit.edu	37	6	30554313	30554313	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30554313A>G	uc003nql.2	+	19	2043	c.1948A>G	c.(1948-1950)ATG>GTG	p.M650V	ABCF1_uc003nqm.2_Missense_Mutation_p.M612V|ABCF1_uc010jsb.2_Intron	NM_001025091	NP_001020262	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F, member 1	650	ABC transporter 2.				inflammatory response|translational initiation	nuclear envelope|nuclear envelope|nucleoplasm|nucleoplasm|polysomal ribosome	ATP binding|ATP binding|ATPase activity|protein binding|ribosome binding|translation activator activity|translation factor activity, nucleic acid binding			ovary(2)	2																		---	---	---	---
GTF2H4	2968	broad.mit.edu	37	6	30879001	30879001	+	Silent	SNP	G	T	T	rs143011675	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30879001G>T	uc003nsa.1	+	7	834	c.627G>T	c.(625-627)CCG>CCT	p.P209P	GTF2H4_uc010jsf.2_Silent_p.P209P|GTF2H4_uc011dmv.1_Silent_p.P153P|GTF2H4_uc003nsb.1_Silent_p.P47P|GTF2H4_uc011dmw.1_Silent_p.P215P|VARS2_uc003nsc.1_5'Flank|VARS2_uc003nsd.2_5'Flank|VARS2_uc011dmx.1_5'Flank|VARS2_uc011dmy.1_5'Flank	NM_001517	NP_001508	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4,	209					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	holo TFIIH complex	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|breast(1)	3													NER					---	---	---	---
BAT2	7916	broad.mit.edu	37	6	31590652	31590652	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31590652A>C	uc003nvb.3	+	2	335	c.86A>C	c.(85-87)AAG>ACG	p.K29T	BAT2_uc011dnv.1_RNA|BAT2_uc003nvc.3_Missense_Mutation_p.K29T|SNORA38_uc003nvd.2_5'Flank|BAT2_uc003nve.2_5'Flank	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	29						cytoplasm|nucleus	protein binding				0																		---	---	---	---
BAT2	7916	broad.mit.edu	37	6	31597497	31597497	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31597497G>A	uc003nvb.3	+	14	2378	c.2129G>A	c.(2128-2130)CGG>CAG	p.R710Q	BAT2_uc011dnv.1_Intron|BAT2_uc003nvc.3_Missense_Mutation_p.R710Q	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	710	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0																		---	---	---	---
C6orf26	401251	broad.mit.edu	37	6	31731318	31731318	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31731318G>A	uc003nxa.3	+	2	300	c.241G>A	c.(241-243)GGG>AGG	p.G81R	MSH5_uc003nwz.3_RNA	NM_001039651	NP_001034740	Q5SSQ6	G7D_HUMAN	hypothetical protein LOC401251	81											0																		---	---	---	---
SLC44A4	80736	broad.mit.edu	37	6	31833884	31833884	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31833884G>A	uc010jti.2	-	14	1319	c.1253C>T	c.(1252-1254)TCG>TTG	p.S418L		NM_025257	NP_079533	Q53GD3	CTL4_HUMAN	choline transporter-like protein 4	418	Extracellular (Potential).					integral to membrane|plasma membrane	choline transmembrane transporter activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4					Choline(DB00122)													---	---	---	---
EGFL8	80864	broad.mit.edu	37	6	32135153	32135153	+	Missense_Mutation	SNP	G	A	A	rs149576421		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32135153G>A	uc003oab.1	+	7	686	c.628G>A	c.(628-630)GCT>ACT	p.A210T	PPT2_uc003nzy.1_RNA|EGFL8_uc003oac.1_Missense_Mutation_p.A210T	NM_030652	NP_085155	Q99944	EGFL8_HUMAN	NG3 protein precursor	210	Potential.					extracellular region|integral to membrane	calcium ion binding				0																		---	---	---	---
HLA-DRA	3122	broad.mit.edu	37	6	32411064	32411064	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32411064T>C	uc003obh.2	+	3	512	c.431T>C	c.(430-432)GTC>GCC	p.V144A	HLA-DRA_uc003obi.2_Missense_Mutation_p.V119A	NM_019111	NP_061984	P01903	DRA_HUMAN	major histocompatibility complex, class II, DR	144	Ig-like C1-type.|Extracellular (Potential).|Alpha-2.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|Golgi apparatus|integral to plasma membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity			ovary(1)|skin(1)	2														T-cell_Lymphoma_(Cutaneous)__Familial_Clustering_of|Kaposi_Sarcoma_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	6	32427865	32427865	+	IGR	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32427865T>C								HLA-DRA (15044 upstream) : HLA-DRB1 (57298 downstream)																																			---	---	---	---
TAP2	6891	broad.mit.edu	37	6	32782287	32782287	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32782287C>T	uc011dqf.1	-	14	2396	c.2274G>A	c.(2272-2274)GGG>GGA	p.G758G	HLA-DOB_uc003oca.2_Silent_p.G151G|HLA-DOB_uc011dqg.1_Silent_p.G151G	NM_018833	NP_061313	Q03519	TAP2_HUMAN	transporter 2, ATP-binding cassette, sub-family	Error:Variant_position_missing_in_Q03519_after_alignment					antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent|cytosol to ER transport|intracellular transport of viral proteins in host cell|peptide antigen transport|positive regulation of antigen processing and presentation of peptide antigen via MHC class I|positive regulation of T cell mediated cytotoxicity	nucleus|plasma membrane|TAP complex	ATP binding|MHC class I protein binding|oligopeptide-transporting ATPase activity|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|tapasin binding				0																		---	---	---	---
COL11A2	1302	broad.mit.edu	37	6	33144778	33144778	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33144778G>A	uc003ocx.1	-	25	2289	c.2061C>T	c.(2059-2061)GAC>GAT	p.D687D	COL11A2_uc010jul.1_Intron|COL11A2_uc003ocy.1_Silent_p.D601D|COL11A2_uc003ocz.1_Silent_p.D580D	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	687	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																		---	---	---	---
B3GALT4	8705	broad.mit.edu	37	6	33245751	33245751	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33245751G>A	uc003odr.2	+	1	835	c.555G>A	c.(553-555)CTG>CTA	p.L185L		NM_003782	NP_003773	O96024	B3GT4_HUMAN	UDP-Gal:betaGlcNAc beta	185	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	ganglioside galactosyltransferase activity|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)|breast(1)	2																		---	---	---	---
UHRF1BP1	54887	broad.mit.edu	37	6	34825149	34825149	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34825149T>C	uc003oju.3	+	12	1709	c.1475T>C	c.(1474-1476)CTT>CCT	p.L492P	UHRF1BP1_uc010jvm.1_RNA|UHRF1BP1_uc010jvn.2_RNA|UHRF1BP1_uc010jvo.2_5'Flank	NM_017754	NP_060224	Q6BDS2	URFB1_HUMAN	ICBP90 binding protein 1	492										ovary(3)	3																		---	---	---	---
MDGA1	266727	broad.mit.edu	37	6	37619917	37619917	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37619917G>A	uc003onu.1	-	7	2361	c.1182C>T	c.(1180-1182)CCC>CCT	p.P394P	MDGA1_uc003onw.3_RNA	NM_153487	NP_705691	Q8NFP4	MDGA1_HUMAN	MAM domain containing	394	Ig-like 4.				brain development|neuron migration|spinal cord association neuron differentiation	anchored to plasma membrane				central_nervous_system(2)	2																		---	---	---	---
ZFAND3	60685	broad.mit.edu	37	6	38120107	38120107	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38120107T>C	uc003onx.2	+	6	1041	c.626T>C	c.(625-627)GTG>GCG	p.V209A		NM_021943	NP_068762	Q9H8U3	ZFAN3_HUMAN	zinc finger, AN1-type domain 3	209							DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38840746	38840746	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38840746C>T	uc003ooe.1	+	49	7251	c.6651C>T	c.(6649-6651)TCC>TCT	p.S2217S		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																		---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42633221	42633221	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42633221A>G	uc011dur.1	+	33	3773	c.3773A>G	c.(3772-3774)CAG>CGG	p.Q1258R	UBR2_uc011dus.1_Missense_Mutation_p.Q903R|UBR2_uc003osh.2_RNA	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	1258					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	42796237	42796237	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42796237G>A	uc003osn.1	+	6	317	c.166G>A	c.(166-168)GAT>AAT	p.D56N	KIAA0240_uc003osm.1_Missense_Mutation_p.D56N|KIAA0240_uc011duw.1_Missense_Mutation_p.D56N|KIAA0240_uc003oso.1_Missense_Mutation_p.D56N|KIAA0240_uc003osp.1_Missense_Mutation_p.D56N	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506	56										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)															---	---	---	---
CUL9	23113	broad.mit.edu	37	6	43152490	43152490	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43152490G>A	uc003ouk.2	+	2	517	c.442G>A	c.(442-444)GTG>ATG	p.V148M	CUL9_uc003ouj.1_Missense_Mutation_p.V148M|CUL9_uc003oul.2_Missense_Mutation_p.V148M|CUL9_uc010jyk.2_Translation_Start_Site|CUL9_uc003oum.1_5'Flank	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	148					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																		---	---	---	---
TDRD6	221400	broad.mit.edu	37	6	46656522	46656522	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46656522C>T	uc003oyj.2	+	1	657	c.657C>T	c.(655-657)AGC>AGT	p.S219S	TDRD6_uc010jze.2_Silent_p.S213S	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	219					cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)|skin(1)	6			Lung(136;0.192)															---	---	---	---
C6orf138	442213	broad.mit.edu	37	6	47846191	47846191	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47846191G>T	uc011dwm.1	-	3	2423	c.2338C>A	c.(2338-2340)CTG>ATG	p.L780M	C6orf138_uc011dwn.1_Missense_Mutation_p.L544M	NM_001013732	NP_001013754	Q6ZW05	CF138_HUMAN	hypothetical protein LOC442213	797	Helical; (Potential).					integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1																		---	---	---	---
KIAA1586	57691	broad.mit.edu	37	6	56919147	56919147	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56919147G>A	uc003pdj.2	+	4	2020	c.1850G>A	c.(1849-1851)CGC>CAC	p.R617H	KIAA1586_uc011dxm.1_Missense_Mutation_p.R590H	NM_020931	NP_065982	Q9HCI6	K1586_HUMAN	hypothetical protein LOC57691	617							nucleic acid binding				0	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)															---	---	---	---
EYS	346007	broad.mit.edu	37	6	66045023	66045023	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66045023C>A	uc011dxu.1	-	11	2154	c.1616G>T	c.(1615-1617)TGC>TTC	p.C539F	EYS_uc003peq.2_Missense_Mutation_p.C539F|EYS_uc003per.1_Missense_Mutation_p.C539F	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	539					response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
COL9A1	1297	broad.mit.edu	37	6	71011710	71011710	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71011710G>A	uc003pfg.3	-	2	241	c.82C>T	c.(82-84)CGC>TGC	p.R28C		NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor	28	Nonhelical region (NC4).				axon guidance|cell adhesion|organ morphogenesis	collagen type IX	metal ion binding			ovary(4)	4																		---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72678706	72678706	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72678706C>T	uc003pga.2	+	2	262	c.185C>T	c.(184-186)GCG>GTG	p.A62V		NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	62	RabBD.				calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73902416	73902416	+	Splice_Site	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73902416T>C	uc003pgk.2	+	13	2183	c.1836_splice	c.e13+2	p.Q612_splice	KCNQ5_uc011dyh.1_Splice_Site_p.Q631_splice|KCNQ5_uc011dyi.1_Splice_Site_p.Q622_splice|KCNQ5_uc010kat.2_Splice_Site_p.Q603_splice|KCNQ5_uc011dyj.1_Splice_Site_p.Q502_splice|KCNQ5_uc011dyk.1_Splice_Site_p.Q362_splice	NM_019842	NP_062816			potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)														---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75797321	75797321	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75797321G>T	uc003phs.2	-	65	9319	c.9153C>A	c.(9151-9153)AGC>AGA	p.S3051R	COL12A1_uc003pht.2_Missense_Mutation_p.S1887R	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	3051	Nonhelical region (NC1).				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75814988	75814988	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75814988A>G	uc003phs.2	-	54	8365	c.8199T>C	c.(8197-8199)CCT>CCC	p.P2733P	COL12A1_uc003pht.2_Silent_p.P1569P	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	2733	Nonhelical region (NC3).				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																		---	---	---	---
SNX14	57231	broad.mit.edu	37	6	86223561	86223561	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86223561T>C	uc003pkr.2	-	26	2803	c.2610A>G	c.(2608-2610)AAA>AAG	p.K870K	SNX14_uc003pkp.2_Silent_p.K733K|SNX14_uc003pkq.2_Silent_p.K476K|SNX14_uc011dzg.1_Silent_p.K818K|SNX14_uc003pks.2_Silent_p.K817K|SNX14_uc003pkt.2_Silent_p.K861K	NM_153816	NP_722523	Q9Y5W7	SNX14_HUMAN	sorting nexin 14 isoform a	870					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)														---	---	---	---
ANKRD6	22881	broad.mit.edu	37	6	90340559	90340559	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90340559G>A	uc003pni.3	+	16	2361	c.2020G>A	c.(2020-2022)GCT>ACT	p.A674T	ANKRD6_uc003pne.3_Missense_Mutation_p.A669T|ANKRD6_uc003pnf.3_Missense_Mutation_p.A639T|ANKRD6_uc011dzy.1_Missense_Mutation_p.A674T|ANKRD6_uc010kcd.2_Missense_Mutation_p.A610T|LYRM2_uc010kce.1_Intron|LYRM2_uc003png.2_Intron|ANKRD6_uc003pnh.3_Missense_Mutation_p.A270T|LYRM2_uc010kcf.1_Intron|ANKRD6_uc003pnj.3_Missense_Mutation_p.A270T	NM_014942	NP_055757	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	674							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	90402442	90402442	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90402442G>A	uc003pnn.1	-	63	10423	c.10307C>T	c.(10306-10308)GCC>GTC	p.A3436V		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	3436					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)														---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90642584	90642584	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90642584G>A	uc011eab.1	-	9	2878	c.2069C>T	c.(2068-2070)TCA>TTA	p.S690L	BACH2_uc003pnw.2_Missense_Mutation_p.S690L	NM_021813	NP_068585	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper	690	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)														---	---	---	---
EPHA7	2045	broad.mit.edu	37	6	93967182	93967182	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93967182T>C	uc003poe.2	-	12	2411	c.2170A>G	c.(2170-2172)AGG>GGG	p.R724G	EPHA7_uc003pof.2_Missense_Mutation_p.R719G|EPHA7_uc011eac.1_Missense_Mutation_p.R720G	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	724	Cytoplasmic (Potential).|Protein kinase.					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)														---	---	---	---
KLHL32	114792	broad.mit.edu	37	6	97587132	97587132	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97587132C>T	uc010kcm.1	+	11	2309	c.1837C>T	c.(1837-1839)CCT>TCT	p.P613S	KLHL32_uc011ead.1_Missense_Mutation_p.P577S|KLHL32_uc003poz.2_Missense_Mutation_p.P169S|KLHL32_uc011eae.1_Missense_Mutation_p.P544S|KLHL32_uc003ppa.2_RNA	NM_052904	NP_443136	Q96NJ5	KLH32_HUMAN	kelch-like 32	613										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)														---	---	---	---
C6orf167	253714	broad.mit.edu	37	6	97711260	97711260	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97711260A>G	uc003ppb.2	-	9	1159	c.893T>C	c.(892-894)GTT>GCT	p.V298A	C6orf167_uc011eaf.1_Missense_Mutation_p.V298A|C6orf167_uc010kcn.1_Missense_Mutation_p.V72A|C6orf167_uc010kco.1_Intron|C6orf167_uc003ppc.2_Missense_Mutation_p.V298A	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714	298					double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)														---	---	---	---
C6orf186	728464	broad.mit.edu	37	6	110620298	110620298	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110620298C>A	uc010kdu.1	-	4	613	c.613G>T	c.(613-615)GTG>TTG	p.V205L	C6orf186_uc003pub.2_Missense_Mutation_p.V8L	NM_001123364	NP_001116836	Q5JXM2	CF186_HUMAN	chromosome 6 open reading frame 186 precursor	205						extracellular region					0																		---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117674208	117674208	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117674208C>A	uc003pxp.1	-	26	4465	c.4266G>T	c.(4264-4266)AAG>AAT	p.K1422N	ROS1_uc011ebi.1_RNA|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	1422	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								---	---	---	---
GJA1	2697	broad.mit.edu	37	6	121768495	121768495	+	Missense_Mutation	SNP	G	A	A	rs111717577		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121768495G>A	uc003pyr.2	+	2	752	c.502G>A	c.(502-504)GCC>ACC	p.A168T	GJA1_uc011ebo.1_Missense_Mutation_p.A69T|GJA1_uc011ebp.1_5'UTR	NM_000165	NP_000156	P17302	CXA1_HUMAN	connexin 43	168	Helical; (Potential).				cell-cell signaling|cellular membrane organization|gap junction assembly|heart development|muscle contraction|positive regulation of I-kappaB kinase/NF-kappaB cascade	connexon complex|Golgi-associated vesicle membrane|integral to plasma membrane|membrane raft	ion transmembrane transporter activity|signal transducer activity			ovary(2)	2				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)													---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128318068	128318068	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128318068G>T	uc003qbk.2	-	17	3109	c.2742C>A	c.(2740-2742)AAC>AAA	p.N914K	PTPRK_uc003qbj.2_Missense_Mutation_p.N915K|PTPRK_uc010kfc.2_Missense_Mutation_p.N915K|PTPRK_uc011ebu.1_Missense_Mutation_p.N931K	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	914	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)														---	---	---	---
ARHGAP18	93663	broad.mit.edu	37	6	129959703	129959703	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129959703G>T	uc003qbr.2	-	3	477	c.388C>A	c.(388-390)CCA>ACA	p.P130T	ARHGAP18_uc011ebw.1_Missense_Mutation_p.P130T	NM_033515	NP_277050	Q8N392	RHG18_HUMAN	Rho GTPase activating protein 18	130					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)														---	---	---	---
L3MBTL3	84456	broad.mit.edu	37	6	130374144	130374144	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130374144C>T	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)														---	---	---	---
REPS1	85021	broad.mit.edu	37	6	139226190	139226190	+	3'UTR	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139226190C>T	uc003qii.2	-	20					REPS1_uc003qig.3_3'UTR|REPS1_uc011edr.1_3'UTR|REPS1_uc003qij.2_3'UTR|REPS1_uc003qik.2_3'UTR	NM_031922	NP_114128			RALBP1 associated Eps domain containing 1							coated pit|plasma membrane	calcium ion binding|SH3 domain binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144811195	144811195	+	Intron	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144811195A>T	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)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146262872	146262872	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146262872G>A	uc003qlf.2	-	10	2776	c.2377C>T	c.(2377-2379)CGT>TGT	p.R793C	SHPRH_uc003qld.2_Missense_Mutation_p.R793C|SHPRH_uc003qle.2_Missense_Mutation_p.R793C|SHPRH_uc003qlg.1_Missense_Mutation_p.R349C|SHPRH_uc003qlj.1_Missense_Mutation_p.R682C	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	793	Helicase ATP-binding; second part.				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)														---	---	---	---
ULBP1	80329	broad.mit.edu	37	6	150290280	150290280	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150290280G>T	uc003qnp.2	+	3	452	c.409G>T	c.(409-411)GGA>TGA	p.G137*		NM_025218	NP_079494	Q9BZM6	N2DL1_HUMAN	UL16 binding protein 1 precursor	137	MHC class I alpha-2 like.				antigen processing and presentation|immune response|natural killer cell activation|regulation of immune response	anchored to membrane|endoplasmic reticulum|MHC class I protein complex	MHC class I receptor activity			pancreas(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.14e-11)														---	---	---	---
C6orf211	79624	broad.mit.edu	37	6	151785658	151785658	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151785658A>T	uc003qok.1	+	4	722	c.463A>T	c.(463-465)ATC>TTC	p.I155F	C6orf211_uc011ees.1_Missense_Mutation_p.I36F	NM_024573	NP_078849	Q9H993	CF211_HUMAN	hypothetical protein LOC79624	155							protein binding				0			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152469223	152469223	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152469223C>A	uc010kiw.2	-	137	25535	c.24933G>T	c.(24931-24933)CAG>CAT	p.Q8311H	SYNE1_uc010kiv.2_Missense_Mutation_p.Q2835H|SYNE1_uc003qos.3_Missense_Mutation_p.Q2835H|SYNE1_uc003qot.3_Missense_Mutation_p.Q8240H|SYNE1_uc003qou.3_Missense_Mutation_p.Q8311H|SYNE1_uc003qop.3_Missense_Mutation_p.Q473H|SYNE1_uc011eez.1_Missense_Mutation_p.Q513H|SYNE1_uc003qoq.3_Missense_Mutation_p.Q513H|SYNE1_uc003qor.3_Missense_Mutation_p.Q1211H	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8311	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153603652	153603652	+	IGR	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153603652C>T								RGS17 (151263 upstream) : OPRM1 (727984 downstream)																																			---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155561718	155561718	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155561718G>A	uc003qqb.2	+	18	4496	c.3223G>A	c.(3223-3225)GGC>AGC	p.G1075S	TIAM2_uc003qqe.2_Missense_Mutation_p.G1075S|TIAM2_uc010kjj.2_Missense_Mutation_p.G608S|TIAM2_uc003qqf.2_Missense_Mutation_p.G451S|TIAM2_uc011efl.1_Missense_Mutation_p.G411S|TIAM2_uc003qqg.2_Missense_Mutation_p.G387S|TIAM2_uc003qqh.2_5'UTR	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1075					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)														---	---	---	---
SYNJ2	8871	broad.mit.edu	37	6	158492720	158492720	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158492720G>T	uc003qqx.1	+	15	2102	c.2027G>T	c.(2026-2028)AGC>ATC	p.S676I	SYNJ2_uc003qqw.1_Missense_Mutation_p.S676I|SYNJ2_uc003qqy.1_Missense_Mutation_p.S389I|SYNJ2_uc003qqz.1_Missense_Mutation_p.S293I|SYNJ2_uc003qra.1_Missense_Mutation_p.S19I	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2	676	Catalytic (By similarity).						nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)														---	---	---	---
SERAC1	84947	broad.mit.edu	37	6	158538748	158538748	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158538748G>A	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)														---	---	---	---
ACAT2	39	broad.mit.edu	37	6	160199806	160199806	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160199806C>T	uc010kjy.2	+	9	1270	c.1139C>T	c.(1138-1140)GCA>GTA	p.A380V	ACAT2_uc011efw.1_Missense_Mutation_p.A409V|TCP1_uc003qsr.2_3'UTR|TCP1_uc003qss.2_3'UTR|TCP1_uc010kjz.2_3'UTR|TCP1_uc003qst.2_3'UTR	NM_005891	NP_005882	Q9BWD1	THIC_HUMAN	acetyl-Coenzyme A acetyltransferase 2	380						mitochondrion|nucleolus	acetyl-CoA C-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)														---	---	---	---
LPA	4018	broad.mit.edu	37	6	161027563	161027563	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161027563C>T	uc003qtl.2	-	18	2851	c.2731G>A	c.(2731-2733)GTC>ATC	p.V911I		NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor	3419	Kringle 30.				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)													---	---	---	---
PHF10	55274	broad.mit.edu	37	6	170118937	170118937	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170118937T>C	uc011egy.1	-	3	351	c.272A>G	c.(271-273)CAA>CGA	p.Q91R	PHF10_uc011egz.1_Missense_Mutation_p.Q91R|PHF10_uc011eha.1_5'Flank	NM_018288	NP_060758	Q8WUB8	PHF10_HUMAN	PHD finger protein 10 isoform a	91	SAY.|Essential to induce neural progenitor proliferation (By similarity).				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)														---	---	---	---
HEATR2	54919	broad.mit.edu	37	7	769421	769421	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:769421C>T	uc010krz.1	+	2	737	c.717C>T	c.(715-717)AAC>AAT	p.N239N	PRKAR1B_uc003siw.1_5'Flank|HEATR2_uc003siz.2_Silent_p.N107N	NM_017802	NP_060272	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	239	HEAT 2.						protein binding			skin(1)	1		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)														---	---	---	---
SUN1	23353	broad.mit.edu	37	7	872217	872217	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:872217C>T	uc011jvp.1	+	2	135	c.56C>T	c.(55-57)ACG>ATG	p.T19M	SUN1_uc010ksa.1_Missense_Mutation_p.T40M|SUN1_uc003sje.1_Missense_Mutation_p.T19M|SUN1_uc003sjf.2_Intron|SUN1_uc011jvq.1_Missense_Mutation_p.T19M	NM_001130965	NP_001124437	O94901	SUN1_HUMAN	unc-84 homolog A isoform a	19	Nuclear.|LMNA-binding.				cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding				0																		---	---	---	---
EIF3B	8662	broad.mit.edu	37	7	2418871	2418871	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2418871C>T	uc003slx.2	+	17	2418	c.2335C>T	c.(2335-2337)CGA>TGA	p.R779*	EIF3B_uc003sly.2_Nonsense_Mutation_p.R779*|EIF3B_uc003sma.2_Nonsense_Mutation_p.R507*|EIF3B_uc003smb.2_RNA	NM_003751	NP_003742	P55884	EIF3B_HUMAN	eukaryotic translation initiation factor 3,	779					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)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5752364	5752364	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5752364T>C	uc003soy.1	-	12	1983	c.1793A>G	c.(1792-1794)TAC>TGC	p.Y598C	RNF216_uc010ksz.1_Missense_Mutation_p.Y220C|RNF216_uc010kta.1_Missense_Mutation_p.Y220C|RNF216_uc011jwj.1_Missense_Mutation_p.Y220C|RNF216_uc003sox.1_Missense_Mutation_p.Y655C	NM_207116	NP_996999	Q9NWF9	RN216_HUMAN	ring finger protein 216 isoform b	598	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)														---	---	---	---
CYTH3	9265	broad.mit.edu	37	7	6210230	6210230	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6210230G>A	uc003spt.2	-	9	863	c.759C>T	c.(757-759)GAC>GAT	p.D253D	CYTH3_uc011jws.1_Silent_p.D168D	NM_004227	NP_004218	O43739	CYH3_HUMAN	cytohesin 3	253					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																		---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21747335	21747335	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21747335C>T	uc003svc.2	+	41	6617	c.6586C>T	c.(6586-6588)CGA>TGA	p.R2196*		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2196	AAA 2 (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				---	---	---	---
IGF2BP3	10643	broad.mit.edu	37	7	23509592	23509592	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23509592G>A	uc003swg.2	-	1	404	c.138C>T	c.(136-138)GAC>GAT	p.D46D	IGF2BP3_uc003swh.1_RNA	NM_006547	NP_006538	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding	46	RRM 1.				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	23811811	23811811	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23811811G>A	uc003sws.3	+	15	1946	c.1879G>A	c.(1879-1881)GAT>AAT	p.D627N	STK31_uc003swt.3_Missense_Mutation_p.D604N|STK31_uc011jze.1_Missense_Mutation_p.D627N|STK31_uc010kuq.2_Missense_Mutation_p.D604N	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a	627							ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9																		---	---	---	---
HOXA3	3200	broad.mit.edu	37	7	27149829	27149829	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27149829G>T	uc011jzl.1	-	2	631	c.431C>A	c.(430-432)CCC>CAC	p.P144H	HOXA3_uc011jzk.1_5'UTR|HOXA3_uc003syk.2_Missense_Mutation_p.P144H	NM_030661	NP_109377	O43365	HXA3_HUMAN	homeobox A3 isoform a	144					angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)	2																		---	---	---	---
C7orf41	222166	broad.mit.edu	37	7	30185810	30185810	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30185810C>T	uc011kab.1	+	2	381	c.180C>T	c.(178-180)AGC>AGT	p.S60S	C7orf41_uc010kvr.1_RNA|C7orf41_uc003tar.1_Silent_p.S60S	NM_152793	NP_690006	Q8N3F0	CG041_HUMAN	hypothetical protein LOC222166	60											0																		---	---	---	---
PDE1C	5137	broad.mit.edu	37	7	31890296	31890296	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31890296G>A	uc003tcm.1	-	8	1279	c.810C>T	c.(808-810)TAC>TAT	p.Y270Y	PDE1C_uc003tcn.1_Silent_p.Y270Y|PDE1C_uc003tco.1_Silent_p.Y330Y|PDE1C_uc003tcr.2_Silent_p.Y270Y|PDE1C_uc003tcs.2_Silent_p.Y270Y	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C	270	Catalytic (By similarity).				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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	38398132	38398132	+	Intron	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38398132T>C	uc003tgp.1	+						uc003tgr.2_Missense_Mutation_p.Y112C					Homo sapiens cDNA FLJ43658 fis, clone SYNOV4004184.																														---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42005174	42005174	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42005174C>A	uc011kbh.1	-	15	3588	c.3497G>T	c.(3496-3498)AGC>ATC	p.S1166I	GLI3_uc011kbg.1_Missense_Mutation_p.S1107I	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	1166					negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19														Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42012141	42012141	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42012141C>A	uc011kbh.1	-	13	1989	c.1898G>T	c.(1897-1899)GGC>GTC	p.G633V	GLI3_uc011kbg.1_Missense_Mutation_p.G574V	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	633					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				---	---	---	---
AEBP1	165	broad.mit.edu	37	7	44151800	44151800	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44151800T>C	uc003tkb.2	+	17	2402	c.2097T>C	c.(2095-2097)TTT>TTC	p.F699F	AEBP1_uc003tkc.3_Silent_p.F274F|AEBP1_uc003tkd.2_Intron	NM_001129	NP_001120	Q8IUX7	AEBP1_HUMAN	adipocyte enhancer binding protein 1 precursor	699	Interaction with PTEN (By similarity).				cell adhesion|muscle organ development|proteolysis|skeletal system development	cytoplasm|extracellular space|nucleus	DNA binding|metallocarboxypeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
ZMIZ2	83637	broad.mit.edu	37	7	44806205	44806205	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44806205C>T	uc003tlr.2	+	18	2721	c.2598C>T	c.(2596-2598)GGC>GGT	p.G866G	ZMIZ2_uc003tlq.2_Silent_p.G808G|ZMIZ2_uc003tls.2_Silent_p.G840G|ZMIZ2_uc003tlt.2_Silent_p.G489G|ZMIZ2_uc010kyj.2_Silent_p.G388G|ZMIZ2_uc003tlu.2_Silent_p.G147G|ZMIZ2_uc010kyk.1_5'Flank	NM_031449	NP_113637	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2 isoform 1	866	Pro-rich.				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	45016545	45016545	+	Missense_Mutation	SNP	C	T	T	rs144045009	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45016545C>T	uc003tmh.2	-	2	365	c.221G>A	c.(220-222)CGG>CAG	p.R74Q	MYO1G_uc003tmg.2_5'Flank|MYO1G_uc010kym.2_Intron|MYO1G_uc003tmi.1_5'UTR|MYO1G_uc003tmj.2_5'UTR	NM_033054	NP_149043	B0I1T2	MYO1G_HUMAN	myosin IG	74	Myosin head-like.					myosin complex|plasma membrane	actin binding|ATP binding|calmodulin binding|motor activity			breast(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48375117	48375117	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48375117G>T	uc003toq.2	+	28	10123	c.10098G>T	c.(10096-10098)ATG>ATT	p.M3366I	ABCA13_uc010kys.1_Missense_Mutation_p.M440I|ABCA13_uc003tos.1_Missense_Mutation_p.M192I	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	3366					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48411974	48411974	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48411974T>G	uc003toq.2	+	33	11038	c.11013T>G	c.(11011-11013)TTT>TTG	p.F3671L	ABCA13_uc010kys.1_Missense_Mutation_p.F745L|ABCA13_uc003tos.1_Missense_Mutation_p.F497L	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	3671					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
COBL	23242	broad.mit.edu	37	7	51097038	51097038	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51097038C>T	uc003tpr.3	-	10	1940	c.1755G>A	c.(1753-1755)GAG>GAA	p.E585E	COBL_uc003tps.2_Silent_p.E642E|COBL_uc011kcl.1_Silent_p.E585E|COBL_uc003tpp.3_Silent_p.E371E|COBL_uc003tpq.3_Silent_p.E526E|COBL_uc003tpo.3_Silent_p.E127E	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	585										skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	70255840	70255840	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70255840C>T	uc003tvw.3	+	19	4381	c.3638C>T	c.(3637-3639)CCG>CTG	p.P1213L	AUTS2_uc003tvx.3_Missense_Mutation_p.P1189L|AUTS2_uc011keg.1_Missense_Mutation_p.P665L	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1	1213										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)														---	---	---	---
TBL2	26608	broad.mit.edu	37	7	72985121	72985121	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72985121T>C	uc003tyh.2	-	7	1194	c.1060A>G	c.(1060-1062)ATT>GTT	p.I354V	TBL2_uc011kex.1_Missense_Mutation_p.I318V|TBL2_uc010lbg.2_Missense_Mutation_p.I259V|TBL2_uc003tyi.2_Missense_Mutation_p.I189V|TBL2_uc011key.1_Missense_Mutation_p.I225V|TBL2_uc010lbh.2_Missense_Mutation_p.I259V	NM_012453	NP_036585	Q9Y4P3	TBL2_HUMAN	transducin (beta)-like 2	354	WD 6.										0		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
MLXIPL	51085	broad.mit.edu	37	7	73011554	73011554	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73011554C>T	uc003tyn.1	-	9	1609	c.1561G>A	c.(1561-1563)GCG>ACG	p.A521T	MLXIPL_uc003tyj.1_5'UTR|MLXIPL_uc003tyk.1_Missense_Mutation_p.A521T|MLXIPL_uc003tyl.1_Missense_Mutation_p.A521T|MLXIPL_uc003tym.1_Missense_Mutation_p.A521T|MLXIPL_uc003tyo.1_RNA|MLXIPL_uc003typ.1_Missense_Mutation_p.A428T|MLXIPL_uc003tyq.1_Missense_Mutation_p.A263T	NM_032951	NP_116569	Q9NP71	WBS14_HUMAN	Williams Beuren syndrome chromosome region 14	521					anatomical structure morphogenesis|energy reserve metabolic process|glucose mediated signaling pathway|intracellular protein kinase cascade|negative regulation of cell cycle arrest|negative regulation of oxidative phosphorylation|negative regulation of peptidyl-serine phosphorylation|positive regulation of cell proliferation|positive regulation of fatty acid biosynthetic process|positive regulation of glycolysis|positive regulation of transcription from RNA polymerase II promoter|triglyceride homeostasis	cytosol|transcription factor complex	carbohydrate response element binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74159243	74159243	+	Missense_Mutation	SNP	G	A	A	rs139477988		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74159243G>A	uc003uau.2	+	21	2267	c.1897G>A	c.(1897-1899)GTC>ATC	p.V633I	GTF2I_uc003uav.2_Missense_Mutation_p.V612I|GTF2I_uc003uaw.2_Missense_Mutation_p.V613I|GTF2I_uc003uay.2_Missense_Mutation_p.V611I|GTF2I_uc003uax.2_Missense_Mutation_p.V592I	NM_032999	NP_127492	P78347	GTF2I_HUMAN	general transcription factor IIi isoform 1	633	GTF2I-like 4.				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																		---	---	---	---
POM121C	100101267	broad.mit.edu	37	7	75066870	75066870	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75066870C>T	uc010lde.1	-	5	1129	c.1129G>A	c.(1129-1131)GCT>ACT	p.A377T	POM121C_uc003udk.3_Missense_Mutation_p.A135T			A8CG34	P121C_HUMAN	Homo sapiens POM121-2 mRNA for nuclear pore membrane protein 121-2, partial cds.	377	Required for targeting to the nucleus and nuclear pore complex.|Pore side (Potential).|Ser-rich.				mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0																		---	---	---	---
SRCRB4D	136853	broad.mit.edu	37	7	76029799	76029799	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76029799G>A	uc003ufb.2	-	4	627	c.279C>T	c.(277-279)AAC>AAT	p.N93N	ZP3_uc003ufc.3_Intron	NM_080744	NP_542782	Q8WTU2	SRB4D_HUMAN	scavenger receptor cysteine rich domain	93	SRCR 1.					extracellular region|membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
PTPN12	5782	broad.mit.edu	37	7	77210825	77210825	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77210825G>A	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																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82390067	82390067	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82390067G>T	uc003uhx.2	-	24	15465	c.15176C>A	c.(15175-15177)TCT>TAT	p.S5059Y		NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4982	C2 2.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
KIAA1324L	222223	broad.mit.edu	37	7	86522383	86522383	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86522383A>G	uc011kha.1	-	20	2904	c.2719T>C	c.(2719-2721)TGC>CGC	p.C907R	KIAA1324L_uc003uif.1_Missense_Mutation_p.C667R|KIAA1324L_uc011kgz.1_Missense_Mutation_p.C793R|KIAA1324L_uc003uie.2_Missense_Mutation_p.C740R	NM_001142749	NP_001136221	A8MWY0	K132L_HUMAN	hypothetical protein LOC222223 isoform 1	907	Extracellular (Potential).					integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)																	---	---	---	---
ADAM22	53616	broad.mit.edu	37	7	87785330	87785330	+	Intron	SNP	C	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87785330C>G	uc003ujn.2	+						ADAM22_uc003ujk.1_Intron|ADAM22_uc003ujl.1_Intron|ADAM22_uc003ujm.2_Intron|ADAM22_uc003ujo.2_Intron|ADAM22_uc003ujp.1_Intron	NM_021723	NP_068369			ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
FZD1	8321	broad.mit.edu	37	7	90894471	90894471	+	Silent	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90894471G>T	uc003ula.2	+	1	689	c.276G>T	c.(274-276)CCG>CCT	p.P92P		NM_003505	NP_003496	Q9UP38	FZD1_HUMAN	frizzled 1 precursor	92	Poly-Pro.|Extracellular (Potential).				autocrine signaling|axonogenesis|brain development|canonical Wnt receptor signaling pathway involved in mesenchymal stem cell differentiation|canonical Wnt receptor signaling pathway involved in osteoblast differentiation|embryo development|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|lung alveolus development|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to drug|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cell surface|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|receptor binding|Wnt receptor activity|Wnt-protein binding				0	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)															---	---	---	---
MTERF	7978	broad.mit.edu	37	7	91503750	91503750	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91503750C>T	uc003ulb.1	-	2	402	c.358G>A	c.(358-360)GTG>ATG	p.V120M	MTERF_uc010let.1_Intron|MTERF_uc003ulc.1_Missense_Mutation_p.V120M|MTERF_uc011khm.1_Missense_Mutation_p.V100M|MTERF_uc010leu.1_Missense_Mutation_p.V100M	NM_006980	NP_008911	Q99551	MTERF_HUMAN	mitochondrial transcription termination factor	120					DNA geometric change|regulation of transcription, DNA-dependent|termination of mitochondrial transcription	mitochondrial nucleoid	double-stranded DNA binding				0	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)															---	---	---	---
COL1A2	1278	broad.mit.edu	37	7	94054966	94054966	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94054966C>T	uc003ung.1	+	43	3297	c.2826C>T	c.(2824-2826)CCC>CCT	p.P942P	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	942					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)			---	---	---	---
DLX6	1750	broad.mit.edu	37	7	96639132	96639132	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96639132C>T	uc003uom.2	+	4	571	c.571C>T	c.(571-573)CGC>TGC	p.R191C	DLX6AS_uc003uol.2_Intron|DLX6AS_uc010lfo.1_Intron	NM_005222	NP_005213	P56179	DLX6_HUMAN	distal-less homeobox 6	101	Homeobox.				nervous system development|skeletal system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)																	---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98581030	98581030	+	Silent	SNP	C	T	T	rs148646770		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98581030C>T	uc003upp.2	+	59	9158	c.8949C>T	c.(8947-8949)GAC>GAT	p.D2983D	TRRAP_uc011kis.1_Silent_p.D2965D|TRRAP_uc003upr.2_Silent_p.D2682D	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	2983	FAT.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ZNF655	79027	broad.mit.edu	37	7	99159544	99159544	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99159544G>A	uc003urh.2	+						ZNF655_uc003urf.2_RNA|ZNF655_uc003urc.2_Missense_Mutation_p.R57H|ZNF655_uc010lfz.2_Intron|ZNF655_uc003ure.2_RNA|ZNF655_uc010lga.2_Intron|ZNF655_uc010lgb.2_Missense_Mutation_p.R57H|ZNF655_uc003uri.2_Intron|ZNF655_uc010lgc.2_Intron|ZNF655_uc003urj.2_Intron	NM_138494	NP_612503			zinc finger protein 655 isoform a						G1 phase|regulation of mitotic cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding|zinc ion binding			ovary(1)	1	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)																	---	---	---	---
ZSCAN21	7589	broad.mit.edu	37	7	99654966	99654966	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99654966G>A	uc003uso.2	+	2	481	c.337G>A	c.(337-339)GCT>ACT	p.A113T	ZSCAN21_uc011kje.1_Missense_Mutation_p.A112T|ZSCAN21_uc003usn.1_Missense_Mutation_p.A112T	NM_145914	NP_666019	Q9Y5A6	ZSC21_HUMAN	zinc finger protein 38	113	SCAN box.				positive regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|protein 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)															---	---	---	---
SPDYE3	441272	broad.mit.edu	37	7	99913460	99913460	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									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																		---	---	---	---
C7orf51	222950	broad.mit.edu	37	7	100087129	100087129	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100087129C>T	uc003uvd.1	+	4	1944	c.1785C>T	c.(1783-1785)ACC>ACT	p.T595T	C7orf51_uc003uve.1_Silent_p.T377T	NM_173564	NP_775835	Q6ZVC0	CG051_HUMAN	hypothetical protein FLJ37538	595										skin(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
TFR2	7036	broad.mit.edu	37	7	100218519	100218519	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100218519C>T	uc003uvv.1	-	18	2408	c.2367G>A	c.(2365-2367)GCG>GCA	p.A789A	TFR2_uc010lhc.1_Silent_p.A330A|TFR2_uc003uvu.1_Silent_p.A618A	NM_003227	NP_003218	Q9UP52	TFR2_HUMAN	transferrin receptor 2	789	Extracellular (Potential).				cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity			ovary(1)|pancreas(1)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)																	---	---	---	---
TFR2	7036	broad.mit.edu	37	7	100226903	100226903	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100226903G>A	uc003uvv.1	-	10	1404	c.1363C>T	c.(1363-1365)CGG>TGG	p.R455W	TFR2_uc010lhc.1_5'UTR|TFR2_uc003uvu.1_Missense_Mutation_p.R284W	NM_003227	NP_003218	Q9UP52	TFR2_HUMAN	transferrin receptor 2	455	Extracellular (Potential).				cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity			ovary(1)|pancreas(1)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)																	---	---	---	---
TRIP6	7205	broad.mit.edu	37	7	100468258	100468258	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100468258C>T	uc003uww.2	+	6	1062	c.892C>T	c.(892-894)CGC>TGC	p.R298C	TRIP6_uc010lhk.1_RNA	NM_003302	NP_003293	Q15654	TRIP6_HUMAN	thyroid receptor-interacting protein 6	298	LIM zinc-binding 1.				focal adhesion assembly|positive regulation of cell migration|regulation of transcription, DNA-dependent|release of cytoplasmic sequestered NF-kappaB|transcription, DNA-dependent	cytoplasm|cytoskeleton|focal adhesion|nucleus	identical protein binding|interleukin-1 receptor binding|kinase binding|thyroid hormone receptor binding|zinc ion binding			central_nervous_system(2)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100550770	100550770	+	RNA	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100550770C>A	uc003uxk.1	+	1		c.21C>A			uc003uxl.1_5'UTR					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																														---	---	---	---
PIK3CG	5294	broad.mit.edu	37	7	106508373	106508373	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106508373C>T	uc003vdv.3	+	2	452	c.367C>T	c.(367-369)CGC>TGC	p.R123C	PIK3CG_uc003vdu.2_Missense_Mutation_p.R123C|PIK3CG_uc003vdw.2_Missense_Mutation_p.R123C	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	123					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38																		---	---	---	---
PIK3CG	5294	broad.mit.edu	37	7	106523539	106523539	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106523539C>A	uc003vdv.3	+	8	2776	c.2691C>A	c.(2689-2691)GGC>GGA	p.G897G	PIK3CG_uc003vdu.2_Silent_p.G897G|PIK3CG_uc003vdw.2_Silent_p.G897G	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	897	PI3K/PI4K.				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38																		---	---	---	---
COG5	10466	broad.mit.edu	37	7	107198538	107198538	+	Silent	SNP	G	A	A	rs138518242		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107198538G>A	uc003ved.2	-	2	735	c.210C>T	c.(208-210)AAC>AAT	p.N70N	COG5_uc003vec.2_Silent_p.N70N|COG5_uc003vee.2_Silent_p.N70N	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform	70					intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4																		---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111377033	111377033	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111377033T>C	uc003vfx.2	-	49	5487	c.5218A>G	c.(5218-5220)AAT>GAT	p.N1740D	DOCK4_uc011kml.1_Missense_Mutation_p.N621D|DOCK4_uc011kmm.1_Missense_Mutation_p.N647D|DOCK4_uc003vfw.2_Missense_Mutation_p.N1190D|DOCK4_uc003vfy.2_Missense_Mutation_p.N1785D|DOCK4_uc003vfv.2_Missense_Mutation_p.N53D	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1740	Ser-rich.				cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)																---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	114284763	114284763	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114284763C>T	uc003vhb.2	+	8	1387	c.1013C>T	c.(1012-1014)GCC>GTC	p.A338V	FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_Missense_Mutation_p.A363V|FOXP2_uc003vha.2_Missense_Mutation_p.A246V|FOXP2_uc011kmu.1_Missense_Mutation_p.A355V|FOXP2_uc011kmv.1_Missense_Mutation_p.A337V|FOXP2_uc010ljz.1_Missense_Mutation_p.A246V|FOXP2_uc003vgx.2_Missense_Mutation_p.A338V|FOXP2_uc003vhd.2_Missense_Mutation_p.A338V|FOXP2_uc003vhc.2_Missense_Mutation_p.A363V	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I	338					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																		---	---	---	---
ZNF800	168850	broad.mit.edu	37	7	127014061	127014061	+	Silent	SNP	T	C	C	rs17868513		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127014061T>C	uc003vlx.1	-	5	1592	c.1329A>G	c.(1327-1329)ACA>ACG	p.T443T	ZNF800_uc003vlw.1_Silent_p.T346T|ZNF800_uc003vly.1_Silent_p.T443T|ZNF800_uc010lla.2_Silent_p.T443T	NM_176814	NP_789784	Q2TB10	ZN800_HUMAN	zinc finger protein 800	443					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
LRRC4	64101	broad.mit.edu	37	7	127669841	127669841	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127669841G>T	uc003vmk.2	-	2	990	c.853C>A	c.(853-855)CTC>ATC	p.L285I	SND1_uc003vmi.2_Intron|SND1_uc010lle.2_Intron	NM_022143	NP_071426	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4 precursor	285	LRR 9.|Extracellular (Potential).					cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4				Lung(243;0.124)														---	---	---	---
SND1	27044	broad.mit.edu	37	7	127732057	127732057	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127732057C>T	uc003vmi.2	+	24	2906	c.2680C>T	c.(2680-2682)CGC>TGC	p.R894C	SND1_uc010lle.2_Missense_Mutation_p.R547C	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1	894					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																		---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128475506	128475506	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128475506C>T	uc003vnz.3	+	2	688	c.479C>T	c.(478-480)ACG>ATG	p.T160M	FLNC_uc003voa.3_Missense_Mutation_p.T160M	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	160	CH 2.|Actin-binding.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
NRF1	4899	broad.mit.edu	37	7	129394908	129394908	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129394908G>A	uc003voz.2	+	11	1516	c.1399G>A	c.(1399-1401)GCC>ACC	p.A467T	NRF1_uc003vpa.2_Missense_Mutation_p.A486T|NRF1_uc011kpa.1_Missense_Mutation_p.A306T|NRF1_uc003vpb.2_Missense_Mutation_p.A467T	NM_005011	NP_005002	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	467	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																		---	---	---	---
CPA5	93979	broad.mit.edu	37	7	129986353	129986353	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129986353G>A	uc010lmd.1	+	4	647	c.27G>A	c.(25-27)ACG>ACA	p.T9T	CPA5_uc003vps.2_Silent_p.T9T|CPA5_uc003vpt.2_Silent_p.T9T|CPA5_uc010lme.1_Silent_p.T9T|CPA5_uc003vpu.1_Silent_p.T9T	NM_001127441	NP_001120913	Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5 isoform 1	9					proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2	Melanoma(18;0.0435)																	---	---	---	---
COPG2	26958	broad.mit.edu	37	7	130148880	130148880	+	Intron	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130148880A>C	uc003vqh.1	-							NM_012133	NP_036265			coatomer protein complex, subunit gamma 2						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)																	---	---	---	---
COPG2	26958	broad.mit.edu	37	7	130148882	130148882	+	Intron	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130148882A>C	uc003vqh.1	-							NM_012133	NP_036265			coatomer protein complex, subunit gamma 2						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)																	---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	131864546	131864546	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131864546A>G	uc003vra.3	-	20	4003	c.3774T>C	c.(3772-3774)ATT>ATC	p.I1258I		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1258	Helical; (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
AKR1B10	57016	broad.mit.edu	37	7	134222416	134222416	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134222416G>A	uc003vrr.2	+							NM_020299	NP_064695			aldo-keto reductase family 1, member B10						cellular aldehyde metabolic process|digestion|steroid metabolic process	cytoplasm	aldo-keto reductase (NADP) activity|protein binding			skin(5)	5																		---	---	---	---
WDR91	29062	broad.mit.edu	37	7	134871064	134871064	+	Missense_Mutation	SNP	C	T	T	rs141164229		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134871064C>T	uc003vsp.2	-	15	2145	c.2083G>A	c.(2083-2085)GGT>AGT	p.G695S	WDR91_uc010lmq.2_Missense_Mutation_p.G284S|WDR91_uc010lmr.2_RNA	NM_014149	NP_054868	A4D1P6	WDR91_HUMAN	WD repeat domain 91	695	WD 6.									breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135277854	135277854	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135277854C>T	uc003vsw.2	+	12	1775	c.1744C>T	c.(1744-1746)CGT>TGT	p.R582C		NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	582					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																		---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137237203	137237203	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137237203C>A	uc003vtt.2	-	20	2060	c.2059G>T	c.(2059-2061)GCC>TCC	p.A687S	DGKI_uc003vtu.2_Missense_Mutation_p.A387S	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	687					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																		---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138522642	138522642	+	3'UTR	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138522642C>T	uc011kql.1	-	20					KIAA1549_uc011kqi.1_3'UTR|KIAA1549_uc003vuk.3_3'UTR|KIAA1549_uc011kqj.1_3'UTR|KIAA1549_uc011kqk.1_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								---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138554434	138554434	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138554434C>T	uc011kql.1	-	14	4674	c.4625G>A	c.(4624-4626)CGC>CAC	p.R1542H	KIAA1549_uc011kqi.1_Missense_Mutation_p.R326H|KIAA1549_uc003vuk.3_Missense_Mutation_p.R1492H|KIAA1549_uc011kqj.1_Missense_Mutation_p.R1542H|KIAA1549_uc011kqk.1_Missense_Mutation_p.R326H	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	1542						integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230								O	BRAF	pilocytic astrocytoma								---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138602725	138602725	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138602725C>T	uc011kql.1	-	2	1696	c.1647G>A	c.(1645-1647)ACG>ACA	p.T549T	KIAA1549_uc003vuk.3_Silent_p.T499T|KIAA1549_uc011kqj.1_Silent_p.T549T	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	549	Ser-rich.					integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230								O	BRAF	pilocytic astrocytoma								---	---	---	---
UBN2	254048	broad.mit.edu	37	7	138968777	138968777	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138968777T>C	uc011kqr.1	+	15	3126	c.3126T>C	c.(3124-3126)TCT>TCC	p.S1042S		NM_173569	NP_775840	Q6ZU65	UBN2_HUMAN	ubinuclein 2	1042	Ser-rich.									ovary(1)|skin(1)	2																		---	---	---	---
MKRN1	23608	broad.mit.edu	37	7	140158906	140158906	+	Silent	SNP	G	A	A	rs1062761		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140158906G>A	uc003vvt.2	-	4	897	c.672C>T	c.(670-672)TAC>TAT	p.Y224Y	MKRN1_uc003vvs.2_Silent_p.Y160Y|MKRN1_uc011krd.1_Intron|MKRN1_uc003vvv.3_Silent_p.Y224Y|MKRN1_uc003vvu.3_Silent_p.Y160Y	NM_013446	NP_038474	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1 isoform 1	224	C3H1-type 3.						ligase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.00956)																	---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140273680	140273680	+	Silent	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140273680G>T	uc010lnj.2	-	4	1519	c.1374C>A	c.(1372-1374)CCC>CCA	p.P458P	DENND2A_uc011kre.1_RNA|DENND2A_uc010lnk.2_Silent_p.P458P|DENND2A_uc003vvw.2_Silent_p.P458P|DENND2A_uc003vvx.2_Silent_p.P458P	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	458										ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
CLCN1	1180	broad.mit.edu	37	7	143039045	143039045	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143039045G>A	uc003wcr.1	+	15	1693	c.1606G>A	c.(1606-1608)GTT>ATT	p.V536I	CLCN1_uc011ktc.1_Missense_Mutation_p.V148I	NM_000083	NP_000074	P35523	CLCN1_HUMAN	chloride channel 1, skeletal muscle	536					muscle contraction	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Melanoma(164;0.205)																	---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	147914604	147914604	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147914604G>A	uc003weu.1	+	19	3751	c.3235G>A	c.(3235-3237)GTC>ATC	p.V1079I		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	1079	Laminin G-like 4.|Extracellular (Potential).				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)			---	---	---	---
ZNF282	8427	broad.mit.edu	37	7	148921287	148921287	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148921287G>A	uc003wfm.2	+	8	1669	c.1564G>A	c.(1564-1566)GAG>AAG	p.E522K	ZNF282_uc011kun.1_Intron|ZNF282_uc003wfo.2_Silent_p.P198P	NM_003575	NP_003566	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	522	C2H2-type 1.				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	148947336	148947336	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148947336C>T	uc003wfp.2	+	2	207	c.111C>T	c.(109-111)ACC>ACT	p.T37T		NM_012256	NP_036388	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	37					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)															---	---	---	---
ZNF212	7988	broad.mit.edu	37	7	148951367	148951367	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148951367C>T	uc003wfp.2	+	5	1445	c.1349C>T	c.(1348-1350)ACG>ATG	p.T450M		NM_012256	NP_036388	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	450					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)															---	---	---	---
KRBA1	84626	broad.mit.edu	37	7	149420936	149420936	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149420936G>A	uc003wfz.2	+	8	1283	c.884G>A	c.(883-885)CGA>CAA	p.R295Q	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	295										ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149522374	149522374	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149522374C>T	uc010lpk.2	+	101	14001	c.14001C>T	c.(13999-14001)TGC>TGT	p.C4667C	SSPO_uc010lpm.1_RNA|SSPO_uc003wgg.2_RNA|SSPO_uc003wgh.2_RNA|SSPO_uc003wgi.1_RNA	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	4667	TIL 6.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
CHPF2	54480	broad.mit.edu	37	7	150934480	150934480	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150934480C>T	uc003wjr.1	+	4	2545	c.1032C>T	c.(1030-1032)ACC>ACT	p.T344T	CHPF2_uc003wjq.1_Silent_p.T336T|MIR671_hsa-mir-671|MI0003760_5'Flank	NM_019015	NP_061888	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	344	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(1)	1																		---	---	---	---
CRYGN	155051	broad.mit.edu	37	7	151135154	151135154	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151135154G>A	uc003wke.2	-	2	294	c.198C>T	c.(196-198)CAC>CAT	p.H66H	CRYGN_uc003wkf.2_Silent_p.H66H|CRYGN_uc003wkg.2_RNA|CRYGN_uc010lqd.1_5'Flank	NM_144727	NP_653328	Q8WXF5	CRGN_HUMAN	gammaN-crystallin	66	Beta/gamma crystallin 'Greek key' 2.										0			OV - Ovarian serous cystadenocarcinoma(82;0.00358)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
GALNT11	63917	broad.mit.edu	37	7	151818747	151818747	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151818747G>A	uc010lqg.1	+	12	2042	c.1812G>A	c.(1810-1812)TGG>TGA	p.W604*	GALNT11_uc011kvm.1_Nonsense_Mutation_p.W523*|GALNT11_uc003wku.2_Nonsense_Mutation_p.W604*	NM_022087	NP_071370	Q8NCW6	GLT11_HUMAN	N-acetylgalactosaminyltransferase 11	604	Lumenal (Potential).|Ricin B-type lectin.					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)														---	---	---	---
MNX1	3110	broad.mit.edu	37	7	156799214	156799214	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156799214G>A	uc003wnd.1	-	2	1114	c.811C>T	c.(811-813)CGC>TGC	p.R271C	MNX1_uc003wmz.2_Intron|MNX1_uc003wna.2_Intron|MNX1_uc010lqq.1_Missense_Mutation_p.R64C|MNX1_uc003wnc.1_Missense_Mutation_p.R59C|MNX1_uc010lqr.1_Intron	NM_005515	NP_005506	P50219	MNX1_HUMAN	motor neuron and pancreas homeobox 1 isoform 1	271	Homeobox.				humoral immune response|regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										Currarino_syndrome				---	---	---	---
ZNF596	169270	broad.mit.edu	37	8	192901	192901	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:192901C>T	uc003wot.2	+	3	315	c.27C>T	c.(25-27)TTC>TTT	p.F9F	ZNF596_uc003wou.2_5'UTR|ZNF596_uc003wov.2_Silent_p.F9F|ZNF596_uc003wow.2_Silent_p.F9F	NM_173539	NP_775810	Q8TC21	ZN596_HUMAN	zinc finger protein 596	9	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(2;4.81e-29)|all_epithelial(2;5.03e-19)|Lung NSC(2;8.68e-08)|all_lung(2;1.52e-07)|Ovarian(12;0.00965)|Colorectal(14;0.0367)|all_neural(12;0.0837)|Myeloproliferative disorder(644;0.116)|all_hematologic(2;0.138)|Acute lymphoblastic leukemia(644;0.242)		Epithelial(5;3.77e-18)|all cancers(2;5.2e-17)|OV - Ovarian serous cystadenocarcinoma(5;5.37e-09)|BRCA - Breast invasive adenocarcinoma(11;1.7e-06)|Colorectal(2;6.51e-05)|READ - Rectum adenocarcinoma(2;0.0276)|COAD - Colon adenocarcinoma(149;0.0702)														---	---	---	---
FBXO25	26260	broad.mit.edu	37	8	400034	400034	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:400034C>T	uc003wox.2	+	6	692	c.426C>T	c.(424-426)GGC>GGT	p.G142G	FBXO25_uc003woy.2_Silent_p.G142G|FBXO25_uc003woz.2_Silent_p.G75G|FBXO25_uc003wpa.2_5'UTR	NM_183421	NP_904357	Q8TCJ0	FBX25_HUMAN	F-box only protein 25 isoform 1	142						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)														---	---	---	---
MYOM2	9172	broad.mit.edu	37	8	2021408	2021408	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2021408C>T	uc003wpx.3	+						MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961			myomesin 2						muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2857580	2857580	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2857580C>T	uc011kwk.1	-	53	8496	c.8106G>A	c.(8104-8106)ACG>ACA	p.T2702T	CSMD1_uc011kwj.1_Silent_p.T2031T|CSMD1_uc010lrg.2_Silent_p.T712T	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2702	Extracellular (Potential).|Sushi 18.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
SGK223	157285	broad.mit.edu	37	8	8176553	8176553	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8176553G>A	uc003wsh.3	-	5	3332	c.3332C>T	c.(3331-3333)GCG>GTG	p.A1111V		NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin	1111	Protein kinase.		A -> T.				ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
SGK223	157285	broad.mit.edu	37	8	8233918	8233918	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8233918C>T	uc003wsh.3	-	2	2001	c.2001G>A	c.(1999-2001)ACG>ACA	p.T667T		NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin	667							ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
MFHAS1	9258	broad.mit.edu	37	8	8747883	8747883	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8747883C>T	uc003wsj.1	-	1	3249	c.2686G>A	c.(2686-2688)GCA>ACA	p.A896T		NM_004225	NP_004216	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified	896											0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	11058385	11058385	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
MTMR9	66036	broad.mit.edu	37	8	11157593	11157593	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11157593A>G	uc003wtm.2	+	3	751	c.353A>G	c.(352-354)GAA>GGA	p.E118G	MTMR9_uc010lrx.2_Missense_Mutation_p.E11G|MTMR9_uc011kxa.1_Missense_Mutation_p.E33G	NM_015458	NP_056273	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	118						cytoplasm	phosphatase activity|protein binding				0			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)														---	---	---	---
MTMR9	66036	broad.mit.edu	37	8	11172485	11172485	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11172485A>G	uc003wtm.2	+	7	1423	c.1025A>G	c.(1024-1026)CAG>CGG	p.Q342R	MTMR9_uc010lrx.2_Missense_Mutation_p.Q235R|MTMR9_uc011kxa.1_Missense_Mutation_p.Q257R	NM_015458	NP_056273	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	342	Myotubularin phosphatase.					cytoplasm	phosphatase activity|protein binding				0			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)														---	---	---	---
FAM167A	83648	broad.mit.edu	37	8	11301555	11301555	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11301555C>T	uc010lry.1	-	2	986	c.366G>A	c.(364-366)TGG>TGA	p.W122*	FAM167A_uc003wtw.2_Nonsense_Mutation_p.W122*	NM_053279	NP_444509	Q96KS9	F167A_HUMAN	hypothetical protein LOC83648	122	Potential.										0																		---	---	---	---
GATA4	2626	broad.mit.edu	37	8	11615981	11615981	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11615981G>A	uc003wuc.2	+	7	1880	c.1326G>A	c.(1324-1326)GCG>GCA	p.A442A	GATA4_uc003wub.1_Silent_p.A236A|GATA4_uc011kxc.1_Silent_p.A443A|uc003wud.1_5'Flank	NM_002052	NP_002043	P43694	GATA4_HUMAN	GATA binding protein 4	442					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)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18725177	18725177	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18725177C>T	uc003wza.2	-							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)														---	---	---	---
EPB49	2039	broad.mit.edu	37	8	21929867	21929867	+	Missense_Mutation	SNP	G	A	A	rs149330702		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21929867G>A	uc011kyt.1	+	9	864	c.635G>A	c.(634-636)CGG>CAG	p.R212Q	EPB49_uc010ltl.2_Missense_Mutation_p.R212Q|EPB49_uc011kys.1_Missense_Mutation_p.R172Q|EPB49_uc010ltn.2_Missense_Mutation_p.R187Q|EPB49_uc011kyu.1_Missense_Mutation_p.R212Q|EPB49_uc011kyv.1_Missense_Mutation_p.R212Q|EPB49_uc010ltq.2_Missense_Mutation_p.R212Q	NM_001114136	NP_001107608	Q08495	DEMA_HUMAN	erythrocyte membrane protein band 4.9 isoform 1	212					actin filament bundle assembly|actin filament capping	actin cytoskeleton|nucleus	actin binding			central_nervous_system(1)	1				Colorectal(74;9.05e-05)|READ - Rectum adenocarcinoma(5;0.0276)|COAD - Colon adenocarcinoma(73;0.0631)														---	---	---	---
HR	55806	broad.mit.edu	37	8	21985180	21985180	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21985180G>A	uc003xas.2	-	3	1440	c.775C>T	c.(775-777)CGG>TGG	p.R259W	HR_uc003xat.2_Missense_Mutation_p.R259W	NM_005144	NP_005135	O43593	HAIR_HUMAN	hairless protein isoform a	259							DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|ovary(1)	2		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)														---	---	---	---
NKX3-1	4824	broad.mit.edu	37	8	23538896	23538896	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23538896T>C	uc011kzx.1	-	2	591	c.543A>G	c.(541-543)CGA>CGG	p.R181R	NKX3-1_uc003xdv.1_Intron	NM_006167	NP_006158	Q99801	NKX31_HUMAN	NK3 homeobox 1	181	Homeobox.				negative regulation of estrogen receptor binding|negative regulation of transcription, DNA-dependent|positive regulation of cell division|positive regulation of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter	nucleus	estrogen receptor activity|estrogen receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region sequence-specific DNA binding				0		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)														---	---	---	---
ADAMDEC1	27299	broad.mit.edu	37	8	24256965	24256965	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24256965C>A	uc003xdz.2	+	10	1209	c.989C>A	c.(988-990)CCA>CAA	p.P330Q	ADAMDEC1_uc010lub.2_Missense_Mutation_p.P251Q|ADAMDEC1_uc011lab.1_Missense_Mutation_p.P251Q	NM_014479	NP_055294	O15204	ADEC1_HUMAN	ADAM-like, decysin 1 isoform 1	330	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)														---	---	---	---
NEFM	4741	broad.mit.edu	37	8	24771893	24771893	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24771893G>A	uc003xed.3	+	1	620	c.587G>A	c.(586-588)CGC>CAC	p.R196H	NEFM_uc011lac.1_Missense_Mutation_p.R196H|NEFM_uc010lue.2_5'Flank|uc010luc.1_Missense_Mutation_p.R59C	NM_005382	NP_005373	P07197	NFM_HUMAN	neurofilament, medium polypeptide 150kDa isoform	196	Rod.|Coil 1B.					neurofilament	protein binding|structural constituent of cytoskeleton			breast(1)	1		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)														---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25246735	25246735	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25246735G>A	uc003xeg.2	+	41	4397	c.4260G>A	c.(4258-4260)TCG>TCA	p.S1420S	PPP2R2A_uc003xek.2_Silent_p.S209S|DOCK5_uc003xei.2_Silent_p.S990S|DOCK5_uc003xej.2_RNA	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1420	DHR-2.					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)														---	---	---	---
PNMA2	10687	broad.mit.edu	37	8	26365705	26365705	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26365705C>T	uc003xez.2	-	3	1337	c.567G>A	c.(565-567)ACG>ACA	p.T189T		NM_007257	NP_009188	Q9UL42	PNMA2_HUMAN	paraneoplastic antigen MA2	189					apoptosis	nucleolus	protein binding				0		all_cancers(63;0.109)|Ovarian(32;2.61e-05)|all_epithelial(46;0.105)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0196)|Epithelial(17;3.13e-11)|Colorectal(74;0.123)														---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27297938	27297938	+	Silent	SNP	C	T	T	rs149334019		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27297938C>T	uc003xfn.1	+	26	2827	c.2019C>T	c.(2017-2019)ACC>ACT	p.T673T	PTK2B_uc003xfo.1_Silent_p.T673T|PTK2B_uc003xfp.1_Silent_p.T673T|PTK2B_uc003xfq.1_Silent_p.T673T|PTK2B_uc003xfr.1_Silent_p.T419T	NM_173174	NP_775266	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a	673	Protein kinase.				apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			lung(3)|ovary(1)|skin(1)	5		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)														---	---	---	---
EPHX2	2053	broad.mit.edu	37	8	27362600	27362600	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27362600G>A	uc003xfu.2	+	4	555	c.474G>A	c.(472-474)ATG>ATA	p.M158I	EPHX2_uc010lut.1_Missense_Mutation_p.M158I|EPHX2_uc010luu.2_Missense_Mutation_p.M158I|EPHX2_uc010luv.2_Missense_Mutation_p.M92I|EPHX2_uc003xfv.2_Missense_Mutation_p.M105I|EPHX2_uc010luw.2_Missense_Mutation_p.M92I|EPHX2_uc011lam.1_Missense_Mutation_p.M14I	NM_001979	NP_001970	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	158	Phosphatase.				aromatic compound catabolic process|cellular calcium ion homeostasis|drug metabolic process|inflammatory response|positive regulation of vasodilation|reactive oxygen species metabolic process|regulation of blood pressure|response to toxin|xenobiotic metabolic process	cytosol|focal adhesion|Golgi apparatus|nucleolus|peroxisome|soluble fraction	epoxide hydrolase activity|metal ion binding|protein homodimerization activity			ovary(1)	1		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)	Tamoxifen(DB00675)													---	---	---	---
CCDC25	55246	broad.mit.edu	37	8	27606032	27606032	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27606032C>A	uc003xgc.2	-	6	441	c.328G>T	c.(328-330)GGC>TGC	p.G110C	CCDC25_uc003xgd.2_Missense_Mutation_p.G42C|CCDC25_uc011lan.1_Intron|CCDC25_uc011lao.1_Intron|CCDC25_uc003xge.2_Intron|CCDC25_uc003xgf.1_RNA	NM_018246	NP_060716	Q86WR0	CCD25_HUMAN	coiled-coil domain containing 25	110											0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)														---	---	---	---
EXTL3	2137	broad.mit.edu	37	8	28574843	28574843	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28574843G>A	uc003xgz.1	+	3	1860	c.1267G>A	c.(1267-1269)GAA>AAA	p.E423K		NM_001440	NP_001431	O43909	EXTL3_HUMAN	exostoses-like 3	423	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)														---	---	---	---
DUSP4	1846	broad.mit.edu	37	8	29195944	29195944	+	Silent	SNP	G	A	A	rs111661543	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29195944G>A	uc003xhm.2	-	3	1044	c.654C>T	c.(652-654)GAC>GAT	p.D218D	DUSP4_uc003xhl.2_Silent_p.D127D	NM_001394	NP_001385	Q13115	DUS4_HUMAN	dual specificity phosphatase 4 isoform 1	218	Tyrosine-protein phosphatase.				endoderm formation|inactivation 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|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	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/threonine phosphatase activity			lung(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)														---	---	---	---
WRN	7486	broad.mit.edu	37	8	30999110	30999110	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30999110G>A	uc003xio.3	+	25	3920	c.3132G>A	c.(3130-3132)ACG>ACA	p.T1044T	WRN_uc010lvk.2_Silent_p.T511T	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	1044					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				---	---	---	---
GPR124	25960	broad.mit.edu	37	8	37689008	37689008	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37689008C>T	uc003xkj.2	+	8	1363	c.1000C>T	c.(1000-1002)CAA>TAA	p.Q334*	GPR124_uc010lvy.2_Nonsense_Mutation_p.Q334*	NM_032777	NP_116166	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124 precursor	334	Extracellular (Potential).|Ig-like.				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)															---	---	---	---
BRF2	55290	broad.mit.edu	37	8	37702376	37702376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37702376C>T	uc003xkk.2	-	4	1002	c.892G>A	c.(892-894)GGT>AGT	p.G298S		NM_018310	NP_060780	Q9HAW0	BRF2_HUMAN	RNA polymerase III transcription initiation	298					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)															---	---	---	---
BAG4	9530	broad.mit.edu	37	8	38066655	38066655	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38066655G>A	uc003xky.1	+	4	1040	c.758G>A	c.(757-759)GGC>GAC	p.G253D	BAG4_uc003xkz.1_Missense_Mutation_p.G217D	NM_004874	NP_004865	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	253					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)																---	---	---	---
HTRA4	203100	broad.mit.edu	37	8	38835575	38835575	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38835575C>T	uc003xmj.2	+	4	990	c.875C>T	c.(874-876)GCA>GTA	p.A292V		NM_153692	NP_710159	P83105	HTRA4_HUMAN	HtrA serine peptidase 4 precursor	292	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)															---	---	---	---
IKBKB	3551	broad.mit.edu	37	8	42176093	42176093	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42176093G>A	uc003xow.1	+	13	1441	c.1264G>A	c.(1264-1266)GCC>ACC	p.A422T	IKBKB_uc010lxh.1_Missense_Mutation_p.A317T|IKBKB_uc011lco.1_RNA|IKBKB_uc010lxj.1_Missense_Mutation_p.A199T|IKBKB_uc003xox.1_Missense_Mutation_p.A143T|IKBKB_uc011lcp.1_RNA|IKBKB_uc011lcq.1_Missense_Mutation_p.A420T|IKBKB_uc010lxi.1_RNA|IKBKB_uc011lcr.1_Missense_Mutation_p.A363T	NM_001556	NP_001547	O14920	IKKB_HUMAN	inhibitor of nuclear factor kappa B kinase beta	422					anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)													---	---	---	---
HOOK3	84376	broad.mit.edu	37	8	42828458	42828458	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42828458C>T	uc003xpr.2	+	12	1391	c.1149C>T	c.(1147-1149)TCC>TCT	p.S383S	HOOK3_uc010lxq.1_Silent_p.S383S	NM_032410	NP_115786	Q86VS8	HOOK3_HUMAN	golgi-associated microtubule-binding protein	383	Potential.				cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)					T	RET	papillary thyroid								---	---	---	---
MCM4	4173	broad.mit.edu	37	8	48887498	48887498	+	Missense_Mutation	SNP	G	A	A	rs140026188		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48887498G>A	uc003xqk.1	+	15	2436	c.2341G>A	c.(2341-2343)GTG>ATG	p.V781M	MCM4_uc003xql.1_Missense_Mutation_p.V781M|MCM4_uc011ldi.1_Missense_Mutation_p.V768M	NM_182746	NP_877423	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	781					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(2)|skin(2)	4		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52321164	52321164	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52321164G>A	uc003xqu.3	-	17	3121	c.3020C>T	c.(3019-3021)GCG>GTG	p.A1007V	PXDNL_uc003xqt.3_RNA	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	1007					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)																---	---	---	---
SOX17	64321	broad.mit.edu	37	8	55370898	55370898	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55370898G>A	uc003xsb.3	+	1	404	c.200G>A	c.(199-201)CGT>CAT	p.R67H		NM_022454	NP_071899	Q9H6I2	SOX17_HUMAN	SRY-box 17	67					angiogenesis|cardiac cell fate determination|endocardial cell differentiation|endocardium formation|endoderm formation|heart formation|heart looping|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell growth|outflow tract morphogenesis|positive regulation of transcription, DNA-dependent|protein destabilization|protein stabilization|regulation of embryonic development|renal system development|vasculogenesis|Wnt receptor signaling pathway	transcription factor complex	beta-catenin binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			lung(1)	1		Lung NSC(129;0.109)|all_epithelial(80;0.176)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;1.9e-07)|Epithelial(17;1.7e-05)|all cancers(17;0.000159)															---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56015724	56015724	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56015724G>A	uc003xsf.2	+	1	708	c.676G>A	c.(676-678)GCG>ACG	p.A226T		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	226						integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
GGH	8836	broad.mit.edu	37	8	63936566	63936566	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63936566G>A	uc003xuw.2	-							NM_003878	NP_003869			gamma-glutamyl hydrolase precursor						glutamine metabolic process	extracellular space|lysosome|melanosome	gamma-glutamyl-peptidase activity				0	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|L-Glutamic Acid(DB00142)													---	---	---	---
PDE7A	5150	broad.mit.edu	37	8	66639133	66639133	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66639133G>T	uc003xvq.2	-	9	909	c.897C>A	c.(895-897)TTC>TTA	p.F299L	PDE7A_uc003xvr.2_Missense_Mutation_p.F299L|PDE7A_uc003xvp.2_Missense_Mutation_p.F273L	NM_002604	NP_002595	Q13946	PDE7A_HUMAN	phosphodiesterase 7A isoform b	299	Catalytic (By similarity).					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)													---	---	---	---
ADHFE1	137872	broad.mit.edu	37	8	67361171	67361171	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67361171C>T	uc003xwb.3	+	8	734	c.700C>T	c.(700-702)CGA>TGA	p.R234*	ADHFE1_uc003xwd.3_RNA|ADHFE1_uc003xwc.3_Nonsense_Mutation_p.R186*|ADHFE1_uc003xwe.3_RNA|ADHFE1_uc003xwf.3_RNA|ADHFE1_uc011les.1_Nonsense_Mutation_p.R164*|ADHFE1_uc011leq.1_RNA|ADHFE1_uc011ler.1_RNA	NM_144650	NP_653251	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	234					2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)															---	---	---	---
C8orf46	254778	broad.mit.edu	37	8	67405939	67405939	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67405939T>C	uc003xwg.2	+	1	449	c.56T>C	c.(55-57)GTG>GCG	p.V19A	C8orf46_uc003xwh.2_RNA|C8orf46_uc011let.1_Missense_Mutation_p.V19A	NM_152765	NP_689978	Q8TAG6	CH046_HUMAN	hypothetical protein LOC254778	19										skin(2)	2			Epithelial(68;0.0224)|BRCA - Breast invasive adenocarcinoma(89;0.0508)|all cancers(69;0.0558)|OV - Ovarian serous cystadenocarcinoma(28;0.226)															---	---	---	---
C8orf45	157777	broad.mit.edu	37	8	67803139	67803139	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67803139A>G	uc003xwz.3	+	10	1284	c.1113A>G	c.(1111-1113)ATA>ATG	p.I371M	C8orf45_uc011lev.1_Missense_Mutation_p.I371M|C8orf45_uc011lew.1_Missense_Mutation_p.I302M|C8orf45_uc011lex.1_Missense_Mutation_p.I129M|C8orf45_uc003xwy.3_Missense_Mutation_p.I371M	NM_173518	NP_775789	Q4G0Z9	CH045_HUMAN	minichromosome maintenance complex	371					DNA replication		ATP binding|DNA binding			ovary(1)	1	Breast(64;0.186)		Epithelial(68;0.00384)|OV - Ovarian serous cystadenocarcinoma(28;0.00913)|all cancers(69;0.0175)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	67998286	67998286	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67998286C>T	uc003xxi.2	+	4	383	c.352C>T	c.(352-354)CGG>TGG	p.R118W	CSPP1_uc003xxg.1_Missense_Mutation_p.R118W|CSPP1_uc003xxh.1_RNA|CSPP1_uc003xxj.2_Missense_Mutation_p.R118W|CSPP1_uc003xxk.2_Translation_Start_Site	NM_001077204	NP_001070672	Q1MSJ5	CSPP1_HUMAN	centrosome spindle pole associated protein 1	118	Potential.					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)															---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68989660	68989660	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68989660T>A	uc003xxv.1	+	15	1625	c.1598T>A	c.(1597-1599)ATG>AAG	p.M533K	PREX2_uc003xxu.1_Missense_Mutation_p.M533K|PREX2_uc011lez.1_Missense_Mutation_p.M468K	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	533	DEP 2.				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	69017427	69017427	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69017427C>T	uc003xxv.1	+						PREX2_uc003xxu.1_Missense_Mutation_p.H924Y|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	69046300	69046300	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69046300A>G	uc003xxv.1	+	32	3800	c.3773A>G	c.(3772-3774)GAG>GGG	p.E1258G		NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	1258					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	69046345	69046345	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69046345C>T	uc003xxv.1	+	32	3845	c.3818C>T	c.(3817-3819)GCC>GTC	p.A1273V		NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	1273					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	69351816	69351816	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69351816A>G	uc010lyz.2	+	2	201	c.152A>G	c.(151-153)AAC>AGC	p.N51S	C8orf34_uc010lyx.1_Missense_Mutation_p.N51S|C8orf34_uc010lyy.1_Missense_Mutation_p.N51S|C8orf34_uc003xyb.2_Missense_Mutation_p.N26S	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	51					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	70501233	70501233	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70501233C>T	uc010lza.1	+	8	1308	c.591C>T	c.(589-591)AAC>AAT	p.N197N	SULF1_uc003xyd.2_Silent_p.N197N|SULF1_uc003xye.2_Silent_p.N197N|SULF1_uc003xyf.2_Silent_p.N197N|SULF1_uc003xyg.2_Silent_p.N197N	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	197					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)															---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70517125	70517125	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70517125C>T	uc010lza.1	+	13	2052	c.1335C>T	c.(1333-1335)TGC>TGT	p.C445C	SULF1_uc003xyd.2_Silent_p.C445C|SULF1_uc003xye.2_Silent_p.C445C|SULF1_uc003xyf.2_Silent_p.C445C|SULF1_uc003xyg.2_Silent_p.C445C|SULF1_uc003xyh.1_RNA	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	445					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)															---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70536319	70536319	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70536319A>G	uc010lza.1	+	15	2454	c.1737A>G	c.(1735-1737)GAA>GAG	p.E579E	SULF1_uc003xyd.2_Silent_p.E579E|SULF1_uc003xye.2_Silent_p.E579E|SULF1_uc003xyf.2_Silent_p.E579E|SULF1_uc003xyg.2_Silent_p.E579E|SULF1_uc003xyh.1_RNA	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	579					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)															---	---	---	---
PRDM14	63978	broad.mit.edu	37	8	70982068	70982068	+	Missense_Mutation	SNP	C	T	T	rs148357006		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70982068C>T	uc003xym.2	-	2	230	c.28G>A	c.(28-30)GTG>ATG	p.V10M		NM_024504	NP_078780	Q9GZV8	PRD14_HUMAN	PR domain containing 14	10					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)															---	---	---	---
EYA1	2138	broad.mit.edu	37	8	72229848	72229848	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72229848G>A	uc003xys.3	-	6	782	c.495C>T	c.(493-495)AGC>AGT	p.S165S	EYA1_uc003xyr.3_Silent_p.S160S|EYA1_uc003xyt.3_Silent_p.S132S|EYA1_uc010lzf.2_Silent_p.S92S|EYA1_uc003xyu.2_Silent_p.S165S|EYA1_uc011lfe.1_Silent_p.S159S|EYA1_uc003xyv.2_Silent_p.S43S	NM_172058	NP_742055	Q99502	EYA1_HUMAN	eyes absent 1 isoform b	165					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)															---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74464497	74464497	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74464497C>T	uc003xzm.2	-	13	1516	c.1280G>A	c.(1279-1281)CGC>CAC	p.R427H	STAU2_uc011lfg.1_Missense_Mutation_p.R255H|STAU2_uc003xzn.2_Missense_Mutation_p.R395H|STAU2_uc011lfh.1_Missense_Mutation_p.R323H|STAU2_uc003xzo.2_Missense_Mutation_p.R427H|STAU2_uc003xzp.2_Missense_Mutation_p.R395H|STAU2_uc011lfi.1_Missense_Mutation_p.R389H|STAU2_uc003xzq.2_Missense_Mutation_p.R207H|STAU2_uc010lzk.2_Missense_Mutation_p.R395H|STAU2_uc010lzl.1_Missense_Mutation_p.R255H	NM_014393	NP_055208	Q9NUL3	STAU2_HUMAN	staufen homolog 2 isoform e	427	Required for dendritic transport (By similarity).				transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)															---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81555314	81555314	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81555314C>T	uc003yby.1	-	8	1315	c.1083G>A	c.(1081-1083)GCG>GCA	p.A361A		NM_001033723	NP_001028895	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	361						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)															---	---	---	---
ATP6V0D2	245972	broad.mit.edu	37	8	87111213	87111213	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87111213C>T	uc003ydp.1	+	1	75	c.6C>T	c.(4-6)CTC>CTT	p.L2L		NM_152565	NP_689778	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0	2					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																		---	---	---	---
DCAF4L2	138009	broad.mit.edu	37	8	88885164	88885164	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88885164C>T	uc003ydz.2	-	1	1133	c.1036G>A	c.(1036-1038)GGC>AGC	p.G346S		NM_152418	NP_689631	Q8NA75	DC4L2_HUMAN	WD repeat domain 21C	346	WD 2.									ovary(1)	1																		---	---	---	---
RIPK2	8767	broad.mit.edu	37	8	90796355	90796355	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90796355T>C	uc003yee.2	+	8	1331	c.1017T>C	c.(1015-1017)CAT>CAC	p.H339H	RIPK2_uc003yef.2_Silent_p.H202H	NM_003821	NP_003812	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	339					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)															---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	93088227	93088227	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93088227G>A	uc003yfd.2	-	1	138	c.54C>T	c.(52-54)GAC>GAT	p.D18D	RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_5'UTR|RUNX1T1_uc011lgi.1_Intron|RUNX1T1_uc003yfh.1_Intron	NM_175634	NP_783552	Q06455	MTG8_HUMAN	acute myelogenous leukemia 1 translocation 1	18					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)															---	---	---	---
KIAA1429	25962	broad.mit.edu	37	8	95501084	95501084	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95501084G>T	uc003ygo.1	-	24	5302	c.5289C>A	c.(5287-5289)TAC>TAA	p.Y1763*	KIAA1429_uc010maz.1_RNA	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	1763					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	95538496	95538496	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95538496A>T	uc003ygo.1	-	8	1989	c.1976T>A	c.(1975-1977)ATT>AAT	p.I659N	KIAA1429_uc003ygp.2_Missense_Mutation_p.I659N|KIAA1429_uc010maz.1_RNA	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	659					mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)															---	---	---	---
UQCRB	7381	broad.mit.edu	37	8	97243341	97243341	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97243341G>A	uc003yhq.3	-	4	382	c.278C>T	c.(277-279)CCG>CTG	p.P93L	UQCRB_uc011lgt.1_RNA|UQCRB_uc010mbc.2_RNA	NM_006294	NP_006285	P14927	QCR7_HUMAN	ubiquinol-cytochrome c reductase binding	93					aerobic respiration|mitochondrial electron transport, ubiquinol to cytochrome c	mitochondrial respiratory chain	ubiquinol-cytochrome-c reductase activity			ovary(1)	1	Breast(36;5.16e-05)																	---	---	---	---
RGS22	26166	broad.mit.edu	37	8	101020597	101020597	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101020597C>T	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron|RGS22_uc011lgz.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)															---	---	---	---
DCAF13	25879	broad.mit.edu	37	8	104427572	104427572	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104427572T>C	uc003yln.2	+	1	631	c.354T>C	c.(352-354)ACT>ACC	p.T118T	SLC25A32_uc003yll.2_5'Flank|SLC25A32_uc011lhr.1_5'Flank|DCAF13_uc003ylm.1_5'UTR|DCAF13_uc003ylo.2_5'UTR	NM_015420	NP_056235	Q9NV06	DCA13_HUMAN	WD repeats and SOF1 domain containing	Error:Variant_position_missing_in_Q9NV06_after_alignment					rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex				breast(1)	1																		---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104897787	104897787	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104897787C>T	uc003yls.2	+	2	535	c.294C>T	c.(292-294)TAC>TAT	p.Y98Y	RIMS2_uc003ylp.2_Silent_p.Y320Y|RIMS2_uc003ylw.2_Silent_p.Y128Y|RIMS2_uc003ylq.2_Silent_p.Y128Y|RIMS2_uc003ylr.2_Silent_p.Y128Y	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	351					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	104922390	104922390	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104922390T>G	uc003yls.2	+	3	1228	c.987T>G	c.(985-987)CAT>CAG	p.H329Q	RIMS2_uc003ylp.2_Missense_Mutation_p.H551Q|RIMS2_uc003ylw.2_Missense_Mutation_p.H359Q|RIMS2_uc003ylq.2_Missense_Mutation_p.H359Q|RIMS2_uc003ylr.2_Intron|RIMS2_uc003ylt.2_5'Flank	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					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)			---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107691480	107691480	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107691480G>A	uc011lht.1	+	3	365	c.266G>A	c.(265-267)CGA>CAA	p.R89Q	OXR1_uc003ymf.2_Missense_Mutation_p.R88Q|OXR1_uc011lhu.1_Missense_Mutation_p.R81Q|OXR1_uc010mcg.2_Intron|OXR1_uc003ymg.1_Missense_Mutation_p.R21Q|OXR1_uc003ymi.1_5'UTR	NM_018002	NP_060472	Q8N573	OXR1_HUMAN	oxidation resistance 1 isoform 1	89					cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110474143	110474143	+	Intron	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110474143A>C	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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113301668	113301668	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113301668C>T	uc003ynu.2	-	57	9233	c.9074G>A	c.(9073-9075)CGT>CAT	p.R3025H	CSMD3_uc003yns.2_Missense_Mutation_p.R2227H|CSMD3_uc003ynt.2_Missense_Mutation_p.R2985H|CSMD3_uc011lhx.1_Missense_Mutation_p.R2856H	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3025	Sushi 21.|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	113308134	113308134	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113308134G>A	uc003ynu.2	-	54	8701	c.8542C>T	c.(8542-8544)CGA>TGA	p.R2848*	CSMD3_uc003yns.2_Nonsense_Mutation_p.R2050*|CSMD3_uc003ynt.2_Nonsense_Mutation_p.R2808*|CSMD3_uc011lhx.1_Nonsense_Mutation_p.R2679*	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2848	Extracellular (Potential).|Sushi 18.					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	113314034	113314034	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113314034T>A	uc003ynu.2	-	53	8587	c.8428A>T	c.(8428-8430)ACC>TCC	p.T2810S	CSMD3_uc003yns.2_Missense_Mutation_p.T2012S|CSMD3_uc003ynt.2_Missense_Mutation_p.T2770S|CSMD3_uc011lhx.1_Missense_Mutation_p.T2641S	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2810	Extracellular (Potential).|Sushi 17.					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	113702263	113702263	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113702263A>C	uc003ynu.2	-	14	2148	c.1989T>G	c.(1987-1989)AGT>AGG	p.S663R	CSMD3_uc003yns.2_5'UTR|CSMD3_uc003ynt.2_Missense_Mutation_p.S623R|CSMD3_uc011lhx.1_Missense_Mutation_p.S559R	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	663	Extracellular (Potential).|Sushi 3.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116617110	116617110	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116617110T>C	uc003ynz.2	-	3	1506	c.1047A>G	c.(1045-1047)GAA>GAG	p.E349E	TRPS1_uc011lhy.1_Silent_p.E353E|TRPS1_uc003yny.2_Silent_p.E362E|TRPS1_uc010mcy.2_Silent_p.E349E	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	349	C2H2-type 2; atypical.				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				---	---	---	---
RAD21	5885	broad.mit.edu	37	8	117866524	117866524	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117866524G>A	uc003yod.2	-	9	1409	c.1121C>T	c.(1120-1122)TCT>TTT	p.S374F		NM_006265	NP_006256	O60216	RAD21_HUMAN	RAD21 homolog	374	Interaction with WAPAL and PDS5B.|Interaction with STAG1.				apoptosis|cell division|chromosome segregation|double-strand break repair|mitotic metaphase/anaphase transition|mitotic prometaphase|protein localization to chromatin|reciprocal meiotic recombination|regulation of transcription from RNA polymerase II promoter	chromosome, centromeric region|cohesin complex|nuclear chromosome|nucleoplasm	protein binding			lung(1)|skin(1)	2	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)																	---	---	---	---
C8orf85	441376	broad.mit.edu	37	8	117950593	117950593	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117950593C>T	uc003yof.2	+	1	130	c.111C>T	c.(109-111)TTC>TTT	p.F37F		NM_001025357	NP_001020528	Q4LEZ3	AARD_HUMAN	alanine and arginine-rich domain-containing	37											0																		---	---	---	---
ENPP2	5168	broad.mit.edu	37	8	120583061	120583061	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120583061G>A	uc003yot.1	-	20	1887	c.1801C>T	c.(1801-1803)CGA>TGA	p.R601*	ENPP2_uc011lic.1_Nonsense_Mutation_p.R139*|ENPP2_uc003yor.1_Nonsense_Mutation_p.R236*|ENPP2_uc003yos.1_Nonsense_Mutation_p.R653*|ENPP2_uc010mdd.1_Nonsense_Mutation_p.R626*	NM_001040092	NP_001035181	Q13822	ENPP2_HUMAN	autotaxin isoform 2 preproprotein	601					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	120754889	120754889	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120754889C>T	uc003you.2	-	25	3492	c.3222G>A	c.(3220-3222)TCG>TCA	p.S1074S		NM_003184	NP_003175	Q6P1X5	TAF2_HUMAN	TBP-associated factor 2	1074					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	120865444	120865444	+	Missense_Mutation	SNP	C	T	T	rs143137070		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120865444C>T	uc003yov.2	-	2	329	c.194G>A	c.(193-195)CGT>CAT	p.R65H		NM_024094	NP_076999	Q9BVC3	DCC1_HUMAN	defective in sister chromatid cohesion 1	65					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)															---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124335285	124335285	+	Nonsense_Mutation	SNP	T	A	A	rs147415119		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124335285T>A	uc003yqh.3	-	27	4132	c.4024A>T	c.(4024-4026)AAA>TAA	p.K1342*	ATAD2_uc011lii.1_Nonsense_Mutation_p.K1133*|ATAD2_uc003yqi.3_RNA	NM_014109	NP_054828	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	1342					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)															---	---	---	---
ANXA13	312	broad.mit.edu	37	8	124707927	124707927	+	Splice_Site	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124707927C>T	uc003yqu.2	-	5	464	c.391_splice	c.e5+1	p.L131_splice	ANXA13_uc003yqt.2_Splice_Site_p.L172_splice	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)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	125131185	125131185	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125131185A>T	uc003yqw.2	+	40	5596	c.5390A>T	c.(5389-5391)AAC>ATC	p.N1797I	uc003yqy.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1797	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)															---	---	---	---
KIAA0196	9897	broad.mit.edu	37	8	126079934	126079934	+	Missense_Mutation	SNP	C	T	T	rs151298198	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126079934C>T	uc003yrt.2	-	10	1507	c.1178G>A	c.(1177-1179)CGT>CAT	p.R393H	KIAA0196_uc011lir.1_Missense_Mutation_p.R245H|KIAA0196_uc003yru.1_5'UTR	NM_014846	NP_055661	Q12768	STRUM_HUMAN	strumpellin	393					cell death	WASH complex				ovary(2)	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)															---	---	---	---
ADCY8	114	broad.mit.edu	37	8	131797706	131797706	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131797706G>A	uc003ytd.3	-	16	3332	c.3076C>T	c.(3076-3078)CGA>TGA	p.R1026*	ADCY8_uc010mds.2_Nonsense_Mutation_p.R895*	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	1026	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 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	131848567	131848567	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131848567G>A	uc003ytd.3	-	12	2887	c.2631C>T	c.(2629-2631)TAC>TAT	p.Y877Y	ADCY8_uc010mds.2_Silent_p.Y746Y	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	877	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)												HNSCC(32;0.087)			---	---	---	---
EFR3A	23167	broad.mit.edu	37	8	133008660	133008660	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133008660T>G	uc003yte.2	+	19	2274	c.2073T>G	c.(2071-2073)GAT>GAG	p.D691E		NM_015137	NP_055952	Q14156	EFR3A_HUMAN	EFR3 homolog A	691						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)															---	---	---	---
TG	7038	broad.mit.edu	37	8	133894824	133894824	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133894824G>A	uc003ytw.2	+	7	897	c.856G>A	c.(856-858)GCA>ACA	p.A286T		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	286	Thyroglobulin type-1 3.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)														---	---	---	---
WISP1	8840	broad.mit.edu	37	8	134237661	134237661	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134237661C>T	uc003yub.2	+	4	715	c.639C>T	c.(637-639)CAC>CAT	p.H213H	WISP1_uc003yuc.2_Silent_p.H126H|WISP1_uc010meb.2_Silent_p.H41H|WISP1_uc010mec.2_Intron|WISP1_uc010med.2_Intron|WISP1_uc003yud.2_Intron	NM_003882	NP_003873	O95388	WISP1_HUMAN	WNT1 inducible signaling pathway protein 1	213					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)															---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139820047	139820047	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139820047C>A	uc003yvd.2	-	10	1905	c.1458G>T	c.(1456-1458)ATG>ATT	p.M486I		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	486	Collagen-like 1.|Pro-rich.|Gly-rich.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)												HNSCC(7;0.00092)			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139890011	139890011	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139890011G>A	uc003yvd.2	-	3	1087	c.640C>T	c.(640-642)CGG>TGG	p.R214W		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	214					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)			---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141753359	141753359	+	Nonsense_Mutation	SNP	G	A	A	rs139298046		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141753359G>A	uc003yvu.2	-	20	1935	c.1705C>T	c.(1705-1707)CGA>TGA	p.R569*	PTK2_uc003yvo.2_Nonsense_Mutation_p.R197*|PTK2_uc011ljq.1_Nonsense_Mutation_p.R264*|PTK2_uc003yvp.2_Nonsense_Mutation_p.R237*|PTK2_uc003yvq.2_Nonsense_Mutation_p.R95*|PTK2_uc003yvr.2_Nonsense_Mutation_p.R509*|PTK2_uc003yvs.2_Nonsense_Mutation_p.R569*|PTK2_uc003yvt.2_Nonsense_Mutation_p.R591*|PTK2_uc003yvv.2_Nonsense_Mutation_p.R469*|PTK2_uc011ljr.1_Nonsense_Mutation_p.R569*	NM_153831	NP_722560	Q05397	FAK1_HUMAN	PTK2 protein tyrosine kinase 2 isoform a	569	Protein kinase.				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)															---	---	---	---
DENND3	22898	broad.mit.edu	37	8	142176464	142176464	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142176464G>A	uc003yvy.2	+	12	1767	c.1489G>A	c.(1489-1491)GCA>ACA	p.A497T	DENND3_uc010mep.2_Missense_Mutation_p.A458T|DENND3_uc003yvz.1_Missense_Mutation_p.A181T	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	497										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)															---	---	---	---
DENND3	22898	broad.mit.edu	37	8	142178455	142178455	+	Silent	SNP	C	T	T	rs147231668		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142178455C>T	uc003yvy.2	+	13	2144	c.1866C>T	c.(1864-1866)AGC>AGT	p.S622S	DENND3_uc010mep.2_Silent_p.S583S|DENND3_uc003yvz.1_Silent_p.S306S	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	622										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)															---	---	---	---
SLC45A4	57210	broad.mit.edu	37	8	142238339	142238339	+	Silent	SNP	C	T	T	rs34650936	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142238339C>T	uc003ywd.1	-	1	335	c.27G>A	c.(25-27)GGG>GGA	p.G9G	SLC45A4_uc003ywc.1_Silent_p.G9G|SLC45A4_uc010meq.1_Intron	NM_001080431	NP_001073900	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4	Error:Variant_position_missing_in_Q5BKX6_after_alignment					transport	integral to membrane				ovary(2)	2	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|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;0.0493)															---	---	---	---
FLJ43860	389690	broad.mit.edu	37	8	142517187	142517187	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142517187G>A	uc003ywi.2	-	1	144	c.63C>T	c.(61-63)GCC>GCT	p.A21A		NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	hypothetical protein LOC389690	21							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)															---	---	---	---
BAI1	575	broad.mit.edu	37	8	143603485	143603485	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143603485C>T	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)																	---	---	---	---
GPIHBP1	338328	broad.mit.edu	37	8	144295734	144295734	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144295734C>A	uc003yxu.1	+	2	165	c.90C>A	c.(88-90)GAC>GAA	p.D30E		NM_178172	NP_835466	Q8IV16	HDBP1_HUMAN	glycosylphosphatidylinositol anchored high	30	Poly-Glu.				cholesterol homeostasis|intracellular protein transport|positive regulation of chylomicron remnant clearance|positive regulation of lipoprotein lipase activity|protein import|protein localization at cell surface|protein stabilization|response to heparin|triglyceride homeostasis	anchored to external side of plasma membrane|apical plasma membrane|basolateral plasma membrane|high-density lipoprotein particle|integral to membrane|intracellular	apolipoprotein binding|chylomicron binding|lipase binding|lipid binding|protein transmembrane transporter activity				0	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
ZNF696	79943	broad.mit.edu	37	8	144375210	144375210	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144375210C>T	uc003yxy.3	+	2	448	c.39C>T	c.(37-39)AGC>AGT	p.S13S		NM_030895	NP_112157	Q9H7X3	ZN696_HUMAN	zinc finger protein 696	13					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)															---	---	---	---
NRBP2	340371	broad.mit.edu	37	8	144919209	144919209	+	Splice_Site	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144919209A>G	uc011lkt.1	-	14	1403	c.1263_splice	c.e14+1	p.K421_splice	NRBP2_uc003yzv.2_Splice_Site_p.K178_splice|NRBP2_uc003yzz.1_Intron|NRBP2_uc003yzw.2_Splice_Site_p.K213_splice|NRBP2_uc010mfl.2_Splice_Site_p.K213_splice|NRBP2_uc010mfm.2_Splice_Site_p.K178_splice|NRBP2_uc011lks.1_Splice_Site_p.K178_splice|NRBP2_uc003yzy.2_Splice_Site_p.K178_splice	NM_178564	NP_848659			nuclear receptor binding protein 2						negative regulation of neuron apoptosis|neuron differentiation	cytoplasm	ATP binding|protein kinase activity			central_nervous_system(2)	2	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;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)															---	---	---	---
EPPK1	83481	broad.mit.edu	37	8	144941617	144941617	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144941617G>A	uc003zaa.1	-	1	5818	c.5805C>T	c.(5803-5805)GCC>GCT	p.A1935A		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	1935	Plectin 32.					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	144998442	144998442	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144998442C>T	uc003zaf.1	-	31	6236	c.6066G>A	c.(6064-6066)GCG>GCA	p.A2022A	PLEC_uc003zab.1_Silent_p.A1885A|PLEC_uc003zac.1_Silent_p.A1889A|PLEC_uc003zad.2_Silent_p.A1885A|PLEC_uc003zae.1_Silent_p.A1853A|PLEC_uc003zag.1_Silent_p.A1863A|PLEC_uc003zah.2_Silent_p.A1871A|PLEC_uc003zaj.2_Silent_p.A1912A	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	2022	Central fibrous rod domain.|Potential.				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																		---	---	---	---
GPR172A	79581	broad.mit.edu	37	8	145583577	145583577	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145583577G>A	uc003zcc.1	+	3	582	c.425G>A	c.(424-426)CGC>CAC	p.R142H	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.R142H|GPR172A_uc003zce.1_Missense_Mutation_p.R142H|GPR172A_uc010mfy.1_Missense_Mutation_p.R142H|GPR172A_uc003zcf.1_Missense_Mutation_p.R142H|GPR172A_uc011llc.1_Missense_Mutation_p.R54H	NM_024531	NP_078807	Q9HAB3	RFT3_HUMAN	G protein-coupled receptor 172A precursor	142						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	145621823	145621823	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145621823C>A	uc003zcj.2	-	25	2891	c.2816G>T	c.(2815-2817)GGC>GTC	p.G939V		NM_013291	NP_037423	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1,	939					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)															---	---	---	---
ZNF34	80778	broad.mit.edu	37	8	145999196	145999196	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145999196G>A	uc003zdy.3	-	6	1240	c.1138C>T	c.(1138-1140)CGA>TGA	p.R380*	ZNF34_uc010mgb.2_Nonsense_Mutation_p.R277*|ZNF34_uc003zdx.3_Nonsense_Mutation_p.R359*	NM_030580	NP_085057	Q8IZ26	ZNF34_HUMAN	zinc finger protein 34	380	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.221)	OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;5.18e-38)|all cancers(56;4.41e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.0179)														---	---	---	---
CBWD1	55871	broad.mit.edu	37	9	164038	164038	+	Splice_Site	SNP	C	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									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)														---	---	---	---
C9orf66	157983	broad.mit.edu	37	9	214857	214857	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:214857C>T	uc003zge.3	-	1	1037	c.540G>A	c.(538-540)GCG>GCA	p.A180A	DOCK8_uc011lls.1_5'Flank|DOCK8_uc003zgf.2_5'Flank	NM_152569	NP_689782	Q5T8R8	CI066_HUMAN	hypothetical protein LOC157983	180										central_nervous_system(1)	1	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)														---	---	---	---
SMARCA2	6595	broad.mit.edu	37	9	2054701	2054701	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2054701G>A	uc003zhc.2	+	6	1250	c.1151G>A	c.(1150-1152)CGG>CAG	p.R384Q	SMARCA2_uc003zhd.2_Missense_Mutation_p.R384Q|SMARCA2_uc010mha.2_Missense_Mutation_p.R375Q	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	384					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	2123835	2123835	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2123835G>T	uc003zhc.2	+	27	3978	c.3879G>T	c.(3877-3879)AGG>AGT	p.R1293S	SMARCA2_uc003zhd.2_Missense_Mutation_p.R1293S|SMARCA2_uc010mha.2_Missense_Mutation_p.R1226S	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	1293					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)														---	---	---	---
KLHL9	55958	broad.mit.edu	37	9	21334793	21334793	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21334793T>C	uc003zoy.2	-	1	637	c.66A>G	c.(64-66)GGA>GGG	p.G22G	KLHL9_uc003zow.2_Intron|KLHL9_uc003zox.2_RNA	NM_018847	NP_061335	Q9P2J3	KLHL9_HUMAN	kelch-like 9	22					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)														---	---	---	---
TEK	7010	broad.mit.edu	37	9	27206739	27206739	+	Missense_Mutation	SNP	C	T	T	rs147231791	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27206739C>T	uc003zqi.3	+	15	2966	c.2524C>T	c.(2524-2526)CGC>TGC	p.R842C	TEK_uc011lno.1_Missense_Mutation_p.R799C|TEK_uc011lnp.1_Missense_Mutation_p.R694C|TEK_uc003zqj.1_Missense_Mutation_p.R776C	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	842	Protein kinase.|Cytoplasmic (Potential).				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)														---	---	---	---
KIAA1161	57462	broad.mit.edu	37	9	34371530	34371530	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34371530G>A	uc003zue.3	-	3	1579	c.1412C>T	c.(1411-1413)CCG>CTG	p.P471L		NM_020702	NP_065753	Q6NSJ0	K1161_HUMAN	hypothetical protein LOC57462	471	Extracellular (Potential).				carbohydrate metabolic process	integral to membrane	hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(1)|breast(1)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)														---	---	---	---
SPAG8	26206	broad.mit.edu	37	9	35812118	35812118	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35812118T>C	uc003zye.2	-	1	142	c.27A>G	c.(25-27)GGA>GGG	p.G9G	SPAG8_uc003zyf.2_5'UTR|SPAG8_uc003zyg.2_Silent_p.G9G	NM_172312	NP_758516	Q99932	SPAG8_HUMAN	sperm associated antigen 8 isoform 2	9						acrosomal vesicle|membrane				ovary(1)	1	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
C9orf128	392307	broad.mit.edu	37	9	35825359	35825359	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35825359G>A	uc010mlc.2	-	3	895	c.610C>T	c.(610-612)CGC>TGC	p.R204C	C9orf128_uc003zyj.2_RNA|C9orf128_uc011lpg.1_Missense_Mutation_p.R204C	NM_001012446	NP_001012448	A6H8Z2	CI128_HUMAN	hypothetical protein LOC392307	204											0	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
CCIN	881	broad.mit.edu	37	9	36171031	36171031	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36171031G>A	uc003zzb.3	+	1	1643	c.1532G>A	c.(1531-1533)TGC>TAC	p.C511Y		NM_005893	NP_005884	Q13939	CALI_HUMAN	calicin	511	Kelch 5.				cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			ovary(1)|skin(1)	2			STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
FRMPD1	22844	broad.mit.edu	37	9	37745690	37745690	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37745690G>A	uc004aag.1	+	16	3705	c.3661G>A	c.(3661-3663)GTC>ATC	p.V1221I	FRMPD1_uc004aah.1_Missense_Mutation_p.V1221I	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1221						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	69440096	69440096	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69440096A>G	uc010mnx.1	+	3	349	c.180A>G	c.(178-180)CAA>CAG	p.Q60Q		NM_001098806	NP_001092276			coiled-coil domain containing 29																														---	---	---	---
PGM5	5239	broad.mit.edu	37	9	70993106	70993106	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70993106A>G	uc004agr.2	+							NM_021965	NP_068800			phosphoglucomutase 5						cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2																		---	---	---	---
PGM5	5239	broad.mit.edu	37	9	70993121	70993121	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70993121C>T	uc004agr.2	+	2	497	c.268C>T	c.(268-270)CGA>TGA	p.R90*		NM_021965	NP_068800	Q15124	PGM5_HUMAN	phosphoglucomutase 5	90					cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2																		---	---	---	---
PGM5	5239	broad.mit.edu	37	9	70993145	70993145	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70993145A>G	uc004agr.2	+	2	521	c.292A>G	c.(292-294)ATC>GTC	p.I98V		NM_021965	NP_068800	Q15124	PGM5_HUMAN	phosphoglucomutase 5	98					cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2																		---	---	---	---
C9orf41	138199	broad.mit.edu	37	9	77598694	77598694	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77598694T>C	uc004ajq.2	-	8	1372	c.1219A>G	c.(1219-1221)AAG>GAG	p.K407E	uc004ajp.2_Intron	NM_152420	NP_689633	Q8N4J0	CI041_HUMAN	hypothetical protein LOC138199	407										ovary(1)|skin(1)	2																		---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78710821	78710821	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78710821G>A	uc004ajz.2	+	8	1448	c.910G>A	c.(910-912)GGC>AGC	p.G304S	PCSK5_uc004ajy.2_Missense_Mutation_p.G304S|PCSK5_uc004aka.2_RNA	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	304	Catalytic.				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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	78973724	78973724	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78973724C>T	uc004akc.1	+	10	1945	c.1725C>T	c.(1723-1725)ATC>ATT	p.I575I						Homo sapiens cDNA FLJ16215 fis, clone CTONG2025610, moderately similar to PC6B.																														---	---	---	---
FLJ46321	389763	broad.mit.edu	37	9	84608469	84608469	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84608469T>C	uc004amn.2	+	4	3131	c.3084T>C	c.(3082-3084)GGT>GGC	p.G1028G		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	1028						integral to membrane					0																		---	---	---	---
FLJ46321	389763	broad.mit.edu	37	9	84609582	84609582	+	Silent	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84609582T>G	uc004amn.2	+	4	4244	c.4197T>G	c.(4195-4197)ACT>ACG	p.T1399T		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	1399						integral to membrane					0																		---	---	---	---
AGTPBP1	23287	broad.mit.edu	37	9	88248234	88248234	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88248234C>T	uc011ltd.1	-	13	1391	c.1358G>A	c.(1357-1359)CGT>CAT	p.R453H	AGTPBP1_uc004aod.3_Missense_Mutation_p.R79H|AGTPBP1_uc011ltc.1_Missense_Mutation_p.R351H|AGTPBP1_uc010mqc.2_Missense_Mutation_p.R413H|AGTPBP1_uc011lte.1_Missense_Mutation_p.R465H	NM_015239	NP_056054	Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	453					C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7																		---	---	---	---
SHC3	53358	broad.mit.edu	37	9	91680487	91680487	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91680487A>G	uc004aqg.2	-	6	1099	c.792T>C	c.(790-792)ACT>ACC	p.T264T		NM_016848	NP_058544	Q92529	SHC3_HUMAN	src homology 2 domain-containing transforming	264	PID.				central nervous system development|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	protein binding|signal transducer activity			lung(3)|skin(1)	4																		---	---	---	---
SYK	6850	broad.mit.edu	37	9	93606314	93606314	+	Missense_Mutation	SNP	G	A	A	rs16906862		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93606314G>A	uc004aqz.2	+	2	339	c.134G>A	c.(133-135)CGC>CAC	p.R45H	SYK_uc004aqy.2_Missense_Mutation_p.R45H|SYK_uc004ara.2_Missense_Mutation_p.R45H|SYK_uc004arb.2_Missense_Mutation_p.R45H|SYK_uc004arc.2_Missense_Mutation_p.R45H|SYK_uc011ltr.1_RNA|SYK_uc011lts.1_RNA|SYK_uc011ltt.1_RNA	NM_003177	NP_003168	P43405	KSYK_HUMAN	spleen tyrosine kinase isoform 1	45	SH2 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								---	---	---	---
AUH	549	broad.mit.edu	37	9	93983200	93983200	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93983200C>T	uc004arf.3	-	7	765	c.730G>A	c.(730-732)GAT>AAT	p.D244N	AUH_uc004arg.3_Missense_Mutation_p.D215N	NM_001698	NP_001689	Q13825	AUHM_HUMAN	AU RNA binding protein/enoyl-Coenzyme A	244					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																		---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94495598	94495598	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94495598G>A	uc004arj.1	-	6	942	c.743C>T	c.(742-744)CCG>CTG	p.P248L	ROR2_uc004ari.1_Missense_Mutation_p.P108L|ROR2_uc004ark.2_Missense_Mutation_p.P248L	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	248	FZ.|Extracellular (Potential).				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																		---	---	---	---
PHF2	5253	broad.mit.edu	37	9	96428129	96428129	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96428129C>T	uc004aub.2	+	15	2246	c.2099C>T	c.(2098-2100)CCG>CTG	p.P700L	PHF2_uc011lug.1_Missense_Mutation_p.P583L|PHF2_uc004auc.2_Missense_Mutation_p.P119L	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2	700					liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)														---	---	---	---
ZNF169	169841	broad.mit.edu	37	9	97062823	97062823	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97062823G>A	uc004aum.1	+	5	1088	c.983G>A	c.(982-984)CGC>CAC	p.R328H		NM_194320	NP_919301	Q14929	ZN169_HUMAN	zinc finger protein 169	328	C2H2-type 4.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)																---	---	---	---
HIATL1	84641	broad.mit.edu	37	9	97203311	97203311	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97203311C>T	uc004aur.2	+	5	709	c.440C>T	c.(439-441)ACG>ATG	p.T147M	HIATL1_uc011luh.1_Missense_Mutation_p.T82M	NM_032558	NP_115947	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1	147	Helical; (Potential).				transmembrane transport	integral to membrane|plasma membrane	protein binding|transporter activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)																---	---	---	---
FBP1	2203	broad.mit.edu	37	9	97382707	97382707	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97382707G>A	uc004auw.3	-	2	568	c.237C>T	c.(235-237)AAC>AAT	p.N79N	FBP1_uc010mrl.2_Silent_p.N79N	NM_000507	NP_000498	P09467	F16P1_HUMAN	fructose-1,6-bisphosphatase 1	79					gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)			Adenosine monophosphate(DB00131)													---	---	---	---
ZNF510	22869	broad.mit.edu	37	9	99521928	99521928	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99521928C>T	uc004awn.1	-	6	1373	c.1184G>A	c.(1183-1185)CGA>CAA	p.R395Q	ZNF510_uc004awo.1_Missense_Mutation_p.R395Q	NM_014930	NP_055745	Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	395					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)																---	---	---	---
TBC1D2	55357	broad.mit.edu	37	9	100961787	100961787	+	Missense_Mutation	SNP	C	T	T	rs145458773	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100961787C>T	uc011lvb.1	-	13	2843	c.2663G>A	c.(2662-2664)CGG>CAG	p.R888Q	TBC1D2_uc004ayp.2_Missense_Mutation_p.R428Q|TBC1D2_uc004ayq.2_Missense_Mutation_p.R877Q|TBC1D2_uc004ayr.2_Missense_Mutation_p.R670Q|TBC1D2_uc004ayo.3_3'UTR	NM_018421	NP_060891	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	888	Potential.					cell junction|cytoplasmic membrane-bounded vesicle|nucleus	Rab GTPase activator activity			ovary(3)	3		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)														---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101304194	101304194	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101304194G>A	uc004ays.2	-	3	747	c.591C>T	c.(589-591)CGC>CGT	p.R197R		NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor	197	Extracellular (Potential).				negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
ANKS6	203286	broad.mit.edu	37	9	101536250	101536250	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101536250G>A	uc004ayu.2	-	9	1751	c.1730C>T	c.(1729-1731)ACG>ATG	p.T577M	ANKS6_uc004ayt.2_Missense_Mutation_p.T276M|ANKS6_uc004ayv.1_Missense_Mutation_p.T39M|ANKS6_uc004ayw.1_Missense_Mutation_p.T159M|ANKS6_uc004ayx.1_RNA|ANKS6_uc004ayy.1_RNA	NM_173551	NP_775822	Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain	577										ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)																---	---	---	---
COL15A1	1306	broad.mit.edu	37	9	101832036	101832036	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101832036G>A	uc004azb.1	+	42	4241	c.4035G>A	c.(4033-4035)GCG>GCA	p.A1345A		NM_001855	NP_001846	P39059	COFA1_HUMAN	alpha 1 type XV collagen precursor	1345	Nonhelical region 10 (NC10).				angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)																---	---	---	---
INVS	27130	broad.mit.edu	37	9	103035177	103035177	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103035177G>T	uc004bap.1	+	12	1815	c.1603G>T	c.(1603-1605)GAG>TAG	p.E535*	INVS_uc010mta.1_Nonsense_Mutation_p.E439*|INVS_uc011lve.1_Nonsense_Mutation_p.E439*|INVS_uc004bao.1_Nonsense_Mutation_p.E535*|INVS_uc004baq.1_Nonsense_Mutation_p.E439*|INVS_uc004bar.1_Nonsense_Mutation_p.E439*|INVS_uc010mtb.1_Nonsense_Mutation_p.E209*	NM_014425	NP_055240	Q9Y283	INVS_HUMAN	inversin isoform a	535	ANK 16.				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)																---	---	---	---
SMC2	10592	broad.mit.edu	37	9	106876290	106876290	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106876290G>A	uc004bbv.2	+	12	1748	c.1460G>A	c.(1459-1461)CGT>CAT	p.R487H	SMC2_uc004bbu.1_Missense_Mutation_p.R487H|SMC2_uc004bbw.2_Missense_Mutation_p.R487H|SMC2_uc011lvl.1_Missense_Mutation_p.R487H|SMC2_uc004bbx.2_Missense_Mutation_p.R487H	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	487	Potential.				cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9																		---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107602806	107602806	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107602806G>A	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)													---	---	---	---
KLF4	9314	broad.mit.edu	37	9	110249320	110249320	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110249320C>T	uc004bdh.2	-	3	1949	c.1328G>A	c.(1327-1329)CGA>CAA	p.R443Q	KLF4_uc004bdf.1_Missense_Mutation_p.R368Q|KLF4_uc004bdg.2_Missense_Mutation_p.R418Q	NM_004235	NP_004226	O43474	KLF4_HUMAN	Kruppel-like factor 4 (gut)	452	C2H2-type 1.				fat cell differentiation|mesodermal cell fate determination|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|stem cell maintenance|transcription from RNA polymerase II promoter	nucleus	RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor recruiting transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(2)|lung(1)	3																		---	---	---	---
EPB41L4B	54566	broad.mit.edu	37	9	112015826	112015826	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112015826G>A	uc004bdz.1	-	12	1469	c.1174C>T	c.(1174-1176)CGG>TGG	p.R392W	EPB41L4B_uc004bea.2_Missense_Mutation_p.R392W	NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	392						cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112687354	112687354	+	Missense_Mutation	SNP	C	T	T	rs150674445		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112687354C>T	uc004bei.2	+	5	578	c.386C>T	c.(385-387)ACG>ATG	p.T129M	PALM2_uc004bef.2_Missense_Mutation_p.T131M|PALM2_uc004beg.2_Missense_Mutation_p.T131M|PALM2_uc004beh.3_Missense_Mutation_p.T129M|PALM2-AKAP2_uc004bek.3_Missense_Mutation_p.T129M|PALM2-AKAP2_uc004bej.3_Missense_Mutation_p.T129M|PALM2-AKAP2_uc004bel.1_Translation_Start_Site	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2	Error:Variant_position_missing_in_Q9Y2D5_after_alignment							enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
RGS3	5998	broad.mit.edu	37	9	116359161	116359161	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116359161G>A	uc004bhq.2	+	26	3734	c.3525G>A	c.(3523-3525)TCG>TCA	p.S1175S	RGS3_uc004bhs.2_Silent_p.S1065S|RGS3_uc004bht.2_Silent_p.S894S|RGS3_uc010muy.2_Silent_p.S568S|RGS3_uc004bhv.2_Silent_p.S496S|RGS3_uc004bhw.2_Silent_p.S145S|RGS3_uc011lxh.1_Silent_p.S485S|RGS3_uc004bhx.2_Silent_p.S496S|RGS3_uc004bhz.2_Silent_p.S517S|RGS3_uc004bia.2_Silent_p.S288S	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6	1175	RGS.				inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
AMBP	259	broad.mit.edu	37	9	116838907	116838907	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116838907C>T	uc004bie.3	-	2	494	c.231G>A	c.(229-231)GCG>GCA	p.A77A	AMBP_uc011lxk.1_Silent_p.A18A|AMBP_uc010mvc.1_RNA	NM_001633	NP_001624	P02760	AMBP_HUMAN	alpha-1-microglobulin/bikunin preproprotein	77					cell adhesion|female pregnancy|heme catabolic process|interspecies interaction between organisms|negative regulation of immune response|negative regulation of JNK cascade|protein-chromophore linkage	extracellular region|plasma membrane	calcium channel inhibitor activity|calcium oxalate binding|heme binding|IgA binding|protein homodimerization activity|serine-type endopeptidase inhibitor activity|transporter activity			skin(1)	1					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)													---	---	---	---
TNFSF8	944	broad.mit.edu	37	9	117692480	117692480	+	Missense_Mutation	SNP	C	A	A	rs139509296		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117692480C>A	uc004bji.1	-	1	291	c.104G>T	c.(103-105)AGC>ATC	p.S35I		NM_001244	NP_001235	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily,	35	Cytoplasmic (Potential).				cell proliferation|cell-cell signaling|immune response|induction of apoptosis|signal transduction	extracellular space|integral to plasma membrane	cytokine activity|tumor necrosis factor receptor binding			lung(3)|skin(2)|ovary(1)	6																		---	---	---	---
TNC	3371	broad.mit.edu	37	9	117853061	117853061	+	Silent	SNP	C	T	T	rs149512169		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117853061C>T	uc004bjj.3	-	2	599	c.237G>A	c.(235-237)CCG>CCA	p.P79P	TNC_uc010mvf.2_Silent_p.P79P	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	79					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	119737508	119737508	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119737508G>A	uc004bjs.1	-	10	1969	c.1868C>T	c.(1867-1869)ACG>ATG	p.T623M	ASTN2_uc004bjr.1_Missense_Mutation_p.T619M|ASTN2_uc004bjt.1_Missense_Mutation_p.T572M	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	623	Extracellular (Potential).					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	120053685	120053685	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120053685C>G	uc004bjs.1	-	2	651	c.550G>C	c.(550-552)GCC>CCC	p.A184P	ASTN2_uc004bjr.1_Missense_Mutation_p.A184P|ASTN2_uc004bjt.1_Missense_Mutation_p.A184P	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	184	Extracellular (Potential).					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
GOLGA1	2800	broad.mit.edu	37	9	127652731	127652731	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127652731C>A	uc004bpc.2	-	16	1776	c.1434G>T	c.(1432-1434)GTG>GTT	p.V478V	GOLGA1_uc010mws.2_RNA	NM_002077	NP_002068	Q92805	GOGA1_HUMAN	golgin 97	478	Potential.|Gln-rich.					Golgi cisterna membrane				ovary(1)	1																		---	---	---	---
SCAI	286205	broad.mit.edu	37	9	127818218	127818218	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127818218C>A	uc004bpe.2	-	3	248	c.167G>T	c.(166-168)AGG>ATG	p.R56M	SCAI_uc004bpd.2_Missense_Mutation_p.R79M|SCAI_uc010mwu.2_RNA	NM_001144877	NP_001138349	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion isoform 2	56	Necessary to inhibit MKL1-induced SRF transcriptional activity (By similarity).				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																		---	---	---	---
RABEPK	10244	broad.mit.edu	37	9	127982827	127982827	+	Missense_Mutation	SNP	C	T	T	rs144370574		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127982827C>T	uc004bpi.2	+	6	547	c.374C>T	c.(373-375)ACG>ATG	p.T125M	RABEPK_uc004bph.1_Missense_Mutation_p.R149C|RABEPK_uc004bpj.2_Missense_Mutation_p.T74M|RABEPK_uc004bpk.2_Missense_Mutation_p.T125M|RABEPK_uc004bpl.1_Missense_Mutation_p.T74M|RABEPK_uc004bpm.2_Missense_Mutation_p.T125M	NM_005833	NP_005824	Q7Z6M1	RABEK_HUMAN	Rab9 effector protein with kelch motifs	125	Kelch 2.				receptor-mediated endocytosis|vesicle docking involved in exocytosis	endosome membrane|plasma membrane				ovary(1)	1																		---	---	---	---
HSPA5	3309	broad.mit.edu	37	9	127998919	127998919	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127998919G>A	uc004bpn.2	-	8	2173	c.1917C>T	c.(1915-1917)GGC>GGT	p.G639G		NM_005347	NP_005338	P11021	GRP78_HUMAN	heat shock 70kDa protein 5	639					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)			---	---	---	---
ZBTB43	23099	broad.mit.edu	37	9	129595780	129595780	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129595780A>G	uc004bql.2	+	3	1265	c.992A>G	c.(991-993)GAT>GGT	p.D331G	ZBTB43_uc010mxf.2_Missense_Mutation_p.D331G	NM_014007	NP_054726	O43298	ZBT43_HUMAN	zinc finger and BTB domain containing 43	331					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ANGPTL2	23452	broad.mit.edu	37	9	129870416	129870416	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129870416G>A	uc004bqr.1	-	2	1095	c.595C>T	c.(595-597)CAG>TAG	p.Q199*	RALGPS1_uc004bqo.1_Intron|RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron|ANGPTL2_uc010mxg.1_Intron	NM_012098	NP_036230	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2 precursor	199	Potential.				multicellular organismal development|signal transduction	extracellular space	receptor binding				0																		---	---	---	---
RPL12	6136	broad.mit.edu	37	9	130210644	130210644	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130210644C>T	uc004bqy.1	-	5	439	c.351G>A	c.(349-351)CGG>CGA	p.R117R	RPL12_uc004bqx.1_RNA|RPL12_uc004bqz.1_Silent_p.R84R	NM_000976	NP_000967	P30050	RL12_HUMAN	ribosomal protein L12	117					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	RNA binding|structural constituent of ribosome				0																		---	---	---	---
SH2D3C	10044	broad.mit.edu	37	9	130507045	130507045	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130507045G>A	uc004bsc.2	-	7	1740	c.1598C>T	c.(1597-1599)GCC>GTC	p.A533V	SH2D3C_uc010mxo.2_Missense_Mutation_p.A373V|SH2D3C_uc004bry.2_Missense_Mutation_p.A375V|SH2D3C_uc004brz.3_Missense_Mutation_p.A179V|SH2D3C_uc011mak.1_Missense_Mutation_p.A179V|SH2D3C_uc004bsa.2_Missense_Mutation_p.A376V|SH2D3C_uc004bsb.2_Missense_Mutation_p.A465V	NM_170600	NP_733745	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C isoform a	533					JNK cascade|small GTPase mediated signal transduction	cytoplasm|membrane	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			ovary(1)	1																		---	---	---	---
NAIF1	203245	broad.mit.edu	37	9	130829391	130829391	+	Translation_Start_Site	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130829391C>A	uc004bta.2	-	1	209	c.-10G>T	c.(-12--8)GAGGG>GATGG		NAIF1_uc004bsz.2_RNA|SLC25A25_uc004btb.2_5'Flank	NM_197956	NP_931045			nuclear apoptosis inducing factor 1						apoptosis|induction of apoptosis	nucleus					0																		---	---	---	---
LRRC8A	56262	broad.mit.edu	37	9	131670129	131670129	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131670129C>T	uc004bwl.3	+	3	940	c.686C>T	c.(685-687)ACG>ATG	p.T229M	LRRC8A_uc010myp.2_Missense_Mutation_p.T229M|LRRC8A_uc010myq.2_Missense_Mutation_p.T229M	NM_019594	NP_062540	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member	229					pre-B cell differentiation	integral to membrane					0																		---	---	---	---
NUP188	23511	broad.mit.edu	37	9	131755602	131755602	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131755602A>G	uc004bws.1	+	26	2789	c.2767A>G	c.(2767-2769)ACT>GCT	p.T923A	NUP188_uc004bwu.2_Missense_Mutation_p.T266A	NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	923					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																OREG0019527	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM78A	286336	broad.mit.edu	37	9	134136213	134136213	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134136213C>T	uc004cak.2	-	2	1188	c.848G>A	c.(847-849)CGG>CAG	p.R283Q	FAM78A_uc004caj.2_Missense_Mutation_p.R280Q	NM_033387	NP_203745	Q5JUQ0	FA78A_HUMAN	hypothetical protein LOC286336	283										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)														---	---	---	---
NTNG2	84628	broad.mit.edu	37	9	135073517	135073517	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135073517G>A	uc004cbh.2	+	3	1154	c.378G>A	c.(376-378)TCG>TCA	p.S126S		NM_032536	NP_115925	Q96CW9	NTNG2_HUMAN	netrin G2 precursor	126	Laminin N-terminal.				axonogenesis	anchored to plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)														---	---	---	---
ADAMTS13	11093	broad.mit.edu	37	9	136321656	136321656	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136321656G>A	uc004cdv.3	+						ADAMTS13_uc004cdp.3_Intron|ADAMTS13_uc004cdt.1_Intron|ADAMTS13_uc004cdu.1_Intron|ADAMTS13_uc004cdw.3_Intron|ADAMTS13_uc004cdx.3_Intron|ADAMTS13_uc004cdz.3_Intron|ADAMTS13_uc004cea.1_Intron|ADAMTS13_uc004ceb.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)														---	---	---	---
SARDH	1757	broad.mit.edu	37	9	136536721	136536721	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136536721C>T	uc004cep.3	-	18	2396	c.2262G>A	c.(2260-2262)GCG>GCA	p.A754A	SARDH_uc004ceo.2_Silent_p.A754A|SARDH_uc011mdn.1_Silent_p.A754A|SARDH_uc011mdo.1_Silent_p.A586A|SARDH_uc004cen.2_Silent_p.A182A	NM_001134707	NP_001128179	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase precursor	754					glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|sarcosine dehydrogenase activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)														---	---	---	---
VAV2	7410	broad.mit.edu	37	9	136660824	136660824	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136660824C>A	uc004ces.2	-	12	1113	c.1067G>T	c.(1066-1068)AGG>ATG	p.R356M	VAV2_uc004cer.2_Missense_Mutation_p.R351M	NM_001134398	NP_001127870	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor isoform	356	DH.				angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)														---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137664692	137664692	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137664692C>T	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	137674515	137674515	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137674515T>C	uc004cfe.2	+	29	2815	c.2433T>C	c.(2431-2433)GGT>GGC	p.G811G		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	811	Triple-helical region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
FCN1	2219	broad.mit.edu	37	9	137803098	137803098	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137803098C>T	uc004cfi.2	-	8	706	c.614G>A	c.(613-615)CGT>CAT	p.R205H		NM_002003	NP_001994	O00602	FCN1_HUMAN	ficolin 1 precursor	205	Fibrinogen C-terminal.				opsonization|signal transduction	collagen|extracellular space	antigen binding|calcium ion binding|receptor binding|sugar binding			large_intestine(1)|ovary(1)	2		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)														---	---	---	---
LHX3	8022	broad.mit.edu	37	9	139092502	139092502	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139092502G>A	uc004cha.2	-	2	274	c.177C>T	c.(175-177)AGC>AGT	p.S59S	LHX3_uc004cgz.2_Silent_p.S64S	NM_178138	NP_835258	Q9UBR4	LHX3_HUMAN	LIM homeobox protein 3 isoform a	59	LIM zinc-binding 1.				inner ear development|organ morphogenesis|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		Myeloproliferative disorder(178;0.0511)		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)														---	---	---	---
SDCCAG3	10807	broad.mit.edu	37	9	139299537	139299537	+	Intron	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139299537C>A	uc004chi.2	-						SDCCAG3_uc004chj.2_Intron|SDCCAG3_uc004chk.2_Intron	NM_001039707	NP_001034796			serologically defined colon cancer antigen 3							cytoplasm					0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)														---	---	---	---
PMPCA	23203	broad.mit.edu	37	9	139310805	139310805	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139310805C>T	uc004chl.2	+	6	600	c.595C>T	c.(595-597)CCT>TCT	p.P199S	PMPCA_uc011mdy.1_Missense_Mutation_p.P199S|PMPCA_uc010nbk.2_RNA|PMPCA_uc010nbl.2_Missense_Mutation_p.P99S|PMPCA_uc011mdz.1_Missense_Mutation_p.P68S|PMPCA_uc004chm.1_5'UTR|PMPCA_uc004chn.1_5'Flank	NM_015160	NP_055975	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	199					proteolysis	mitochondrial inner membrane|mitochondrial matrix	metalloendopeptidase activity|zinc ion binding				0		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)														---	---	---	---
INPP5E	56623	broad.mit.edu	37	9	139328514	139328514	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139328514C>T	uc004cho.2	-	3	1394	c.1009G>A	c.(1009-1011)GGG>AGG	p.G337R	INPP5E_uc010nbm.2_Missense_Mutation_p.G337R	NM_019892	NP_063945	Q9NRR6	INP5E_HUMAN	inositol polyphosphate-5-phosphatase E	337						cilium axoneme|cytoskeleton|Golgi cisterna membrane	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity			skin(1)	1		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)														---	---	---	---
LCN10	414332	broad.mit.edu	37	9	139635288	139635288	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139635288G>A	uc010nbq.2	-	3	495	c.436C>T	c.(436-438)CAT>TAT	p.H146Y	LCN10_uc004civ.2_Missense_Mutation_p.H159Y|LCN10_uc011med.1_Intron|LCN10_uc011mee.1_Intron|LCN10_uc011mef.1_Intron|LCN10_uc004ciw.2_RNA			Q6JVE6	LCN10_HUMAN	SubName: Full=LCN10 protein;	146					transport	extracellular region	binding			large_intestine(1)	1	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.32e-06)|Epithelial(140;7.83e-05)														---	---	---	---
C9orf139	401563	broad.mit.edu	37	9	139927540	139927540	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139927540C>T	uc004ckp.1	+	2	1539	c.25C>T	c.(25-27)CCC>TCC	p.P9S	FUT7_uc004ckq.2_5'Flank	NM_207511	NP_997394	Q6ZV77	CI139_HUMAN	hypothetical protein LOC401563	9											0	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.99e-05)|Epithelial(140;0.000493)														---	---	---	---
ANAPC2	29882	broad.mit.edu	37	9	140079368	140079368	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140079368G>A	uc004clr.1	-	4	1118	c.1045C>T	c.(1045-1047)CGA>TGA	p.R349*	ANAPC2_uc004clq.1_Nonsense_Mutation_p.R208*	NM_013366	NP_037498	Q9UJX6	ANC2_HUMAN	anaphase-promoting complex subunit 2	349					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cyclin catabolic process|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of synapse maturation|positive regulation of synaptic plasticity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination|regulation of cyclin-dependent protein kinase activity	anaphase-promoting complex|cytosol|nucleoplasm	ubiquitin protein ligase binding|ubiquitin-protein ligase activity			ovary(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)														---	---	---	---
ENTPD8	377841	broad.mit.edu	37	9	140331728	140331728	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140331728G>A	uc004cmw.2	-	4	462	c.278C>T	c.(277-279)GCA>GTA	p.A93V	C9orf167_uc011mew.1_Intron|ENTPD8_uc004cmx.2_Missense_Mutation_p.A93V|ENTPD8_uc004cmy.2_Missense_Mutation_p.A93V	NM_001033113	NP_001028285	Q5MY95	ENTP8_HUMAN	ectonucleoside triphosphate diphosphohydrolase 8	93	Extracellular (Potential).					integral to membrane|plasma membrane	ATP binding			skin(1)	1	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000224)|Epithelial(140;0.000898)														---	---	---	---
NELF	26012	broad.mit.edu	37	9	140347017	140347017	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140347017C>T	uc004cna.2	-	11	1385	c.1153G>A	c.(1153-1155)GAG>AAG	p.E385K	C9orf167_uc011mew.1_Intron|NELF_uc011mex.1_Missense_Mutation_p.E182K|NELF_uc010nci.2_Missense_Mutation_p.E129K|NELF_uc011mey.1_RNA|NELF_uc011mez.1_Missense_Mutation_p.E362K|NELF_uc004cmz.2_Missense_Mutation_p.E383K|NELF_uc004cnc.2_Missense_Mutation_p.E360K|NELF_uc004cnb.2_Missense_Mutation_p.E355K	NM_001130969	NP_001124441	Q6X4W1	NELF_HUMAN	nasal embryonic LHRH factor isoform a	385						nucleus|plasma membrane					0	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000222)|Epithelial(140;0.000888)														---	---	---	---
PNPLA7	375775	broad.mit.edu	37	9	140392668	140392668	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140392668A>G	uc004cnf.2	-	16	2049	c.1712T>C	c.(1711-1713)CTG>CCG	p.L571P	C9orf167_uc011mew.1_Intron|PNPLA7_uc011mfa.1_Intron|PNPLA7_uc010ncj.1_Missense_Mutation_p.L596P	NM_152286	NP_689499	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	571	cNMP 2.				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	140637989	140637989	+	Intron	SNP	C	T	T	rs75421798	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140637989C>T	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)														---	---	---	---
EHMT1	79813	broad.mit.edu	37	9	140676805	140676805	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140676805G>A	uc011mfc.1	+	15	2375	c.2338G>A	c.(2338-2340)GCG>ACG	p.A780T	EHMT1_uc004coa.2_Missense_Mutation_p.A780T|EHMT1_uc004cob.1_Missense_Mutation_p.A749T	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	780	ANK 2.				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	140772539	140772539	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140772539C>T	uc004cog.2	+	1	299	c.154C>T	c.(154-156)CGC>TGC	p.R52C	uc004cof.1_Intron	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	52	Cytoplasmic (Potential).				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)													---	---	---	---
PFKP	5214	broad.mit.edu	37	10	3155672	3155672	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3155672G>A	uc001igp.2	+	13	1369	c.1333G>A	c.(1333-1335)GCC>ACC	p.A445T	PFKP_uc001igq.2_Missense_Mutation_p.A437T|PFKP_uc009xhr.2_Missense_Mutation_p.A407T|PFKP_uc009xhs.1_Missense_Mutation_p.A229T|PFKP_uc009xht.2_Missense_Mutation_p.A183T|PFKP_uc009xhu.2_5'UTR	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet	445					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)														---	---	---	---
ITIH5	80760	broad.mit.edu	37	10	7608295	7608295	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7608295C>T	uc001ijq.2	-	13	2304	c.2225G>A	c.(2224-2226)CGC>CAC	p.R742H	ITIH5_uc001ijp.2_Missense_Mutation_p.R528H	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	742					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
ITIH5	80760	broad.mit.edu	37	10	7627891	7627891	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7627891A>T	uc001ijq.2	-	8	1160	c.1081T>A	c.(1081-1083)TAC>AAC	p.Y361N	ITIH5_uc001ijp.2_Missense_Mutation_p.Y147N|ITIH5_uc001ijr.1_Missense_Mutation_p.Y361N	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	361	VWFA.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
UPF2	26019	broad.mit.edu	37	10	11990443	11990443	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11990443T>A	uc001ila.2	-	15	3573	c.3099A>T	c.(3097-3099)GAA>GAT	p.E1033D	UPF2_uc001ilb.2_Missense_Mutation_p.E1033D|UPF2_uc001ilc.2_Missense_Mutation_p.E1033D	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	1033	Glu-rich.|Sufficient for interaction with EIF4A1 and EIF1.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)																---	---	---	---
UPF2	26019	broad.mit.edu	37	10	12070898	12070898	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12070898C>T	uc001ila.2	-	2	1465	c.991G>A	c.(991-993)GCA>ACA	p.A331T	UPF2_uc001ilb.2_Missense_Mutation_p.A331T|UPF2_uc001ilc.2_Missense_Mutation_p.A331T|UPF2_uc009xiz.1_Missense_Mutation_p.A331T	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	331	MIF4G 1.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)																---	---	---	---
CUBN	8029	broad.mit.edu	37	10	16893340	16893340	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16893340A>G	uc001ioo.2	-	60	9609	c.9557T>C	c.(9556-9558)GTA>GCA	p.V3186A	CUBN_uc009xjq.1_RNA	NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	3186	CUB 24.				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	17147455	17147455	+	Splice_Site	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17147455C>T	uc001ioo.2	-	11	1282	c.1230_splice	c.e11+1	p.I410_splice		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)													---	---	---	---
VIM	7431	broad.mit.edu	37	10	17278320	17278320	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17278320T>C	uc001iou.2	+	9	1714	c.1301T>C	c.(1300-1302)GTT>GCT	p.V434A	VIM_uc001iov.1_Intron|VIM_uc001iow.1_RNA|VIM_uc001iox.1_Missense_Mutation_p.V434A|VIM_uc001ioy.1_Missense_Mutation_p.V347A|VIM_uc001ioz.1_RNA|VIM_uc001ipb.1_RNA|VIM_uc009xjv.1_Missense_Mutation_p.V392A|VIM_uc001ipc.1_Intron	NM_003380	NP_003371	P08670	VIME_HUMAN	vimentin	434	Tail.				cellular component disassembly involved in apoptosis|cellular component movement|interspecies interaction between organisms|muscle filament sliding	cytosol|intermediate filament	protein C-terminus binding|structural constituent of cytoskeleton			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4																		---	---	---	---
SLC39A12	221074	broad.mit.edu	37	10	18242199	18242199	+	5'UTR	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18242199C>T	uc001ipo.2	+	2					SLC39A12_uc001ipn.2_5'UTR|SLC39A12_uc001ipp.2_5'UTR|SLC39A12_uc010qck.1_Intron	NM_001145195	NP_001138667			solute carrier family 39 (zinc transporter),						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)|breast(1)	2																		---	---	---	---
GPR158	57512	broad.mit.edu	37	10	25887748	25887748	+	Missense_Mutation	SNP	C	T	T	rs146528842		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25887748C>T	uc001isj.2	+	11	3253	c.3193C>T	c.(3193-3195)CGC>TGC	p.R1065C	GPR158_uc001isk.2_Missense_Mutation_p.R440C	NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	1065	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8																		---	---	---	---
SVIL	6840	broad.mit.edu	37	10	29839766	29839766	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29839766G>A	uc001iut.1	-	6	1340	c.587C>T	c.(586-588)CCG>CTG	p.P196L	SVIL_uc001iuu.1_Missense_Mutation_p.P196L|SVIL_uc009xld.1_Missense_Mutation_p.P196L	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	196					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)																---	---	---	---
EPC1	80314	broad.mit.edu	37	10	32581920	32581920	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32581920C>T	uc001iwg.1	-	4	932	c.662G>A	c.(661-663)CGA>CAA	p.R221Q	EPC1_uc001iwi.3_Missense_Mutation_p.R171Q|EPC1_uc009xlt.2_Missense_Mutation_p.R171Q|EPC1_uc001iwh.1_Missense_Mutation_p.R221Q	NM_025209	NP_079485	Q9H2F5	EPC1_HUMAN	enhancer of polycomb 1	221					histone H2A acetylation|histone H4 acetylation|negative regulation of gene expression, epigenetic|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear membrane|Piccolo NuA4 histone acetyltransferase complex				ovary(3)|central_nervous_system(1)	4		Prostate(175;0.0199)																---	---	---	---
ZNF33A	7581	broad.mit.edu	37	10	38344404	38344404	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38344404G>A	uc001izh.2	+	5	1527	c.1349G>A	c.(1348-1350)CGT>CAT	p.R450H	ZNF33A_uc001izg.2_Missense_Mutation_p.R451H|ZNF33A_uc010qev.1_Missense_Mutation_p.R457H|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	450	C2H2-type 5.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
SLC18A3	6572	broad.mit.edu	37	10	50819067	50819067	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50819067C>T	uc001jhw.2	+	1	721	c.281C>T	c.(280-282)ACG>ATG	p.T94M	CHAT_uc001jhv.1_Intron|CHAT_uc001jhx.1_5'Flank|CHAT_uc001jhy.1_5'Flank	NM_003055	NP_003046	Q16572	VACHT_HUMAN	vesicular acetylcholine transporter	94	Lumenal, vesicle (Potential).				neurotransmitter secretion	clathrin sculpted acetylcholine transport vesicle membrane|integral to plasma membrane|membrane fraction	acetylcholine transmembrane transporter activity			ovary(2)	2																		---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55664973	55664973	+	Intron	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55664973T>G	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	55782869	55782869	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55782869C>T	uc001jju.1	-	19	2704	c.2309G>A	c.(2308-2310)AGC>AAC	p.S770N	PCDH15_uc010qhq.1_Missense_Mutation_p.S775N|PCDH15_uc010qhr.1_Missense_Mutation_p.S770N|PCDH15_uc010qhs.1_Missense_Mutation_p.S782N|PCDH15_uc010qht.1_Missense_Mutation_p.S777N|PCDH15_uc010qhu.1_Missense_Mutation_p.S770N|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.S770N|PCDH15_uc010qhw.1_Missense_Mutation_p.S733N|PCDH15_uc010qhx.1_Missense_Mutation_p.S699N|PCDH15_uc010qhy.1_Missense_Mutation_p.S775N|PCDH15_uc010qhz.1_Missense_Mutation_p.S770N|PCDH15_uc010qia.1_Missense_Mutation_p.S748N|PCDH15_uc010qib.1_Missense_Mutation_p.S748N|PCDH15_uc001jjw.2_Missense_Mutation_p.S770N	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	770	Extracellular (Potential).|Cadherin 7.				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)			---	---	---	---
FAM13C	220965	broad.mit.edu	37	10	61029761	61029761	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61029761T>G	uc001jkn.2	-	8	835	c.701A>C	c.(700-702)AAC>ACC	p.N234T	FAM13C_uc001jko.2_Missense_Mutation_p.N234T|FAM13C_uc010qid.1_Missense_Mutation_p.N151T|FAM13C_uc010qie.1_Missense_Mutation_p.N151T|FAM13C_uc010qif.1_Missense_Mutation_p.N256T|FAM13C_uc001jkp.2_Missense_Mutation_p.N151T	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1	234										ovary(2)	2																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	61835974	61835974	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61835974C>T	uc001jky.2	-	37	4857	c.4665G>A	c.(4663-4665)GCG>GCA	p.A1555A	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	1555	Ser-rich.				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
TET1	80312	broad.mit.edu	37	10	70450964	70450964	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70450964C>T	uc001jok.3	+	12	6309	c.5804C>T	c.(5803-5805)ACG>ATG	p.T1935M		NM_030625	NP_085128	Q8NFU7	TET1_HUMAN	CXXC finger 6	1935					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																		---	---	---	---
SRGN	5552	broad.mit.edu	37	10	70856875	70856875	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70856875C>T	uc001joz.2	+	2	201	c.115C>T	c.(115-117)CGC>TGC	p.R39C		NM_002727	NP_002718	P10124	SRGN_HUMAN	serglycin precursor	39					apoptosis|biomineral tissue development|maintenance of granzyme B location in T cell secretory granule|maintenance of protease location in mast cell secretory granule|negative regulation of bone mineralization|negative regulation of cytokine secretion|platelet activation|platelet degranulation|protein maturation by peptide bond cleavage	extracellular space|mast cell granule|platelet alpha granule lumen					0																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71124621	71124621	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71124621C>T	uc001jpl.3	+	4	559	c.458C>T	c.(457-459)ACG>ATG	p.T153M	HK1_uc001jpg.3_Missense_Mutation_p.T141M|HK1_uc001jph.3_Missense_Mutation_p.T157M|HK1_uc001jpi.3_Missense_Mutation_p.T157M|HK1_uc001jpj.3_Missense_Mutation_p.T188M|HK1_uc001jpk.3_Missense_Mutation_p.T152M|HK1_uc009xqd.2_Missense_Mutation_p.T31M	NM_000188	NP_000179	P19367	HXK1_HUMAN	hexokinase 1 isoform HKI	153	Regulatory.				glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71142254	71142254	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71142254G>A	uc001jpl.3	+	10	1378	c.1277G>A	c.(1276-1278)CGT>CAT	p.R426H	HK1_uc001jpg.3_Missense_Mutation_p.R414H|HK1_uc001jph.3_Missense_Mutation_p.R430H|HK1_uc001jpi.3_Missense_Mutation_p.R430H|HK1_uc001jpj.3_Missense_Mutation_p.R461H|HK1_uc001jpk.3_Missense_Mutation_p.R425H|HK1_uc009xqd.2_Missense_Mutation_p.R304H	NM_000188	NP_000179	P19367	HXK1_HUMAN	hexokinase 1 isoform HKI	426	ATP 1.|Regulatory.				glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73491893	73491893	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73491893G>A	uc001jrx.3	+	31	4242	c.3865G>A	c.(3865-3867)GCC>ACC	p.A1289T	CDH23_uc001jrz.2_Missense_Mutation_p.A905T|C10orf105_uc001jsb.1_Intron|CDH23_uc001jsc.1_Missense_Mutation_p.A97T	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	1289	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																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73572286	73572286	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73572286G>A	uc001jrx.3	+	65	9807	c.9430G>A	c.(9430-9432)GCC>ACC	p.A3144T	CDH23_uc001jsg.3_Missense_Mutation_p.A904T|CDH23_uc001jsh.3_Missense_Mutation_p.A904T|CDH23_uc001jsi.3_Missense_Mutation_p.A904T|CDH23_uc001jsj.3_Missense_Mutation_p.A41T|CDH23_uc010qjr.1_Missense_Mutation_p.A41T	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	3144	Cytoplasmic (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																		---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78839229	78839229	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78839229G>A	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)													---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	80968205	80968205	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80968205C>T	uc001kaf.2	+	6	745	c.173C>T	c.(172-174)ACG>ATG	p.T58M	ZMIZ1_uc001kae.2_Missense_Mutation_p.T58M	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17	58					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)															---	---	---	---
CDHR1	92211	broad.mit.edu	37	10	85968128	85968128	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85968128G>A	uc001kcv.2	+	11	1162	c.1162G>A	c.(1162-1164)GAC>AAC	p.D388N	CDHR1_uc001kcw.2_Missense_Mutation_p.D388N|CDHR1_uc009xst.2_Missense_Mutation_p.D147N	NM_033100	NP_149091	Q96JP9	CDHR1_HUMAN	protocadherin 21 precursor	388	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion		calcium ion binding|receptor activity			ovary(1)	1																		---	---	---	---
CDHR1	92211	broad.mit.edu	37	10	85970853	85970853	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85970853G>A	uc001kcv.2	+	13	1417	c.1417G>A	c.(1417-1419)GAC>AAC	p.D473N	CDHR1_uc001kcw.2_Missense_Mutation_p.D473N|CDHR1_uc009xst.2_Intron|CDHR1_uc001kcx.2_5'Flank	NM_033100	NP_149091	Q96JP9	CDHR1_HUMAN	protocadherin 21 precursor	473	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion		calcium ion binding|receptor activity			ovary(1)	1																		---	---	---	---
LDB3	11155	broad.mit.edu	37	10	88428474	88428474	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88428474G>T	uc001kdv.2	+	1	49	c.26G>T	c.(25-27)GGG>GTG	p.G9V	LDB3_uc010qml.1_Missense_Mutation_p.G9V|LDB3_uc010qmm.1_Missense_Mutation_p.G9V|LDB3_uc001kdu.2_Missense_Mutation_p.G9V|LDB3_uc009xsz.2_5'UTR|LDB3_uc001kdr.2_Missense_Mutation_p.G9V|LDB3_uc009xsy.2_Missense_Mutation_p.G9V|LDB3_uc001kds.2_Missense_Mutation_p.G9V|LDB3_uc001kdt.2_RNA	NM_007078	NP_009009	O75112	LDB3_HUMAN	LIM domain binding 3 isoform 1	9	PDZ.					cytoskeleton|perinuclear region of cytoplasm|pseudopodium	zinc ion binding			ovary(1)	1																		---	---	---	---
MMRN2	79812	broad.mit.edu	37	10	88703011	88703011	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88703011G>A	uc001kea.2	-	6	1657	c.1530C>T	c.(1528-1530)GAC>GAT	p.D510D	MMRN2_uc010qmn.1_Silent_p.D153D|MMRN2_uc009xtb.2_Silent_p.D467D	NM_024756	NP_079032	Q9H8L6	MMRN2_HUMAN	multimerin 2 precursor	510						extracellular space				large_intestine(1)	1																		---	---	---	---
AGAP11	119385	broad.mit.edu	37	10	88768422	88768422	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88768422C>T	uc001kee.2	+	12	1617	c.413C>T	c.(412-414)ACA>ATA	p.T138I	AGAP11_uc001kef.2_Intron	NM_133447	NP_597704	Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase	138	PH.				regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
ANKRD22	118932	broad.mit.edu	37	10	90591679	90591679	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90591679C>T	uc001kfj.3	-	2	494	c.126G>A	c.(124-126)ACG>ACA	p.T42T		NM_144590	NP_653191	Q5VYY1	ANR22_HUMAN	ankyrin repeat domain 22	42	ANK 1.										0		Colorectal(252;0.0163)		Colorectal(12;6.29e-05)|COAD - Colon adenocarcinoma(12;7.69e-05)														---	---	---	---
ACTA2	59	broad.mit.edu	37	10	90701549	90701549	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90701549G>A	uc001kfp.2	-	5	563	c.447C>T	c.(445-447)CGC>CGT	p.R149R	STAMBPL1_uc010qmx.1_Intron|ACTA2_uc010qmy.1_Silent_p.R104R|ACTA2_uc001kfq.2_Silent_p.R149R	NM_001613	NP_001604	P62736	ACTA_HUMAN	alpha 2 actin	149			R -> C (in AAT6).		response to virus	cytosol	ATP binding				0		Colorectal(252;0.0161)		Colorectal(12;0.000123)|COAD - Colon adenocarcinoma(12;0.00018)														---	---	---	---
KIF20B	9585	broad.mit.edu	37	10	91483813	91483813	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91483813T>C	uc001kgs.1	+	14	1887	c.1815T>C	c.(1813-1815)GTT>GTC	p.V605V	KIF20B_uc001kgr.1_Silent_p.V605V|KIF20B_uc001kgt.1_5'UTR	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1	605					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																		---	---	---	---
PCGF5	84333	broad.mit.edu	37	10	92982626	92982626	+	Translation_Start_Site	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92982626C>T	uc001khh.2	+	2	245	c.-2C>T	c.(-4-0)CACGA>CATGA		PCGF5_uc001khg.2_RNA|PCGF5_uc010qnk.1_Translation_Start_Site|PCGF5_uc001khi.2_Translation_Start_Site	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																		---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93744029	93744029	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93744029C>T	uc001khr.2	+	19	2393	c.2295C>T	c.(2293-2295)GAC>GAT	p.D765D	BTAF1_uc001khs.1_Silent_p.D435D|BTAF1_uc001kht.1_Silent_p.D203D	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription	765					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)																---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95069835	95069835	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95069835C>T	uc001kin.2	-	53	6212	c.6089G>A	c.(6088-6090)GGC>GAC	p.G2030D	MYOF_uc001kio.2_Missense_Mutation_p.G2017D|MYOF_uc009xue.2_RNA	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	2030	Helical; (Potential).				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
PDE6C	5146	broad.mit.edu	37	10	95394529	95394529	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95394529C>T	uc001kiu.3	+	9	1272	c.1134C>T	c.(1132-1134)GAC>GAT	p.D378D		NM_006204	NP_006195	P51160	PDE6C_HUMAN	phosphodiesterase 6C	378	GAF 2.				visual perception	plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|metal ion binding			ovary(2)|kidney(1)|skin(1)	4		Colorectal(252;0.123)																---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97096789	97096789	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97096789C>T	uc001kkp.2	-	28	3173	c.3128G>A	c.(3127-3129)CGT>CAT	p.R1043H	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_Missense_Mutation_p.R997H|SORBS1_uc010qoe.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3	1043					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)														---	---	---	---
ALDH18A1	5832	broad.mit.edu	37	10	97397115	97397115	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97397115G>A	uc001kkz.2	-	4	624	c.382C>T	c.(382-384)CGC>TGC	p.R128C	ALDH18A1_uc001kky.2_Missense_Mutation_p.R128C|ALDH18A1_uc010qog.1_Missense_Mutation_p.R17C|ALDH18A1_uc010qoh.1_Intron	NM_002860	NP_002851	P54886	P5CS_HUMAN	pyrroline-5-carboxylate synthetase isoform 1	128	Glutamate 5-kinase.				proline biosynthetic process	mitochondrial inner membrane	ATP binding|glutamate 5-kinase activity|glutamate-5-semialdehyde dehydrogenase activity			pancreas(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)	L-Glutamic Acid(DB00142)													---	---	---	---
SLIT1	6585	broad.mit.edu	37	10	98764573	98764573	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98764573G>A	uc001kmw.2	-	33	3839	c.3587C>T	c.(3586-3588)ACG>ATG	p.T1196M		NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor	1196	Laminin G-like.				axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)														---	---	---	---
RRP12	23223	broad.mit.edu	37	10	99141494	99141494	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99141494G>A	uc001knf.2	-	11	1437	c.1298C>T	c.(1297-1299)ACT>ATT	p.T433I	RRP12_uc009xvm.2_Missense_Mutation_p.T151I|RRP12_uc010qou.1_Missense_Mutation_p.T372I|RRP12_uc009xvn.2_Missense_Mutation_p.T333I	NM_015179	NP_055994	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog isoform 1	433						integral to membrane|nuclear membrane|nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)														---	---	---	---
DHDPSL	112817	broad.mit.edu	37	10	99358872	99358872	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99358872G>A	uc001kny.2	+	3	726	c.367G>A	c.(367-369)GTC>ATC	p.V123I	DHDPSL_uc001knx.2_Missense_Mutation_p.V123I|DHDPSL_uc001knz.2_Intron|PI4K2A_uc010qoy.1_Intron	NM_138413	NP_612422	Q86XE5	HOGA1_HUMAN	DHDPS-like protein isoform 1	123					glyoxylate catabolic process	mitochondrion	4-hydroxy-2-oxoglutarate aldolase activity				0																		---	---	---	---
CRTAC1	55118	broad.mit.edu	37	10	99695979	99695979	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99695979G>A	uc001kou.1	-	3	725	c.369C>T	c.(367-369)GAC>GAT	p.D123D	CRTAC1_uc001kov.2_Silent_p.D112D|CRTAC1_uc001kot.1_Translation_Start_Site	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	123	FG-GAP 2; atypical.					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)														---	---	---	---
CNNM1	26507	broad.mit.edu	37	10	101090324	101090324	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101090324C>T	uc001kpp.3	+	1	1469	c.1180C>T	c.(1180-1182)CGG>TGG	p.R394W	CNNM1_uc009xwe.2_Missense_Mutation_p.R394W|CNNM1_uc010qpi.1_Missense_Mutation_p.R394W|CNNM1_uc009xwf.2_Missense_Mutation_p.R394W	NM_020348	NP_065081	Q9NRU3	CNNM1_HUMAN	cyclin M1	394	DUF21.				ion transport	integral to membrane|plasma membrane					0		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)														---	---	---	---
LBX1	10660	broad.mit.edu	37	10	102987489	102987489	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102987489C>T	uc001ksx.2	-	2	529	c.384G>A	c.(382-384)TCG>TCA	p.S128S	uc010qpy.1_5'Flank	NM_006562	NP_006553	P52954	LBX1_HUMAN	ladybird homeobox 1	128	Homeobox.				muscle organ development		sequence-specific DNA binding				0		Colorectal(252;0.234)		Epithelial(162;3.22e-09)|all cancers(201;1.79e-07)														---	---	---	---
POLL	27343	broad.mit.edu	37	10	103340084	103340084	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103340084G>A	uc001ktg.1	-	7	2050	c.1284C>T	c.(1282-1284)GTC>GTT	p.V428V	DPCD_uc010qpz.1_Intron|POLL_uc001ktd.1_Silent_p.V101V|POLL_uc001kte.1_Silent_p.V120V|POLL_uc001kth.1_Silent_p.V153V|POLL_uc001kti.1_Silent_p.V428V|POLL_uc001ktj.1_Silent_p.V428V|POLL_uc001ktf.2_Silent_p.V336V|POLL_uc001ktk.1_Silent_p.V167V|POLL_uc010qqa.1_Silent_p.V167V|POLL_uc010qqb.1_RNA|POLL_uc001ktm.2_Silent_p.V428V|POLL_uc001ktl.2_Silent_p.V340V|POLL_uc010qqc.1_Silent_p.V120V	NM_013274	NP_037406	Q9UGP5	DPOLL_HUMAN	DNA-directed DNA polymerase lambda	428	Involved in primer binding (By similarity).				DNA replication|nucleotide-excision repair|somatic hypermutation of immunoglobulin genes	nucleus	DNA binding|DNA-directed DNA polymerase activity|lyase activity|metal ion binding				0		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)									DNA_polymerases_(catalytic_subunits)					---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104679333	104679333	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104679333C>T	uc001kwm.2	+	1	1220	c.1096C>T	c.(1096-1098)CGG>TGG	p.R366W	CNNM2_uc001kwn.2_Missense_Mutation_p.R366W|CNNM2_uc001kwl.2_Missense_Mutation_p.R366W	NM_017649	NP_060119	Q9H8M5	CNNM2_HUMAN	cyclin M2 isoform 1	366	DUF21.				ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
SH3PXD2A	9644	broad.mit.edu	37	10	105361883	105361883	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105361883C>T	uc001kxj.1	-	14	3148	c.3008G>A	c.(3007-3009)CGC>CAC	p.R1003H	SH3PXD2A_uc010qqr.1_Intron|SH3PXD2A_uc010qqs.1_Missense_Mutation_p.R838H|SH3PXD2A_uc010qqt.1_Missense_Mutation_p.R880H|SH3PXD2A_uc009xxn.1_Missense_Mutation_p.R838H|SH3PXD2A_uc010qqu.1_Missense_Mutation_p.R946H	NM_014631	NP_055446	Q5TCZ1	SPD2A_HUMAN	SH3 multiple domains 1	1031					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)														---	---	---	---
COL17A1	1308	broad.mit.edu	37	10	105824282	105824282	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105824282G>A	uc001kxr.2	-	10	849	c.680C>T	c.(679-681)GCG>GTG	p.A227V	COL17A1_uc010qqv.1_Missense_Mutation_p.A211V|COL17A1_uc009xxp.1_Missense_Mutation_p.A227V	NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	227	Cytoplasmic (Potential).|Nonhelical region (NC16).|Necessary for interaction with DST and for the recruitment of DST to hemidesmosome.				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)														---	---	---	---
TDRD1	56165	broad.mit.edu	37	10	115963151	115963151	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115963151C>T	uc001lbg.1	+	8	959	c.806C>T	c.(805-807)ACG>ATG	p.T269M	TDRD1_uc001lbf.2_Missense_Mutation_p.T260M|TDRD1_uc001lbh.1_Missense_Mutation_p.T260M|TDRD1_uc001lbi.1_Missense_Mutation_p.T260M|TDRD1_uc010qsc.1_Translation_Start_Site|TDRD1_uc001lbj.2_Translation_Start_Site	NM_198795	NP_942090	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	269					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)														---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117045787	117045787	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117045787T>A	uc001lcg.2	+	15	2681	c.2295T>A	c.(2293-2295)AGT>AGA	p.S765R		NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor	765	C-type lectin.|Extracellular (Potential).					integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)														---	---	---	---
VAX1	11023	broad.mit.edu	37	10	118897444	118897444	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118897444C>T	uc009xyx.2	-	1	369	c.124G>A	c.(124-126)GCC>ACC	p.A42T	VAX1_uc001ldb.1_Missense_Mutation_p.A42T	NM_001112704	NP_001106175	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1 isoform a	42						nucleus	sequence-specific DNA binding			ovary(2)	2				all cancers(201;0.0108)														---	---	---	---
INPP5F	22876	broad.mit.edu	37	10	121557041	121557041	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121557041T>G	uc001leo.2	+	8	1103	c.937T>G	c.(937-939)TTG>GTG	p.L313V		NM_014937	NP_055752	Q9Y2H2	SAC2_HUMAN	inositol polyphosphate-5-phosphatase F	313	SAC.						phosphoric ester hydrolase activity			ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)														---	---	---	---
FGFR2	2263	broad.mit.edu	37	10	123325038	123325038	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123325038G>A	uc010qtk.1	-	3	937	c.290C>T	c.(289-291)GCC>GTC	p.A97V	FGFR2_uc010qtg.1_Missense_Mutation_p.A97V|FGFR2_uc010qth.1_Intron|FGFR2_uc010qti.1_Intron|FGFR2_uc010qtj.1_Missense_Mutation_p.A97V|FGFR2_uc010qtl.1_Missense_Mutation_p.A97V|FGFR2_uc010qtm.1_Intron|FGFR2_uc001lfl.3_Missense_Mutation_p.A97V|FGFR2_uc001lfm.2_Intron|FGFR2_uc001lfn.3_Intron|FGFR2_uc010qtn.1_Missense_Mutation_p.A116V|FGFR2_uc010qto.1_Intron|FGFR2_uc001lfo.1_Missense_Mutation_p.A116V|FGFR2_uc010qtp.1_Missense_Mutation_p.A116V|FGFR2_uc010qtq.1_Missense_Mutation_p.A116V	NM_000141	NP_000132	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2 isoform 1	97	Ig-like C2-type 1.|Extracellular (Potential).				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	p.A97T(1)		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				---	---	---	---
HMX3	340784	broad.mit.edu	37	10	124896865	124896865	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124896865G>A	uc010quc.1	+	2	692	c.692G>A	c.(691-693)CGC>CAC	p.R231H		NM_001105574	NP_001099044	A6NHT5	HMX3_HUMAN	H6 family homeobox 3	231	Homeobox.				cell differentiation	nucleus	sequence-specific DNA binding transcription factor activity				0		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.122)|COAD - Colon adenocarcinoma(40;0.141)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128836060	128836060	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128836060G>A	uc001ljt.2	+	19	1991	c.1927G>A	c.(1927-1929)GAT>AAT	p.D643N	DOCK1_uc010qun.1_Missense_Mutation_p.D664N	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	643	DHR-1.				apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
FAM196A	642938	broad.mit.edu	37	10	128974539	128974539	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128974539G>A	uc001lju.1	-	1	162	c.121C>T	c.(121-123)CGG>TGG	p.R41W	DOCK1_uc001ljt.2_Intron|DOCK1_uc010qun.1_Intron|FAM196A_uc010quo.1_Missense_Mutation_p.R41W|FAM196A_uc001ljv.1_Missense_Mutation_p.R41W|FAM196A_uc009yap.1_Missense_Mutation_p.R41W	NM_001039762	NP_001034851	Q6ZSG2	F196A_HUMAN	hypothetical protein LOC642938	41										ovary(2)	2																		---	---	---	---
FAM196A	642938	broad.mit.edu	37	10	128974569	128974569	+	Missense_Mutation	SNP	C	T	T	rs150536495		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128974569C>T	uc001lju.1	-	1	132	c.91G>A	c.(91-93)GCC>ACC	p.A31T	DOCK1_uc001ljt.2_Intron|DOCK1_uc010qun.1_Intron|FAM196A_uc010quo.1_Missense_Mutation_p.A31T|FAM196A_uc001ljv.1_Missense_Mutation_p.A31T|FAM196A_uc009yap.1_Missense_Mutation_p.A31T	NM_001039762	NP_001034851	Q6ZSG2	F196A_HUMAN	hypothetical protein LOC642938	31										ovary(2)	2																		---	---	---	---
NKX6-2	84504	broad.mit.edu	37	10	134598438	134598438	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134598438G>A	uc001llr.2	-	3	901	c.816C>T	c.(814-816)GGC>GGT	p.G272G		NM_177400	NP_796374	Q9C056	NKX62_HUMAN	NK6 transcription factor related, locus 2	272						nucleus	sequence-specific DNA binding transcription factor activity				0		all_cancers(35;2.79e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0584)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;4.06e-05)|Epithelial(32;5.53e-05)|all cancers(32;5.99e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	134664801	134664801	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134664801G>A	uc010qux.1	-	32	4761	c.4761C>T	c.(4759-4761)AAC>AAT	p.N1587N		NM_017609	NP_060079			Homo sapiens cDNA, FLJ17989.																														---	---	---	---
B4GALNT4	338707	broad.mit.edu	37	11	375665	375665	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:375665G>A	uc001lpb.2	+	10	886	c.877G>A	c.(877-879)GTG>ATG	p.V293M		NM_178537	NP_848632	Q76KP1	B4GN4_HUMAN	beta	293	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
ANO9	338440	broad.mit.edu	37	11	418466	418466	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:418466G>A	uc001lpi.2	-	23	2339	c.2254C>T	c.(2254-2256)CAG>TAG	p.Q752*	SIGIRR_uc001lpf.2_5'Flank|SIGIRR_uc001lpe.1_5'Flank|ANO9_uc001lph.2_Nonsense_Mutation_p.Q445*|ANO9_uc010qvv.1_Nonsense_Mutation_p.Q608*	NM_001012302	NP_001012302	A1A5B4	ANO9_HUMAN	tumor protein p53 inducible protein 5	752	Cytoplasmic (Potential).					chloride channel complex	chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4																		---	---	---	---
PTDSS2	81490	broad.mit.edu	37	11	479107	479107	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:479107C>T	uc001lpj.2	+	4	566	c.390C>T	c.(388-390)TGC>TGT	p.C130C	PTDSS2_uc009ybv.1_Silent_p.C130C	NM_030783	NP_110410	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	130	Helical; (Potential).					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)													---	---	---	---
PHRF1	57661	broad.mit.edu	37	11	598418	598418	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:598418G>A	uc001lqe.2	+	9	1071	c.940G>A	c.(940-942)GAG>AAG	p.E314K	PHRF1_uc010qwc.1_Missense_Mutation_p.E314K|PHRF1_uc010qwd.1_Missense_Mutation_p.E313K|PHRF1_uc010qwe.1_Missense_Mutation_p.E310K|PHRF1_uc009ybz.1_Missense_Mutation_p.E105K	NM_020901	NP_065952	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	314	Arg-rich.						RNA polymerase binding|zinc ion binding				0																		---	---	---	---
PHRF1	57661	broad.mit.edu	37	11	608437	608437	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:608437G>A	uc001lqe.2	+	14	3112	c.2981G>A	c.(2980-2982)CGC>CAC	p.R994H	PHRF1_uc010qwc.1_Missense_Mutation_p.R993H|PHRF1_uc010qwd.1_Missense_Mutation_p.R992H|PHRF1_uc010qwe.1_Missense_Mutation_p.R990H|PHRF1_uc009ybz.1_Missense_Mutation_p.R784H|PHRF1_uc009yca.1_RNA	NM_020901	NP_065952	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	994	Arg-rich.						RNA polymerase binding|zinc ion binding				0																		---	---	---	---
DEAF1	10522	broad.mit.edu	37	11	686948	686948	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:686948G>A	uc001lqq.1	-	5	1407	c.714C>T	c.(712-714)ACC>ACT	p.T238T	DEAF1_uc009ycf.1_RNA	NM_021008	NP_066288	O75398	DEAF1_HUMAN	deformed epidermal autoregulatory factor 1	238	SAND.				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)														---	---	---	---
MUC6	4588	broad.mit.edu	37	11	1017547	1017547	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1017547G>A	uc001lsw.2	-	31	5305	c.5254C>T	c.(5254-5256)CAC>TAC	p.H1752Y		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	1752	Thr-rich.|Approximate repeats.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1154250	1154250	+	Silent	SNP	C	T	T	rs79836765		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1154250C>T	uc009ycr.1	+	3	222	c.96C>T	c.(94-96)TCC>TCT	p.S32S		NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					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)														---	---	---	---
TSPAN32	10077	broad.mit.edu	37	11	2339137	2339137	+	Missense_Mutation	SNP	C	T	T	rs147063227		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2339137C>T	uc001lvy.1	+	10	1083	c.946C>T	c.(946-948)CGG>TGG	p.R316W	TSPAN32_uc009ydl.1_RNA|TSPAN32_uc001lvz.1_Missense_Mutation_p.R286W|TSPAN32_uc001lwb.1_3'UTR|TSPAN32_uc001lwc.1_Missense_Mutation_p.R261W|TSPAN32_uc001lwd.1_Missense_Mutation_p.R248W	NM_139022	NP_620591	Q96QS1	TSN32_HUMAN	tumor-suppressing subtransferable candidate 6	316					cell-cell signaling	integral to membrane				central_nervous_system(1)	1		all_epithelial(84;4.89e-05)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.00791)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000533)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)														---	---	---	---
CARS	833	broad.mit.edu	37	11	3062131	3062131	+	Silent	SNP	G	A	A	rs61737270	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3062131G>A	uc001lxh.2	-	3	275	c.201C>T	c.(199-201)CAC>CAT	p.H67H	CARS_uc001lxe.2_Silent_p.H57H|CARS_uc001lxf.2_Silent_p.H150H|CARS_uc001lxg.2_Silent_p.H67H|CARS_uc010qxo.1_Silent_p.H150H|CARS_uc010qxp.1_Silent_p.H80H|uc001lxi.1_RNA	NM_001751	NP_001742	P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase isoform b	67	HIGH region.				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								---	---	---	---
OSBPL5	114879	broad.mit.edu	37	11	3140844	3140844	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3140844G>A	uc001lxk.2	-	7	782	c.624C>T	c.(622-624)AGC>AGT	p.S208S	OSBPL5_uc010qxq.1_Silent_p.S119S|OSBPL5_uc009ydw.2_Silent_p.S140S|OSBPL5_uc001lxl.2_Silent_p.S140S|OSBPL5_uc009ydx.2_Silent_p.S232S	NM_020896	NP_065947	Q9H0X9	OSBL5_HUMAN	oxysterol-binding protein-like protein 5 isoform	208	PH.				cholesterol metabolic process|cholesterol transport|Golgi to plasma membrane transport	cytosol	oxysterol binding|protein binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)														---	---	---	---
NUP98	4928	broad.mit.edu	37	11	3697469	3697469	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3697469T>C	uc001lyh.2	-	33	5614	c.5323A>G	c.(5323-5325)ATG>GTG	p.M1775V	NUP98_uc001lyi.2_Missense_Mutation_p.M1701V|NUP98_uc001lyg.2_Missense_Mutation_p.M740V	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1	1792					carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)				T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								---	---	---	---
OR51F1	256892	broad.mit.edu	37	11	4790804	4790804	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4790804C>T	uc010qyl.1	-	1	344	c.344G>A	c.(343-345)GGA>GAA	p.G115E		NM_001004752	NP_001004752	A6NLW9	A6NLW9_HUMAN	olfactory receptor, family 51, subfamily F,	115						integral to membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.87e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0045)|LUSC - Lung squamous cell carcinoma(625;0.192)														---	---	---	---
OR51G1	79324	broad.mit.edu	37	11	4945161	4945161	+	Missense_Mutation	SNP	C	T	T	rs145607331	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4945161C>T	uc010qyr.1	-	1	409	c.409G>A	c.(409-411)GTC>ATC	p.V137I		NM_001005237	NP_001005237	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G,	137	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR51V1	283111	broad.mit.edu	37	11	5221347	5221347	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5221347C>T	uc010qyz.1	-	1	584	c.584G>A	c.(583-585)CGC>CAC	p.R195H		NM_001004760	NP_001004760	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V,	195	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
FAM160A2	84067	broad.mit.edu	37	11	6244371	6244371	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6244371A>G	uc001mcl.3	-	4	1234	c.875T>C	c.(874-876)CTG>CCG	p.L292P	FAM160A2_uc001mck.3_Missense_Mutation_p.L292P|FAM160A2_uc001mcm.2_Missense_Mutation_p.L292P	NM_001098794	NP_001092264	Q8N612	F16A2_HUMAN	hypothetical protein LOC84067 isoform 2	292					early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|protein transport	FHF complex	protein binding			skin(2)	2																		---	---	---	---
SMPD1	6609	broad.mit.edu	37	11	6413002	6413002	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6413002C>T	uc001mcw.2	+	2	881	c.707C>T	c.(706-708)CCG>CTG	p.P236L	SMPD1_uc001mcv.1_Intron|SMPD1_uc009yex.2_RNA|SMPD1_uc001mcx.2_Missense_Mutation_p.P236L|SMPD1_uc009yew.2_Missense_Mutation_p.P235L	NM_000543	NP_000534	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid	234					cell death|ceramide biosynthetic process|negative regulation of MAP kinase activity|nervous system development|positive regulation of protein dephosphorylation|signal transduction|sphingomyelin catabolic process|termination of signal transduction	lysosome	hydrolase activity, acting on glycosyl bonds|sphingomyelin phosphodiesterase activity				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Desipramine(DB01151)													---	---	---	---
APBB1	322	broad.mit.edu	37	11	6432180	6432180	+	Missense_Mutation	SNP	C	T	T	rs139345068		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6432180C>T	uc001mdb.1	-	2	498	c.398G>A	c.(397-399)CGA>CAA	p.R133Q	APBB1_uc001mdc.1_Missense_Mutation_p.R133Q|APBB1_uc010rah.1_Intron	NM_001164	NP_001155	O00213	APBB1_HUMAN	amyloid beta A4 precursor protein-binding,	133					apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription factor binding			breast(2)	2		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)														---	---	---	---
OR10A2	341276	broad.mit.edu	37	11	6891003	6891003	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6891003G>A	uc001meu.1	+	1	18	c.18G>A	c.(16-18)CTG>CTA	p.L6L		NM_001004460	NP_001004460	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A,	6	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)														---	---	---	---
OR10A2	341276	broad.mit.edu	37	11	6891024	6891024	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6891024A>G	uc001meu.1	+	1	39	c.39A>G	c.(37-39)TTA>TTG	p.L13L		NM_001004460	NP_001004460	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A,	13	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)														---	---	---	---
OR10A2	341276	broad.mit.edu	37	11	6891030	6891030	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6891030T>C	uc001meu.1	+	1	45	c.45T>C	c.(43-45)TTT>TTC	p.F15F		NM_001004460	NP_001004460	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A,	15	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)														---	---	---	---
OVCH2	341277	broad.mit.edu	37	11	7716409	7716409	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7716409G>T	uc010rbf.1	-	13	1293	c.1293C>A	c.(1291-1293)TGC>TGA	p.C431*		NM_198185	NP_937828			ovochymase 2 precursor												0				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)												OREG0020725	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NRIP3	56675	broad.mit.edu	37	11	9009687	9009687	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9009687T>C	uc001mhg.2	-	2	431	c.317A>G	c.(316-318)GAC>GGC	p.D106G	NRIP3_uc010rbu.1_Missense_Mutation_p.D106G	NM_020645	NP_065696	Q9NQ35	NRIP3_HUMAN	nuclear receptor interacting protein 3	106					proteolysis		aspartic-type endopeptidase activity				0				Epithelial(150;4.77e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0241)														---	---	---	---
DENND5A	23258	broad.mit.edu	37	11	9191462	9191462	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9191462G>A	uc001mhl.2	-	10	2347	c.2092C>T	c.(2092-2094)CGG>TGG	p.R698W	DENND5A_uc001mhk.2_Missense_Mutation_p.R41W|DENND5A_uc010rbw.1_Missense_Mutation_p.R698W|DENND5A_uc010rbx.1_RNA	NM_015213	NP_056028	Q6IQ26	DEN5A_HUMAN	RAB6 interacting protein 1	698										liver(1)	1																		---	---	---	---
RPS13	6207	broad.mit.edu	37	11	17098745	17098745	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17098745C>T	uc001mmp.2	-	3	153	c.121G>A	c.(121-123)GCC>ACC	p.A41T		NM_001017	NP_001008	P62277	RS13_HUMAN	ribosomal protein S13	41					endocrine pancreas development|negative regulation of RNA splicing|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	mRNA binding|protein binding|structural constituent of ribosome				0																		---	---	---	---
MYOD1	4654	broad.mit.edu	37	11	17742486	17742486	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17742486G>A	uc001mni.2	+	2	888	c.668G>A	c.(667-669)CGG>CAG	p.R223Q		NM_002478	NP_002469	P15172	MYOD1_HUMAN	myogenic differentiation 1	223					muscle cell fate commitment|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|skeletal muscle tissue development	nuclear chromatin|transcription factor complex	E-box binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription coactivator activity			breast(2)|ovary(1)	3																		---	---	---	---
SPTY2D1	144108	broad.mit.edu	37	11	18633072	18633072	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18633072C>T	uc001moy.2	-	5	2132	c.1916G>A	c.(1915-1917)CGT>CAT	p.R639H		NM_194285	NP_919261	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1	639										breast(1)	1																		---	---	---	---
MRGPRX1	259249	broad.mit.edu	37	11	18955510	18955510	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18955510G>A	uc001mpg.2	-	1	1040	c.822C>T	c.(820-822)TTC>TTT	p.F274F		NM_147199	NP_671732	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	274	Helical; Name=7; (Potential).				acute-phase response	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(2)|central_nervous_system(1)	3																		---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35456304	35456304	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35456304C>T	uc001mwg.2	-	10	1425	c.1382G>A	c.(1381-1383)CGC>CAC	p.R461H	PAMR1_uc001mwf.2_Missense_Mutation_p.R478H|PAMR1_uc010rew.1_Missense_Mutation_p.R350H|PAMR1_uc010rex.1_Missense_Mutation_p.R421H	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform	461	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
API5	8539	broad.mit.edu	37	11	43351532	43351532	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43351532G>A	uc010rfh.1	+	10	1318	c.1145G>A	c.(1144-1146)CGG>CAG	p.R382Q	API5_uc010rfg.1_Missense_Mutation_p.R371Q|API5_uc001mxf.2_Missense_Mutation_p.R382Q|API5_uc010rfi.1_Missense_Mutation_p.R328Q|API5_uc001mxg.2_Missense_Mutation_p.R256Q	NM_001142930	NP_001136402	Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5 isoform a	382	Leucine-zipper.				anti-apoptosis|apoptosis	cytoplasm|spliceosomal complex	fibroblast growth factor binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
ACCS	84680	broad.mit.edu	37	11	44102762	44102762	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44102762C>A	uc009yks.1	+	12	1147	c.1003C>A	c.(1003-1005)CTG>ATG	p.L335M	EXT2_uc010rfo.1_Intron|ACCS_uc001mxx.2_Missense_Mutation_p.L335M	NM_001127219	NP_001120691	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase	335							1-aminocyclopropane-1-carboxylate synthase activity|protein homodimerization activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			breast(2)|ovary(1)|lung(1)	4																		---	---	---	---
CHST1	8534	broad.mit.edu	37	11	45671251	45671251	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45671251C>T	uc001mys.1	-	4	1894	c.1223G>A	c.(1222-1224)CGC>CAC	p.R408H		NM_003654	NP_003645	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6)	408	Lumenal (Potential).				galactose metabolic process|inflammatory response|keratan sulfate metabolic process	Golgi membrane|integral to membrane	keratan sulfotransferase activity			skin(4)|pancreas(1)	5				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)														---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46419227	46419227	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46419227G>A	uc010rgu.1	-	18	4030	c.3670C>T	c.(3670-3672)CGA>TGA	p.R1224*	AMBRA1_uc010rgt.1_3'UTR|AMBRA1_uc009ylc.1_Nonsense_Mutation_p.R1195*|AMBRA1_uc001ncu.1_Nonsense_Mutation_p.R1134*|AMBRA1_uc001ncv.2_Nonsense_Mutation_p.R1227*|AMBRA1_uc001ncw.2_Nonsense_Mutation_p.R1105*|AMBRA1_uc001ncx.2_Nonsense_Mutation_p.R1164*	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated	1224					autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46564257	46564257	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46564257G>A	uc010rgu.1	-	7	1670	c.1310C>T	c.(1309-1311)CCG>CTG	p.P437L	AMBRA1_uc010rgt.1_Missense_Mutation_p.P3L|AMBRA1_uc009ylc.1_Missense_Mutation_p.P437L|AMBRA1_uc001ncu.1_Missense_Mutation_p.P347L|AMBRA1_uc001ncv.2_Missense_Mutation_p.P347L|AMBRA1_uc001ncw.2_Missense_Mutation_p.P347L|AMBRA1_uc001ncx.2_Missense_Mutation_p.P437L	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated	437					autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46568814	46568814	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46568814T>G	uc010rgu.1	-	4	587	c.227A>C	c.(226-228)AAT>ACT	p.N76T	AMBRA1_uc009ylc.1_Missense_Mutation_p.N76T|AMBRA1_uc001ncu.1_Missense_Mutation_p.N76T|AMBRA1_uc001ncv.2_Missense_Mutation_p.N76T|AMBRA1_uc001ncw.2_Missense_Mutation_p.N76T|AMBRA1_uc001ncx.2_Missense_Mutation_p.N76T	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated	76	WD 1.				autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
OR4B1	119765	broad.mit.edu	37	11	48238681	48238681	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48238681T>C	uc010rhs.1	+	1	320	c.320T>C	c.(319-321)GTT>GCT	p.V107A		NM_001005470	NP_001005470	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B,	107	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
OR4X1	390113	broad.mit.edu	37	11	48286043	48286043	+	Missense_Mutation	SNP	G	A	A	rs61915300		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48286043G>A	uc010rht.1	+	1	631	c.631G>A	c.(631-633)GTG>ATG	p.V211M		NM_001004726	NP_001004726	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X,	211	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035844	55035844	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035844T>C	uc010rid.1	+	4	660	c.574T>C	c.(574-576)TAC>CAC	p.Y192H		NM_024114	NP_077019	Q8IWZ4	TRI48_HUMAN	tripartite motif-containing 48	176						intracellular	zinc ion binding				0																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035854	55035854	+	Intron	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035854T>A	uc010rid.1	+							NM_024114	NP_077019			tripartite motif-containing 48							intracellular	zinc ion binding				0																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035855	55035855	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035855A>G	uc010rid.1	+							NM_024114	NP_077019			tripartite motif-containing 48							intracellular	zinc ion binding				0																		---	---	---	---
OR8K5	219453	broad.mit.edu	37	11	55927379	55927379	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55927379G>A	uc010rja.1	-	1	415	c.415C>T	c.(415-417)CGA>TGA	p.R139*		NM_001004058	NP_001004058	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K,	139	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)|skin(1)	4	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)																---	---	---	---
OR8H1	219469	broad.mit.edu	37	11	56058017	56058017	+	Silent	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56058017A>T	uc010rje.1	-	1	522	c.522T>A	c.(520-522)CGT>CGA	p.R174R		NM_001005199	NP_001005199	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H,	174	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3	Esophageal squamous(21;0.00448)																	---	---	---	---
GLYATL1	92292	broad.mit.edu	37	11	58723451	58723451	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58723451G>A	uc001nnf.2	+	8	1236	c.860G>A	c.(859-861)TGT>TAT	p.C287Y	uc001nng.1_Intron|GLYATL1_uc001nnh.1_Missense_Mutation_p.C318Y|GLYATL1_uc001nni.1_Missense_Mutation_p.C287Y|GLYATL1_uc001nnj.1_Missense_Mutation_p.C287Y			Q969I3	GLYL1_HUMAN	SubName: Full=Glycine acyltransferase family-C; SubName: Full=Glycine-N-acyltransferase-like 1, isoform CRA_a;	287						mitochondrion	glycine N-acyltransferase activity			ovary(1)	1					Glycine(DB00145)													---	---	---	---
OSBP	5007	broad.mit.edu	37	11	59344046	59344046	+	3'UTR	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59344046C>T	uc001noc.1	-	14						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	59406604	59406604	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59406604T>C	uc001noe.3	-	18	2351	c.2208A>G	c.(2206-2208)CCA>CCG	p.P736P		NM_152716	NP_689929	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog	736	Region C.				cytoplasmic mRNA processing body assembly|deadenylation-dependent decapping of nuclear-transcribed mRNA	cytoplasmic mRNA processing body	protein binding|RNA binding			ovary(1)	1																		---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62285596	62285596	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62285596G>A	uc001ntl.2	-	5	16593	c.16293C>T	c.(16291-16293)GGC>GGT	p.G5431G	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	5431					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)																---	---	---	---
TUT1	64852	broad.mit.edu	37	11	62349015	62349015	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62349015G>A	uc001nto.2	-	3	584	c.546C>T	c.(544-546)CCC>CCT	p.P182P		NM_022830	NP_073741	Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6	144					mRNA cleavage|mRNA polyadenylation|snRNA processing	nuclear speck|nucleolus	ATP binding|enzyme binding|mRNA 3'-UTR binding|polynucleotide adenylyltransferase activity|RNA uridylyltransferase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
TTC9C	283237	broad.mit.edu	37	11	62496491	62496491	+	Silent	SNP	G	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62496491G>C	uc001nuy.2	+	1	540	c.171G>C	c.(169-171)CCG>CCC	p.P57P	HNRNPUL2_uc001nuu.1_5'Flank|HNRNPUL2_uc001nuw.2_5'Flank|TTC9C_uc001nux.2_Silent_p.P190P	NM_173810	NP_776171	Q8N5M4	TTC9C_HUMAN	tetratricopeptide repeat domain 9C	57							binding			ovary(1)|pancreas(1)	2																		---	---	---	---
MARK2	2011	broad.mit.edu	37	11	63676573	63676573	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63676573A>G	uc001nxw.2	+	19	2810	c.2231A>G	c.(2230-2232)GAC>GGC	p.D744G	MARK2_uc001nxx.2_Missense_Mutation_p.D675G|MARK2_uc001nxy.2_Missense_Mutation_p.D665G|MARK2_uc001nxv.3_Missense_Mutation_p.D680G|MARK2_uc001nxz.3_Missense_Mutation_p.D701G|MARK2_uc009yoy.2_Missense_Mutation_p.D655G	NM_001039469	NP_001034558	Q7KZI7	MARK2_HUMAN	MAP/microtubule affinity-regulating kinase 2	744	KA1.				cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress	plasma membrane	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3																		---	---	---	---
NAALADL1	10004	broad.mit.edu	37	11	64813303	64813303	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64813303C>T	uc001ocn.2	-	17	2043	c.2027G>A	c.(2026-2028)CGC>CAC	p.R676H	NAALADL1_uc010rnw.1_Missense_Mutation_p.R152H|NAALADL1_uc009ypz.2_RNA	NM_005468	NP_005459	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic	676	Extracellular (Potential).				proteolysis	apical plasma membrane|integral to membrane	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity				0																		---	---	---	---
PCNXL3	399909	broad.mit.edu	37	11	65392970	65392970	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65392970C>T	uc001oey.2	+	18	3124	c.3124C>T	c.(3124-3126)CGC>TGC	p.R1042C	PCNXL3_uc009yqn.2_Missense_Mutation_p.R2C|PCNXL3_uc001oez.2_5'Flank	NM_032223	NP_115599	Q9H6A9	PCX3_HUMAN	pecanex-like 3	1042						integral to membrane					0																		---	---	---	---
DKFZp761E198	91056	broad.mit.edu	37	11	65547392	65547392	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65547392A>G	uc001ofo.3	-	1	431	c.401T>C	c.(400-402)CTC>CCC	p.L134P		NM_138368	NP_612377	Q2VPB7	YK046_HUMAN	hypothetical protein LOC91056	134	Leu-rich.						protein binding				0				READ - Rectum adenocarcinoma(159;0.167)														---	---	---	---
GAL3ST3	89792	broad.mit.edu	37	11	65810630	65810630	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65810630C>T	uc001ogv.2	-	2	804	c.644G>A	c.(643-645)CGC>CAC	p.R215H	GAL3ST3_uc001ogw.2_Missense_Mutation_p.R215H	NM_033036	NP_149025	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	215	Lumenal (Potential).				monosaccharide metabolic process|oligosaccharide metabolic process|poly-N-acetyllactosamine metabolic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi cisterna membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|carbohydrate binding|galactosylceramide sulfotransferase activity|proteoglycan sulfotransferase activity			ovary(1)	1																		---	---	---	---
PACS1	55690	broad.mit.edu	37	11	65998373	65998373	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65998373G>A	uc001oha.1	+	13	1722	c.1588G>A	c.(1588-1590)GAC>AAC	p.D530N	PACS1_uc010rou.1_Missense_Mutation_p.D66N	NM_018026	NP_060496	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1	530					interspecies interaction between organisms|regulation of defense response to virus by virus|viral reproduction	cytosol	protein binding			ovary(6)	6																		---	---	---	---
RIN1	9610	broad.mit.edu	37	11	66099763	66099763	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66099763C>T	uc001ohn.1	-	10	2463	c.2336G>A	c.(2335-2337)CGG>CAG	p.R779Q	RIN1_uc010roy.1_Missense_Mutation_p.R410Q|RIN1_uc009yrd.1_Missense_Mutation_p.R472Q|RIN1_uc010roz.1_Missense_Mutation_p.R674Q|RIN1_uc010rpa.1_Missense_Mutation_p.R613Q	NM_004292	NP_004283	Q13671	RIN1_HUMAN	ras inhibitor RIN1	779					endocytosis|signal transduction	cytoplasm|cytoskeleton|plasma membrane	GTPase activator activity|protein binding			lung(2)|breast(1)	3																		---	---	---	---
DPP3	10072	broad.mit.edu	37	11	66249741	66249741	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66249741C>T	uc001oig.1	+	2	132	c.70C>T	c.(70-72)CGC>TGC	p.R24C	DPP3_uc001oif.1_Missense_Mutation_p.R24C|DPP3_uc010rpe.1_Missense_Mutation_p.R43C	NM_005700	NP_005691	Q9NY33	DPP3_HUMAN	dipeptidyl peptidase III	24					proteolysis	cytoplasm	aminopeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity			ovary(1)|skin(1)	2																		---	---	---	---
RBM14	10432	broad.mit.edu	37	11	66393068	66393068	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66393068C>T	uc001oit.2	+	2	1860	c.1721C>T	c.(1720-1722)CCG>CTG	p.P574L	RBM14_uc009yrh.2_Intron|RBM14_uc009yri.2_Intron|RBM4_uc009yrj.2_Intron|RBM4_uc009yrk.2_Intron	NM_006328	NP_006319	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	574					DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|histone deacetylation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus	mediator complex|ribonucleoprotein complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|protein binding, bridging|RNA binding|RNA polymerase II transcription cofactor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
KDM2A	22992	broad.mit.edu	37	11	67017609	67017609	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67017609G>T	uc001ojw.2	+	17	2972	c.2108G>T	c.(2107-2109)CGG>CTG	p.R703L	KDM2A_uc001ojx.2_RNA|KDM2A_uc001ojy.2_Missense_Mutation_p.R397L|KDM2A_uc010rpn.1_Missense_Mutation_p.R264L|KDM2A_uc001ojz.1_Missense_Mutation_p.R161L|KDM2A_uc001oka.2_5'Flank	NM_012308	NP_036440	Q9Y2K7	KDM2A_HUMAN	F-box and leucine-rich repeat protein 11	703					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			ovary(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
ADRBK1	156	broad.mit.edu	37	11	67051736	67051736	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67051736C>T	uc009yrn.1	+	18	1812	c.1546C>T	c.(1546-1548)CGG>TGG	p.R516W	ADRBK1_uc009yrm.1_Intron	NM_001619	NP_001610	P25098	ARBK1_HUMAN	beta-adrenergic receptor kinase 1	516	AGC-kinase C-terminal.				activation of phospholipase C activity|cardiac muscle contraction|desensitization of G-protein coupled receptor protein signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of striated muscle contraction|negative regulation of the force of heart contraction by chemical signal|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of catecholamine secretion|tachykinin receptor signaling pathway	cytosol|soluble fraction	alpha-2A adrenergic receptor binding|ATP binding|beta-adrenergic receptor kinase activity|Edg-2 lysophosphatidic acid receptor binding|G-protein coupled receptor kinase activity|signal transducer activity			large_intestine(1)	1			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)													---	---	---	---
LRP5	4041	broad.mit.edu	37	11	68205952	68205952	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68205952A>C	uc001ont.2	+	20	4225	c.4150A>C	c.(4150-4152)AGC>CGC	p.S1384R	LRP5_uc009ysg.2_Missense_Mutation_p.S794R	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	1384	Extracellular (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7																		---	---	---	---
MYEOV	26579	broad.mit.edu	37	11	69063312	69063312	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69063312G>A	uc001oov.2	+	3	845	c.395G>A	c.(394-396)CGG>CAG	p.R132Q	MYEOV_uc001oox.2_Intron|MYEOV_uc009ysl.2_Missense_Mutation_p.R132Q|MYEOV_uc001oow.2_Missense_Mutation_p.R74Q	NM_138768	NP_620123	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	132											0	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)														---	---	---	---
LRTOMT	220074	broad.mit.edu	37	11	71806464	71806464	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71806464C>T	uc001orr.2	+	6	855	c.477C>T	c.(475-477)TTC>TTT	p.F159F	LRTOMT_uc009ysz.2_RNA|LRTOMT_uc010rqt.1_3'UTR|LRTOMT_uc010rqu.1_Silent_p.F141F|LRTOMT_uc009yta.2_RNA|LRTOMT_uc010rqv.1_Intron|LRTOMT_uc010rqw.1_Intron|LRTOMT_uc001ors.3_Intron|LRTOMT_uc010rqs.1_Intron	NM_145309	NP_660352	Q96E66	LRC51_HUMAN	leucine rich transmembrane and	159	LRRCT.					cytoplasm					0																		---	---	---	---
FOLR2	2350	broad.mit.edu	37	11	71931995	71931995	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71931995T>G	uc009ytd.2	+	3	401	c.232T>G	c.(232-234)TTT>GTT	p.F78V	FOLR2_uc009yte.2_Missense_Mutation_p.F78V|FOLR2_uc001ose.3_Missense_Mutation_p.F78V|FOLR2_uc009ytf.2_Missense_Mutation_p.F78V	NM_001113534	NP_001107006	P14207	FOLR2_HUMAN	folate receptor 2 precursor	78					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)													---	---	---	---
C2CD3	26005	broad.mit.edu	37	11	73785348	73785348	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73785348G>A	uc001ouu.2	-	24	5128	c.4901C>T	c.(4900-4902)ACG>ATG	p.T1634M	C2CD3_uc001out.2_RNA	NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1634	C2 2.					centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)																	---	---	---	---
GDPD5	81544	broad.mit.edu	37	11	75146602	75146602	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75146602G>A	uc001owo.3	-	18	2305	c.1768C>T	c.(1768-1770)CGA>TGA	p.R590*	GDPD5_uc001owp.3_Nonsense_Mutation_p.R590*|GDPD5_uc001own.3_Nonsense_Mutation_p.R345*|GDPD5_uc009yuc.2_Nonsense_Mutation_p.R452*|GDPD5_uc009yud.2_Nonsense_Mutation_p.R471*	NM_030792	NP_110419	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain	590	Cytoplasmic (Potential).				glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1																		---	---	---	---
GDPD5	81544	broad.mit.edu	37	11	75160010	75160010	+	Intron	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75160010G>T	uc001owo.3	-						GDPD5_uc001owp.3_Intron|GDPD5_uc001own.3_Intron|GDPD5_uc009yuc.2_Intron|GDPD5_uc009yud.2_Intron|GDPD5_uc009yue.1_Intron	NM_030792	NP_110419			glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1																		---	---	---	---
PCF11	51585	broad.mit.edu	37	11	82878449	82878449	+	Intron	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82878449C>A	uc001ozx.3	+						PCF11_uc010rsu.1_Intron	NM_015885	NP_056969			pre-mRNA cleavage complex II protein Pcf11						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	86133684	86133684	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86133684G>A	uc001pbx.1	+	15	2314	c.1886G>A	c.(1885-1887)CGC>CAC	p.R629H	CCDC81_uc001pbw.1_Missense_Mutation_p.R539H|CCDC81_uc010rtq.1_Missense_Mutation_p.R412H|CCDC81_uc001pby.1_Missense_Mutation_p.R364H	NM_001156474	NP_001149946	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81 isoform 1	629										skin(1)	1		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)																---	---	---	---
ME3	10873	broad.mit.edu	37	11	86270753	86270753	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86270753C>T	uc001pbz.2	-	2	550	c.296G>A	c.(295-297)CGG>CAG	p.R99Q	ME3_uc001pca.2_Missense_Mutation_p.R99Q|ME3_uc009yvk.2_Missense_Mutation_p.R99Q|ME3_uc010rtr.1_RNA	NM_001014811	NP_001014811	Q16798	MAON_HUMAN	mitochondrial malic enzyme 3 precursor	99					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)													---	---	---	---
GRM5	2915	broad.mit.edu	37	11	88780385	88780385	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88780385G>A	uc001pcq.2	-	1	856	c.656C>T	c.(655-657)ACA>ATA	p.T219I	GRM5_uc009yvm.2_Missense_Mutation_p.T219I|GRM5_uc009yvn.1_Missense_Mutation_p.T219I	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a	219	Extracellular (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)													---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92088438	92088438	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92088438G>C	uc001pdj.3	+	1	3177	c.3160G>C	c.(3160-3162)GAA>CAA	p.E1054Q		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1054	Cadherin 10.|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)			---	---	---	---
CWC15	51503	broad.mit.edu	37	11	94704653	94704653	+	Splice_Site	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94704653T>C	uc001pfd.3	-	3	255	c.132_splice	c.e3-1	p.R44_splice	CWC15_uc009ywl.1_Intron|KDM4D_uc001pfe.2_5'Flank	NM_016403	NP_057487			CWC15 homolog						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)																---	---	---	---
CCDC82	79780	broad.mit.edu	37	11	96086838	96086838	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96086838T>C	uc009ywp.2	-	7	1850	c.1607A>G	c.(1606-1608)TAC>TGC	p.Y536C	CCDC82_uc009ywq.2_Missense_Mutation_p.Y536C|CCDC82_uc001pfx.3_Missense_Mutation_p.Y536C|CCDC82_uc009ywr.2_Missense_Mutation_p.Y536C	NM_024725	NP_079001	Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	536							protein binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)														---	---	---	---
KIAA1377	57562	broad.mit.edu	37	11	101834523	101834523	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101834523G>A	uc001pgm.2	+	6	3027	c.2757G>A	c.(2755-2757)CCG>CCA	p.P919P	KIAA1377_uc001pgn.2_Silent_p.P875P|KIAA1377_uc010run.1_Silent_p.P720P|KIAA1377_uc009yxa.1_Silent_p.P720P	NM_020802	NP_065853	Q9P2H0	K1377_HUMAN	hypothetical protein LOC57562	919							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)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103058206	103058206	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103058206G>A	uc001pho.2	+	43	7175	c.7031G>A	c.(7030-7032)CGT>CAT	p.R2344H	DYNC2H1_uc001phn.1_Missense_Mutation_p.R2344H|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2344	AAA 3 (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)														---	---	---	---
ATM	472	broad.mit.edu	37	11	108098419	108098419	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108098419G>A	uc001pkb.1	+	2	453	c.68G>A	c.(67-69)CGA>CAA	p.R23Q	ATM_uc009yxr.1_Missense_Mutation_p.R23Q|ATM_uc001pkc.1_Missense_Mutation_p.R23Q	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	23			R -> Q (in a colorectal adenocarcinoma sample; somatic mutation).		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	p.R23Q(1)		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)			---	---	---	---
EXPH5	23086	broad.mit.edu	37	11	108385068	108385068	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108385068A>C	uc001pkk.2	-	6	1277	c.1166T>G	c.(1165-1167)CTG>CGG	p.L389R	EXPH5_uc010rvy.1_Missense_Mutation_p.L201R|EXPH5_uc010rvz.1_Missense_Mutation_p.L233R|EXPH5_uc010rwa.1_Missense_Mutation_p.L313R	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	389					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)														---	---	---	---
RDX	5962	broad.mit.edu	37	11	110108291	110108291	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110108291G>A	uc001pku.2	-	11	1487	c.1177C>T	c.(1177-1179)CGT>TGT	p.R393C	RDX_uc009yxx.1_RNA|RDX_uc009yxy.2_Missense_Mutation_p.R393C|RDX_uc009yxz.2_Missense_Mutation_p.R46C|RDX_uc009yya.2_Intron|RDX_uc001pks.2_5'Flank|RDX_uc001pkt.2_Missense_Mutation_p.R47C|RDX_uc010rwe.1_Missense_Mutation_p.R257C	NM_002906	NP_002897	P35241	RADI_HUMAN	radixin	393	Glu-rich.				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)														---	---	---	---
HTR3B	9177	broad.mit.edu	37	11	113803030	113803030	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113803030C>T	uc001pok.2	+	5	455	c.388C>T	c.(388-390)CCT>TCT	p.P130S	HTR3B_uc001pol.2_Missense_Mutation_p.P119S	NM_006028	NP_006019	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B	130	Extracellular (Potential).				synaptic transmission	integral to plasma membrane|postsynaptic membrane	serotonin receptor activity|serotonin-activated cation-selective channel activity				0		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)														---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115088648	115088648	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115088648G>A	uc001ppi.3	-	6	914	c.785C>T	c.(784-786)GCG>GTG	p.A262V	CADM1_uc001ppf.3_Missense_Mutation_p.A262V|CADM1_uc001ppk.3_Missense_Mutation_p.A262V|CADM1_uc001ppj.3_Missense_Mutation_p.A262V|CADM1_uc001ppl.2_Missense_Mutation_p.A262V|CADM1_uc001pph.3_Missense_Mutation_p.A14V	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1	262	Ig-like C2-type 2.|Extracellular (Potential).				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)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117335741	117335741	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117335741T>C	uc001prh.1	-	17	3364	c.3362A>G	c.(3361-3363)CAG>CGG	p.Q1121R		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1061	Extracellular (Potential).|Fibronectin type-III 2.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
CXCR5	643	broad.mit.edu	37	11	118764511	118764511	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118764511G>A	uc001pue.3	+	2	368	c.258G>A	c.(256-258)ACG>ACA	p.T86T	CXCR5_uc001puf.2_Silent_p.T41T	NM_001716	NP_001707	P32302	CXCR5_HUMAN	Burkitt lymphoma receptor 1 isoform 1	86	Cytoplasmic (Potential).				B cell activation|cellular component movement	integral to plasma membrane	C-X-C chemokine receptor activity			breast(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)														---	---	---	---
HYOU1	10525	broad.mit.edu	37	11	118920545	118920545	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118920545T>G	uc001puu.2	-	15	1863	c.1670A>C	c.(1669-1671)GAG>GCG	p.E557A	HYOU1_uc001put.2_Missense_Mutation_p.E522A|HYOU1_uc010ryu.1_Missense_Mutation_p.E577A|HYOU1_uc010ryv.1_Missense_Mutation_p.E446A|HYOU1_uc001pux.3_Missense_Mutation_p.E557A|HYOU1_uc010ryw.1_RNA|HYOU1_uc001puw.1_Missense_Mutation_p.E557A	NM_006389	NP_006380	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1 precursor	557						endoplasmic reticulum lumen	ATP binding|protein binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)														---	---	---	---
TRIM29	23650	broad.mit.edu	37	11	119993703	119993703	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119993703G>A	uc001pwz.2	-	5	1518	c.1394C>T	c.(1393-1395)CCG>CTG	p.P465L	TRIM29_uc001pwx.2_5'Flank|TRIM29_uc001pwy.2_5'UTR|TRIM29_uc010rzi.1_Missense_Mutation_p.P204L|TRIM29_uc010rzj.1_Missense_Mutation_p.P198L|TRIM29_uc001pxa.2_RNA	NM_012101	NP_036233	Q14134	TRI29_HUMAN	tripartite motif protein TRIM29	465					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)														---	---	---	---
TRIM29	23650	broad.mit.edu	37	11	120008291	120008291	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120008291C>T	uc001pwz.2	-	1	573	c.449G>A	c.(448-450)CGG>CAG	p.R150Q	TRIM29_uc001pxa.2_RNA	NM_012101	NP_036233	Q14134	TRI29_HUMAN	tripartite motif protein TRIM29	150					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)														---	---	---	---
TECTA	7007	broad.mit.edu	37	11	120998453	120998453	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120998453C>T	uc010rzo.1	+							NM_005422	NP_005413			tectorin alpha precursor						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)														---	---	---	---
ZNF202	7753	broad.mit.edu	37	11	123596771	123596771	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123596771T>C	uc001pzd.1	-	9	2281	c.1881A>G	c.(1879-1881)GGA>GGG	p.G627G	ZNF202_uc001pzc.1_Silent_p.G403G|ZNF202_uc001pze.1_Silent_p.G627G|ZNF202_uc001pzf.1_Silent_p.G627G	NM_003455	NP_003446	O95125	ZN202_HUMAN	zinc finger protein 202	627	C2H2-type 8.				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)														---	---	---	---
OR10G4	390264	broad.mit.edu	37	11	123887208	123887208	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123887208G>T	uc010sac.1	+	1	927	c.927G>T	c.(925-927)CAG>CAT	p.Q309H		NM_001004462	NP_001004462	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G,	309	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		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;0.0401)														---	---	---	---
OR10G7	390265	broad.mit.edu	37	11	123909240	123909240	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123909240C>A	uc001pzq.1	-	1	469	c.469G>T	c.(469-471)GTC>TTC	p.V157F		NM_001004463	NP_001004463	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G,	157	Helical; Name=4; (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)														---	---	---	---
VSIG2	23584	broad.mit.edu	37	11	124619649	124619649	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124619649G>A	uc001qas.2	-	4	617	c.541C>T	c.(541-543)CGT>TGT	p.R181C	VSIG2_uc001qat.2_Missense_Mutation_p.R181C	NM_014312	NP_055127	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2	181	Extracellular (Potential).|Ig-like C2-type.					integral to plasma membrane|membrane fraction				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.215)	Breast(109;0.00663)|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;0.0215)														---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	128840874	128840874	+	Missense_Mutation	SNP	G	A	A	rs112097648		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128840874G>A	uc009zcp.2	-	22	4192	c.4192C>T	c.(4192-4194)CGC>TGC	p.R1398C	ARHGAP32_uc009zcq.1_3'UTR|ARHGAP32_uc009zco.2_Missense_Mutation_p.R357C|ARHGAP32_uc001qez.2_Missense_Mutation_p.R1049C	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1	1398	Interaction with GAB2.				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																		---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132307147	132307147	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132307147G>A	uc001qgs.2	-	4	683	c.633C>T	c.(631-633)CCC>CCT	p.P211P	OPCML_uc001qgu.2_Silent_p.P204P|OPCML_uc010sck.1_Silent_p.P211P|OPCML_uc001qgt.2_Silent_p.P210P|OPCML_uc010scl.1_Silent_p.P170P	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion	211	Ig-like C2-type 2.				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)														---	---	---	---
IQSEC3	440073	broad.mit.edu	37	12	280307	280307	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:280307C>T	uc001qhw.1	+	10	2191	c.2185C>T	c.(2185-2187)CCG>TCG	p.P729S	IQSEC3_uc001qhu.1_Missense_Mutation_p.P729S	NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	1032					regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)														---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1481092	1481092	+	Silent	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1481092G>T	uc001qjb.2	+	16	3115	c.2874G>T	c.(2872-2874)GTG>GTT	p.V958V	ERC1_uc001qiz.2_RNA|ERC1_uc001qjc.2_Silent_p.V930V|ERC1_uc001qja.2_RNA|ERC1_uc001qjd.2_RNA|ERC1_uc001qjf.2_Silent_p.V958V|ERC1_uc010sdv.1_Silent_p.V666V|ERC1_uc001qje.2_RNA	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon	958	Potential.				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)															---	---	---	---
WNT5B	81029	broad.mit.edu	37	12	1755092	1755092	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1755092G>A	uc009zdq.2	+	5	996	c.754G>A	c.(754-756)GCG>ACG	p.A252T	WNT5B_uc001qjj.2_Missense_Mutation_p.A252T|WNT5B_uc001qjk.2_Missense_Mutation_p.A252T|WNT5B_uc001qjl.2_Missense_Mutation_p.A252T	NM_032642	NP_116031	Q9H1J7	WNT5B_HUMAN	wingless-type MMTV integration site family,	252					angiogenesis|anterior/posterior pattern formation|cell migration involved in gastrulation|cellular response to retinoic acid|chondrocyte differentiation|convergent extension involved in axis elongation|convergent extension involved in gastrulation|dorsal/ventral axis specification|endocrine pancreas development|fat cell differentiation|lens fiber cell development|negative regulation of canonical Wnt receptor signaling pathway|neuron differentiation|positive regulation of cell migration|positive regulation of fat cell differentiation|respiratory system development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)															---	---	---	---
TEAD4	7004	broad.mit.edu	37	12	3128323	3128323	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3128323G>A	uc010sej.1	+	8	844	c.567G>A	c.(565-567)CCG>CCA	p.P189P	TEAD4_uc010sek.1_Silent_p.P146P|TEAD4_uc001qln.2_Silent_p.P61P	NM_003213	NP_003204	Q15561	TEAD4_HUMAN	TEA domain family member 4 isoform 1	190					hippo signaling cascade|muscle organ development|skeletal system development		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)															---	---	---	---
PEX5	5830	broad.mit.edu	37	12	7362774	7362774	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7362774G>A	uc009zfu.1	+	17	2455	c.1875G>A	c.(1873-1875)GCG>GCA	p.A625A	PEX5_uc001qsw.2_Silent_p.A625A|PEX5_uc010sgc.1_Silent_p.A640A|PEX5_uc001qsu.2_Silent_p.A588A|PEX5_uc010sgd.1_Silent_p.A646A|PEX5_uc001qsv.2_Silent_p.A617A	NM_001131026	NP_001124498	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5 isoform d	625					protein import into peroxisome matrix, translocation|protein targeting to peroxisome|protein tetramerization|protein transport	cytosol|peroxisomal matrix|peroxisomal membrane	peroxisome matrix targeting signal-1 binding|protein C-terminus binding|protein N-terminus binding			ovary(1)	1																		---	---	---	---
ACSM4	341392	broad.mit.edu	37	12	7475033	7475033	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7475033C>T	uc001qsx.1	+	7	1021	c.1021C>T	c.(1021-1023)CGG>TGG	p.R341W		NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	341					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0																		---	---	---	---
CD163	9332	broad.mit.edu	37	12	7649629	7649629	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7649629G>A	uc001qsz.3	-	5	1007	c.879C>T	c.(877-879)GAC>GAT	p.D293D	CD163_uc001qta.3_Silent_p.D293D|CD163_uc009zfw.2_Silent_p.D293D	NM_004244	NP_004235	Q86VB7	C163A_HUMAN	CD163 antigen isoform a	293	SRCR 3.|Extracellular (Potential).				acute-phase response	extracellular region|integral to plasma membrane	protein binding|scavenger receptor activity			ovary(6)|pancreas(1)|skin(1)	8																		---	---	---	---
SLC2A14	144195	broad.mit.edu	37	12	7980085	7980085	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7980085A>G	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)														---	---	---	---
KLRG1	10219	broad.mit.edu	37	12	9144878	9144878	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9144878G>A	uc001qvh.2	+	2	170	c.159G>A	c.(157-159)GTG>GTA	p.V53V	KLRG1_uc001qvg.2_Silent_p.V53V	NM_005810	NP_005801	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G,	53	Helical; Signal-anchor for type II membrane protein; (Potential).				cell surface receptor linked signaling pathway|cellular defense response|inflammatory response|regulation of immune response	integral to membrane	receptor activity|sugar binding			central_nervous_system(1)	1																		---	---	---	---
A2M	2	broad.mit.edu	37	12	9231878	9231878	+	Silent	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9231878G>T	uc001qvk.1	-	25	3194	c.3081C>A	c.(3079-3081)ACC>ACA	p.T1027T	A2M_uc001qvj.1_Silent_p.T69T|A2M_uc009zgk.1_Silent_p.T877T	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	1027					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)													---	---	---	---
A2M	2	broad.mit.edu	37	12	9246145	9246145	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9246145C>T	uc001qvk.1	-	18	2269	c.2156G>A	c.(2155-2157)CGC>CAC	p.R719H	A2M_uc009zgk.1_Missense_Mutation_p.R569H	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	719	Bait region.|Inhibitory.				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	9318694	9318694	+	Nonsense_Mutation	SNP	G	A	A	rs150067154		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9318694G>A	uc001qvl.2	-	18	2241	c.2212C>T	c.(2212-2214)CGA>TGA	p.R738*	PZP_uc009zgl.2_Nonsense_Mutation_p.R607*|PZP_uc010sgo.1_RNA|PZP_uc009zgm.1_Nonsense_Mutation_p.R70*	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5																		---	---	---	---
PZP	5858	broad.mit.edu	37	12	9353635	9353635	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9353635C>A	uc001qvl.2	-	6	552	c.523G>T	c.(523-525)GCA>TCA	p.A175S	PZP_uc009zgl.2_Missense_Mutation_p.A44S	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5																		---	---	---	---
MAGOHB	55110	broad.mit.edu	37	12	10762434	10762434	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10762434C>T	uc001qyq.1	-	3	312	c.260G>A	c.(259-261)CGA>CAA	p.R87Q	MAGOHB_uc001qyr.1_RNA	NM_018048	NP_060518	Q96A72	MGN2_HUMAN	mago-nashi homolog B	87					mRNA processing|mRNA transport|RNA splicing	nucleus	RNA binding			breast(1)	1																		---	---	---	---
DUSP16	80824	broad.mit.edu	37	12	12630345	12630345	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12630345C>T	uc001rao.1	-	7	2052	c.1420G>A	c.(1420-1422)GCC>ACC	p.A474T	DUSP16_uc001ram.1_5'Flank|DUSP16_uc001ran.1_Missense_Mutation_p.A326T	NM_030640	NP_085143	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16	474					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)														---	---	---	---
STRAP	11171	broad.mit.edu	37	12	16055920	16055920	+	3'UTR	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16055920T>C	uc001rdc.3	+	10					STRAP_uc010shw.1_3'UTR|STRAP_uc001rdd.3_3'UTR	NM_007178	NP_009109			serine/threonine kinase receptor associated						mRNA processing|RNA splicing	cell junction|mitochondrion|spliceosomal complex	identical protein binding			skin(1)	1		Hepatocellular(102;0.121)																---	---	---	---
PDE3A	5139	broad.mit.edu	37	12	20806894	20806894	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20806894C>A	uc001reh.1	+	15	2961	c.2939C>A	c.(2938-2940)GCC>GAC	p.A980D		NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A	980	Catalytic (By similarity).				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	22005053	22005053	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22005053C>T	uc001rfi.1	-	22	2767	c.2747G>A	c.(2746-2748)CGG>CAG	p.R916Q	ABCC9_uc001rfh.2_Missense_Mutation_p.R916Q|ABCC9_uc001rfj.1_Missense_Mutation_p.R880Q	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	916	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)													---	---	---	---
SOX5	6660	broad.mit.edu	37	12	23999074	23999074	+	Silent	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23999074G>T	uc001rfw.2	-	3	426	c.324C>A	c.(322-324)ACC>ACA	p.T108T	SOX5_uc001rfx.2_Silent_p.T95T|SOX5_uc001rfy.2_Silent_p.T95T|SOX5_uc010siv.1_Silent_p.T95T|SOX5_uc010siw.1_RNA|SOX5_uc001rfz.1_Silent_p.T60T|SOX5_uc001rga.2_Silent_p.T73T	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	108					transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
RASSF8	11228	broad.mit.edu	37	12	26217838	26217838	+	Missense_Mutation	SNP	C	T	T	rs146204306	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26217838C>T	uc001rgx.2	+	3	732	c.511C>T	c.(511-513)CGT>TGT	p.R171C	RASSF8_uc001rgy.2_Missense_Mutation_p.R171C|RASSF8_uc001rgz.2_Missense_Mutation_p.R171C|RASSF8_uc009zjd.1_Missense_Mutation_p.R171C|RASSF8_uc009zje.1_Missense_Mutation_p.R171C	NM_007211	NP_009142	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family	171					signal transduction						0	Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26752167	26752167	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26752167G>A	uc001rhg.2	-	30	4330	c.3913C>T	c.(3913-3915)CGC>TGC	p.R1305C		NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	1305	Cytoplasmic (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
KLHDC5	57542	broad.mit.edu	37	12	27950929	27950929	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27950929G>A	uc001rij.2	+	3	1425	c.1348G>A	c.(1348-1350)GGC>AGC	p.G450S	KLHDC5_uc009zjj.2_RNA	NM_020782	NP_065833	Q9P2K6	KLDC5_HUMAN	kelch domain containing 5	450	Kelch 6.									ovary(1)|central_nervous_system(1)	2	Lung SC(9;0.0873)																	---	---	---	---
FAR2	55711	broad.mit.edu	37	12	29423430	29423430	+	Silent	SNP	G	A	A	rs149661674		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29423430G>A	uc001ris.3	+	2	195	c.48G>A	c.(46-48)ACG>ACA	p.T16T	FAR2_uc001rit.2_Silent_p.T16T|FAR2_uc009zjm.2_Intron	NM_018099	NP_060569	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	16					ether lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor				0																		---	---	---	---
DDX11	1663	broad.mit.edu	37	12	31249595	31249595	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31249595G>A	uc001rjt.1	+	16	1797	c.1546G>A	c.(1546-1548)GGA>AGA	p.G516R	DDX11_uc001rjr.1_Missense_Mutation_p.G516R|DDX11_uc001rjs.1_Missense_Mutation_p.G516R|DDX11_uc001rju.1_Missense_Mutation_p.G194R|DDX11_uc001rjv.1_Missense_Mutation_p.G516R|DDX11_uc001rjw.1_Missense_Mutation_p.G490R|DDX11_uc009zjn.1_RNA	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11	516					G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)														Multiple Myeloma(12;0.14)			---	---	---	---
CPNE8	144402	broad.mit.edu	37	12	39223184	39223184	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39223184A>G	uc001rls.1	-	6	488	c.404T>C	c.(403-405)ATA>ACA	p.I135T		NM_153634	NP_705898	Q86YQ8	CPNE8_HUMAN	copine VIII	135										pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)																---	---	---	---
PRICKLE1	144165	broad.mit.edu	37	12	42859016	42859016	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42859016C>T	uc010skv.1	-	7	1107	c.820G>A	c.(820-822)GCC>ACC	p.A274T	PRICKLE1_uc001rnl.2_Missense_Mutation_p.A274T|PRICKLE1_uc010skw.1_Missense_Mutation_p.A274T|PRICKLE1_uc001rnm.2_Missense_Mutation_p.A274T	NM_001144881	NP_001138353	Q96MT3	PRIC1_HUMAN	prickle homolog 1	274	LIM zinc-binding 3.				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)														---	---	---	---
ARID2	196528	broad.mit.edu	37	12	46246296	46246296	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46246296C>T	uc001ros.1	+	15	4390	c.4390C>T	c.(4390-4392)CGC>TGC	p.R1464C	ARID2_uc001ror.2_Missense_Mutation_p.R1464C|ARID2_uc009zkg.1_Missense_Mutation_p.R920C|ARID2_uc009zkh.1_Missense_Mutation_p.R1091C|ARID2_uc001rou.1_Missense_Mutation_p.R798C	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)														---	---	---	---
ZNF641	121274	broad.mit.edu	37	12	48737355	48737355	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48737355G>C	uc001rrn.1	-	6	883	c.718C>G	c.(718-720)CCC>GCC	p.P240A	ZNF641_uc001rro.1_Missense_Mutation_p.P226A|ZNF641_uc010sls.1_Missense_Mutation_p.P217A	NM_152320	NP_689533	Q96N77	ZN641_HUMAN	zinc finger protein 641	240	Transactivation.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
PRPF40B	25766	broad.mit.edu	37	12	50025223	50025223	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50025223G>T	uc001rur.1	+	2	122	c.58G>T	c.(58-60)GGG>TGG	p.G20W	PRPF40B_uc001rup.1_Missense_Mutation_p.G42W|PRPF40B_uc001ruq.1_Missense_Mutation_p.G14W|PRPF40B_uc001rus.1_5'Flank	NM_001031698	NP_001026868	Q6NWY9	PR40B_HUMAN	Huntingtin interacting protein C isoform 1	20	Pro-rich.				mRNA processing|RNA splicing	nuclear speck				skin(2)|ovary(1)|pancreas(1)|kidney(1)	5																		---	---	---	---
RACGAP1	29127	broad.mit.edu	37	12	50386088	50386088	+	Silent	SNP	G	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50386088G>C	uc001rvt.2	-	16	1828	c.1518C>G	c.(1516-1518)GCC>GCG	p.A506A	RACGAP1_uc009zlm.1_Silent_p.A506A|RACGAP1_uc001rvs.2_Silent_p.A506A|RACGAP1_uc001rvu.2_Silent_p.A506A	NM_013277	NP_037409	Q9H0H5	RGAP1_HUMAN	Rac GTPase activating protein 1	506	Rho-GAP.				blood coagulation|cytokinesis, actomyosin contractile ring assembly|cytokinesis, initiation of separation|embryo development|microtubule-based movement|neuroblast proliferation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|spermatogenesis|sulfate transport	acrosomal vesicle|cytosol|microtubule|midbody|nucleus|spindle	alpha-tubulin binding|beta-tubulin binding|gamma-tubulin binding|GTPase activator activity|metal ion binding			kidney(1)	1																		---	---	---	---
SLC11A2	4891	broad.mit.edu	37	12	51394196	51394196	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51394196G>A	uc001rxe.3	-	6	533	c.436C>T	c.(436-438)CGA>TGA	p.R146*	SLC11A2_uc001rxd.3_Translation_Start_Site|SLC11A2_uc001rxc.3_Nonsense_Mutation_p.R146*|SLC11A2_uc001rxf.2_RNA|SLC11A2_uc010smx.1_Nonsense_Mutation_p.R142*|SLC11A2_uc001rxh.1_Nonsense_Mutation_p.R146*|SLC11A2_uc001rxj.1_Nonsense_Mutation_p.R146*|SLC11A2_uc001rxi.2_Nonsense_Mutation_p.R146*|SLC11A2_uc001rxk.1_Nonsense_Mutation_p.R175*|SLC11A2_uc010smy.1_Nonsense_Mutation_p.R109*	NM_000617	NP_000608	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled	146	Cytoplasmic (Potential).				activation of caspase activity|cellular iron ion homeostasis|cellular response to oxidative stress|detection of oxygen|ferrous iron import|multicellular organismal iron ion homeostasis|response to hypoxia|response to iron ion	apical plasma membrane|basal part of cell|cell surface|cytoplasmic vesicle|early endosome|late endosome|late endosome membrane|lysosomal membrane|lysosome|nucleus|paraferritin complex|perinuclear region of cytoplasm|perinuclear region of cytoplasm|plasma membrane|recycling endosome|trans-Golgi network	cadmium ion transmembrane transporter activity|cadmium ion transmembrane transporter activity|cobalt ion transmembrane transporter activity|copper ion transmembrane transporter activity|ferrous iron transmembrane transporter activity|ferrous iron transmembrane transporter activity|lead ion transmembrane transporter activity|lead ion transmembrane transporter activity|manganese ion transmembrane transporter activity|manganese ion transmembrane transporter activity|nickel ion transmembrane transporter activity|protein binding|solute:hydrogen symporter activity|vanadium ion transmembrane transporter activity|zinc ion transmembrane transporter activity			large_intestine(1)	1																		---	---	---	---
KRT85	3891	broad.mit.edu	37	12	52761184	52761184	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52761184C>T	uc001sag.2	-	1	126	c.6G>A	c.(4-6)TCG>TCA	p.S2S		NM_002283	NP_002274	P78386	KRT85_HUMAN	keratin 85	2	Head.				epidermis development	keratin filament	protein binding|structural molecule activity			ovary(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
CALCOCO1	57658	broad.mit.edu	37	12	54107930	54107930	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54107930G>A	uc001sef.2	-	12	1722	c.1578C>T	c.(1576-1578)GCC>GCT	p.A526A	CALCOCO1_uc001see.2_Silent_p.A27A|CALCOCO1_uc010som.1_Silent_p.A441A|CALCOCO1_uc010son.1_Silent_p.A403A|CALCOCO1_uc001seh.2_Silent_p.A526A|CALCOCO1_uc009znd.2_Silent_p.A526A|CALCOCO1_uc001seg.2_Silent_p.A351A|CALCOCO1_uc010soo.1_Silent_p.A519A	NM_020898	NP_065949	Q9P1Z2	CACO1_HUMAN	coiled-coil transcriptional coactivator isoform	526	C-terminal AD (CTNNB1 binding site) (By similarity).				steroid hormone receptor signaling pathway|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm	armadillo repeat domain binding|beta-catenin binding|ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|sequence-specific DNA binding|transcription regulatory region DNA binding			ovary(1)	1																		---	---	---	---
HOXC13	3229	broad.mit.edu	37	12	54338837	54338837	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54338837C>T	uc001sei.2	+	2	905	c.790C>T	c.(790-792)CGC>TGC	p.R264C	HOXC13_uc010sop.1_RNA	NM_017410	NP_059106	P31276	HXC13_HUMAN	homeobox C13	264	Homeobox.					nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1								T	NUP98	AML								---	---	---	---
HOXC12	3228	broad.mit.edu	37	12	54350327	54350327	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54350327G>A	uc010soq.1	+	2	826	c.826G>A	c.(826-828)GAG>AAG	p.E276K		NM_173860	NP_776272	P31275	HXC12_HUMAN	homeobox C12	276					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
PA2G4	5036	broad.mit.edu	37	12	56504448	56504448	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56504448C>T	uc001sjm.2	+	9	1233	c.814C>T	c.(814-816)CGT>TGT	p.R272C	PA2G4_uc009zol.2_Missense_Mutation_p.R272C|PA2G4_uc009zom.2_Missense_Mutation_p.R272C	NM_006191	NP_006182	Q9UQ80	PA2G4_HUMAN	ErbB3-binding protein 1	272					cell cycle arrest|cell proliferation|negative regulation of transcription, DNA-dependent|regulation of translation|rRNA processing	cytoplasm|nucleolus|ribonucleoprotein complex	DNA binding|RNA binding|sequence-specific DNA binding transcription factor activity|ubiquitin protein ligase binding				0			OV - Ovarian serous cystadenocarcinoma(18;0.0739)															---	---	---	---
SMARCC2	6601	broad.mit.edu	37	12	56563355	56563355	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56563355G>A	uc001skb.2	-	24	2686	c.2580C>T	c.(2578-2580)ACC>ACT	p.T860T	SMARCC2_uc001skd.2_Silent_p.T891T|SMARCC2_uc001ska.2_Silent_p.T891T|SMARCC2_uc001skc.2_Silent_p.T890T|SMARCC2_uc010sqf.1_Silent_p.T780T	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	860					chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)															---	---	---	---
OBFC2B	79035	broad.mit.edu	37	12	56622977	56622977	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56622977C>T	uc001ski.2	+	7	740	c.616C>T	c.(616-618)CGG>TGG	p.R206W	OBFC2B_uc001skk.2_Missense_Mutation_p.R231W|OBFC2B_uc001skj.2_Missense_Mutation_p.R222W	NM_024068	NP_076973	Q9BQ15	SOSB1_HUMAN	oligonucleotide/oligosaccharide-binding fold	206					double-strand break repair via homologous recombination|G2/M transition checkpoint|response to ionizing radiation	SOSS complex	protein binding|single-stranded DNA binding			ovary(1)	1													Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
PAN2	9924	broad.mit.edu	37	12	56718087	56718087	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56718087G>A	uc001skx.2	-	12	2292	c.1919C>T	c.(1918-1920)GCT>GTT	p.A640V	PAN2_uc001skw.2_5'Flank|PAN2_uc001skz.2_Missense_Mutation_p.A640V|PAN2_uc001sky.2_Missense_Mutation_p.A640V	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog	640					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																		---	---	---	---
BAZ2A	11176	broad.mit.edu	37	12	56995134	56995134	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56995134G>A	uc001slq.1	-	21	4324	c.4130C>T	c.(4129-4131)ACG>ATG	p.T1377M	BAZ2A_uc001slp.1_Missense_Mutation_p.T1375M|BAZ2A_uc001slo.1_Missense_Mutation_p.T205M|BAZ2A_uc009zov.1_Missense_Mutation_p.T347M|BAZ2A_uc009zow.1_Missense_Mutation_p.T1345M	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1377	Pro-rich.				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																		---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57578171	57578171	+	Missense_Mutation	SNP	C	T	T	rs148823753	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57578171C>T	uc001snd.2	+	38	6588	c.6122C>T	c.(6121-6123)ACG>ATG	p.T2041M		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	2041	LDL-receptor class B 19.|Extracellular (Potential).				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)													---	---	---	---
SHMT2	6472	broad.mit.edu	37	12	57625344	57625344	+	Splice_Site	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57625344G>A	uc001snf.1	+	3	321	c.311_splice	c.e3+1	p.R104_splice	SHMT2_uc001sng.1_Splice_Site|SHMT2_uc001snh.1_Intron|SHMT2_uc009zpk.1_Splice_Site_p.R104_splice|SHMT2_uc001sni.1_Splice_Site_p.R83_splice|SHMT2_uc010srg.1_Intron|SHMT2_uc001snj.1_Intron|SHMT2_uc010srh.1_Splice_Site_p.R83_splice|SHMT2_uc001snk.1_Intron|SHMT2_uc010sri.1_Splice_Site_p.R83_splice|SHMT2_uc001snl.2_Splice_Site|SHMT2_uc010srj.1_5'Flank	NM_005412	NP_005403			serine hydroxymethyltransferase 2							microtubule cytoskeleton|mitochondrial nucleoid	glycine hydroxymethyltransferase activity|methyltransferase activity			ovary(1)|central_nervous_system(1)	2					Glycine(DB00145)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)													---	---	---	---
ARHGAP9	64333	broad.mit.edu	37	12	57867953	57867953	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57867953C>T	uc001sod.2	-	19	2253	c.2060G>A	c.(2059-2061)CGG>CAG	p.R687Q	ARHGAP9_uc001sny.2_Intron|ARHGAP9_uc001snz.2_Missense_Mutation_p.R413Q|ARHGAP9_uc001soa.2_Missense_Mutation_p.R286Q|ARHGAP9_uc001sob.2_Missense_Mutation_p.R597Q|ARHGAP9_uc001soc.2_Missense_Mutation_p.R597Q|ARHGAP9_uc001soe.1_Missense_Mutation_p.R676Q	NM_032496	NP_115885	Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9 isoform 1	616	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			lung(1)	1			GBM - Glioblastoma multiforme(3;3.37e-34)															---	---	---	---
ARHGAP9	64333	broad.mit.edu	37	12	57869407	57869407	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57869407G>A	uc001sod.2	-						ARHGAP9_uc001sny.2_5'Flank|ARHGAP9_uc001snz.2_Intron|ARHGAP9_uc001soa.2_Intron|ARHGAP9_uc001sob.2_Intron|ARHGAP9_uc001soc.2_Intron|ARHGAP9_uc001soe.1_Intron	NM_032496	NP_115885			Rho GTPase activating protein 9 isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			lung(1)	1			GBM - Glioblastoma multiforme(3;3.37e-34)															---	---	---	---
C12orf66	144577	broad.mit.edu	37	12	64609628	64609628	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64609628G>A	uc001srw.3	-	2	410	c.351C>T	c.(349-351)CAC>CAT	p.H117H	C12orf66_uc009zql.2_Silent_p.H64H	NM_152440	NP_689653	Q96MD2	CL066_HUMAN	hypothetical protein LOC144577	117										ovary(1)	1																		---	---	---	---
TMBIM4	51643	broad.mit.edu	37	12	66546105	66546105	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66546105C>T	uc001stc.2	-	3	334	c.258G>A	c.(256-258)GCG>GCA	p.A86A	LLPH_uc010ssx.1_RNA|TMBIM4_uc001std.2_Silent_p.A55A|TMBIM4_uc009zqr.2_Silent_p.A133A|TMBIM4_uc001ste.2_RNA|TMBIM4_uc001stf.2_Silent_p.A86A|TMBIM4_uc009zqs.2_Silent_p.A86A	NM_016056	NP_057140	Q9HC24	TMBI4_HUMAN	transmembrane BAX inhibitor motif containing 4	86	Helical; (Potential).					integral to membrane	protein binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(28;0.0745)														---	---	---	---
GRIP1	23426	broad.mit.edu	37	12	66771012	66771012	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66771012G>A	uc001stk.2	-	20	2760	c.2519C>T	c.(2518-2520)TCT>TTT	p.S840F	GRIP1_uc010sta.1_Missense_Mutation_p.S784F|GRIP1_uc001stj.2_Missense_Mutation_p.S622F|GRIP1_uc001stl.1_Missense_Mutation_p.S732F|GRIP1_uc001stm.2_Missense_Mutation_p.S840F	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	892					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)														---	---	---	---
LGR5	8549	broad.mit.edu	37	12	71974201	71974201	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71974201A>G	uc001swl.2	+	16	1598	c.1550A>G	c.(1549-1551)CAA>CGA	p.Q517R	LGR5_uc001swm.2_Missense_Mutation_p.Q493R|LGR5_uc001swn.1_RNA	NM_003667	NP_003658	O75473	LGR5_HUMAN	leucine-rich repeat-containing G protein-coupled	517	Extracellular (Potential).					integral to plasma membrane	protein-hormone receptor activity			lung(4)|skin(3)|ovary(1)|pancreas(1)	9																		---	---	---	---
NAP1L1	4673	broad.mit.edu	37	12	76461164	76461164	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76461164C>T	uc001sxw.2	-	4	605	c.193G>A	c.(193-195)GGA>AGA	p.G65R	NAP1L1_uc001sxv.2_Missense_Mutation_p.G23R|NAP1L1_uc001sxz.2_Missense_Mutation_p.G23R|NAP1L1_uc001sxx.2_Missense_Mutation_p.G65R|NAP1L1_uc001sxy.2_Intron|NAP1L1_uc010sty.1_Missense_Mutation_p.G23R|NAP1L1_uc010stz.1_Intron|NAP1L1_uc010sua.1_Missense_Mutation_p.G65R|NAP1L1_uc001syb.2_Missense_Mutation_p.G65R|NAP1L1_uc001sya.2_Missense_Mutation_p.G23R|NAP1L1_uc001syc.2_Missense_Mutation_p.G65R	NM_139207	NP_631946	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	65					DNA replication|nucleosome assembly|positive regulation of cell proliferation	chromatin assembly complex|melanosome	protein binding			ovary(1)|skin(1)	2		Colorectal(145;0.09)																---	---	---	---
E2F7	144455	broad.mit.edu	37	12	77440093	77440093	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77440093C>T	uc001sym.3	-	5	790	c.554G>A	c.(553-555)CGC>CAC	p.R185H	E2F7_uc001syn.2_Missense_Mutation_p.R185H	NM_203394	NP_976328	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	185	Potential.			R->A: Loss of DNA-binding and inhibition of E2F1-dependent activation.	cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3																		---	---	---	---
LIN7A	8825	broad.mit.edu	37	12	81283062	81283062	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81283062G>T	uc001szj.1	-	2	362	c.169C>A	c.(169-171)CTT>ATT	p.L57I	LIN7A_uc001szk.1_RNA	NM_004664	NP_004655	O14910	LIN7A_HUMAN	lin-7 homolog A	57	L27.				exocytosis|protein complex assembly|protein transport	basolateral plasma membrane|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	L27 domain binding			ovary(1)|skin(1)	2																		---	---	---	---
TMTC2	160335	broad.mit.edu	37	12	83324294	83324294	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83324294G>A	uc001szt.2	+	4	2000	c.1568G>A	c.(1567-1569)CGC>CAC	p.R523H	TMTC2_uc001szr.1_Missense_Mutation_p.R523H|TMTC2_uc001szs.1_Missense_Mutation_p.R523H|TMTC2_uc010suk.1_Missense_Mutation_p.R278H	NM_152588	NP_689801	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat	523	TPR 2.					endoplasmic reticulum|integral to membrane	binding			ovary(2)	2																		---	---	---	---
SLC6A15	55117	broad.mit.edu	37	12	85266867	85266867	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85266867G>A	uc001szv.2	-	7	1601	c.1108C>T	c.(1108-1110)CAA>TAA	p.Q370*	SLC6A15_uc010sul.1_Nonsense_Mutation_p.Q263*|SLC6A15_uc001szw.1_Nonsense_Mutation_p.Q78*	NM_182767	NP_877499	Q9H2J7	S6A15_HUMAN	solute carrier family 6, member 15 isoform 1	370	Extracellular (Potential).				cellular nitrogen compound metabolic process|leucine transport|proline transport	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			pancreas(2)|ovary(1)	3																		---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85547850	85547850	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85547850G>A	uc001tac.2	+	23	4809	c.4698G>A	c.(4696-4698)TCG>TCA	p.S1566S		NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1566										ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
KERA	11081	broad.mit.edu	37	12	91449951	91449951	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91449951A>G	uc001tbl.2	-	2	727	c.108T>C	c.(106-108)ACT>ACC	p.T36T		NM_007035	NP_008966	O60938	KERA_HUMAN	keratocan precursor	36	LRRNT.				response to stimulus|visual perception	proteinaceous extracellular matrix				skin(1)	1																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104030991	104030991	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104030991G>A	uc001tjw.2	+	7	872	c.686G>A	c.(685-687)CGA>CAA	p.R229Q		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	229	Extracellular (Potential).|EGF-like 3.				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	104149257	104149257	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104149257A>G	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																		---	---	---	---
TXNRD1	7296	broad.mit.edu	37	12	104733053	104733053	+	Splice_Site	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104733053T>C	uc010swk.1	+	16	1903	c.1881_splice	c.e16+2	p.E627_splice	TXNRD1_uc010swl.1_Splice_Site_p.E477_splice|TXNRD1_uc010swm.1_Splice_Site_p.E529_splice|TXNRD1_uc010swn.1_Splice_Site_p.E477_splice|TXNRD1_uc010swo.1_Splice_Site_p.E477_splice|TXNRD1_uc010swp.1_Splice_Site_p.E439_splice|TXNRD1_uc010swq.1_Splice_Site_p.E527_splice|TXNRD1_uc001tku.2_Splice_Site|TXNRD1_uc009zun.2_Splice_Site_p.E543_splice	NM_001093771	NP_001087240			thioredoxin reductase 1 isoform 3						cell redox homeostasis|cellular lipid metabolic process|electron transport chain|nucleobase, nucleoside and nucleotide interconversion|signal transduction|transport	cytosol|nucleolus	electron carrier activity|flavin adenine dinucleotide binding|NADP binding|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity				0																		---	---	---	---
KIAA1033	23325	broad.mit.edu	37	12	105512217	105512217	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105512217G>A	uc001tld.2	+						KIAA1033_uc010swr.1_Intron|KIAA1033_uc010sws.1_Intron	NM_015275	NP_056090			hypothetical protein LOC23325						endosome transport	WASH complex				kidney(1)|central_nervous_system(1)	2																		---	---	---	---
USP30	84749	broad.mit.edu	37	12	109509471	109509471	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109509471C>T	uc010sxi.1	+	5	639	c.535C>T	c.(535-537)CGC>TGC	p.R179C	USP30_uc001tnu.3_Missense_Mutation_p.R148C	NM_032663	NP_116052	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	179	Cytoplasmic (Potential).				ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial outer membrane	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(1)	1																		---	---	---	---
C12orf34	84915	broad.mit.edu	37	12	110206924	110206924	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110206924G>A	uc001tpd.1	+	3	1749	c.1190G>A	c.(1189-1191)TGC>TAC	p.C397Y	MGC14436_uc010sxs.1_Intron|MGC14436_uc001tpe.2_Intron|C12orf34_uc001tpf.1_Missense_Mutation_p.C397Y	NM_032829	NP_116218	Q5U5X8	CL034_HUMAN	hypothetical protein LOC84915	397										ovary(1)	1																		---	---	---	---
C12orf51	283450	broad.mit.edu	37	12	112696395	112696395	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112696395C>T	uc009zwc.2	-	13	1755	c.1737G>A	c.(1735-1737)GCG>GCA	p.A579A	C12orf51_uc010syk.1_Silent_p.A402A|C12orf51_uc001tts.2_Silent_p.A402A|C12orf51_uc001ttt.3_Silent_p.A400A	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2																		---	---	---	---
TBX5	6910	broad.mit.edu	37	12	114793517	114793517	+	Silent	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114793517G>T	uc001tvo.2	-	9	1872	c.1377C>A	c.(1375-1377)ACC>ACA	p.T459T	TBX5_uc001tvp.2_Silent_p.T459T|TBX5_uc001tvq.2_Silent_p.T409T	NM_181486	NP_852259	Q99593	TBX5_HUMAN	T-box 5 isoform 1	459				MDRLPYQHFSAHFTSGPLVPRLAGMANHGSPQLGEGMFQHQ TS -> WTGYPTSTSPLTSPRGPWSLGWLAWQPWLPTAGRG NVPSTRPP (in Ref. 1; CAA70592).	cardiac left ventricle formation|cell migration involved in coronary vasculogenesis|cell-cell signaling|embryonic arm morphogenesis|induction of apoptosis|negative regulation of cardiac muscle cell proliferation|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|pericardium development|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|ventricular septum development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(6)|pancreas(1)|skin(1)	8	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)														---	---	---	---
NOS1	4842	broad.mit.edu	37	12	117672425	117672425	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117672425C>T	uc001twm.1	-	21	3866	c.3180G>A	c.(3178-3180)CCG>CCA	p.P1060P		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	1060	FAD-binding FR-type.				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)													---	---	---	---
NOS1	4842	broad.mit.edu	37	12	117728174	117728174	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117728174G>A	uc001twm.1	-	4	1596	c.910C>T	c.(910-912)CGC>TGC	p.R304C		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	304					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)													---	---	---	---
PRKAB1	5564	broad.mit.edu	37	12	120110208	120110208	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120110208G>A	uc009zwu.2	+	3	365	c.262G>A	c.(262-264)GGA>AGA	p.G88R	PRKAB1_uc001txg.2_Missense_Mutation_p.G88R	NM_006253	NP_006244	Q9Y478	AAKB1_HUMAN	AMP-activated protein kinase beta 1	88					cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol					0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.166)	Adenosine monophosphate(DB00131)|Metformin(DB00331)													---	---	---	---
GCN1L1	10985	broad.mit.edu	37	12	120585995	120585995	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120585995C>T	uc001txo.2	-	37	4715	c.4702G>A	c.(4702-4704)GTT>ATT	p.V1568I		NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis	1568	HEAT 9.				regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
PXN	5829	broad.mit.edu	37	12	120651713	120651713	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120651713G>A	uc001txt.2	-	11	1572	c.1441C>T	c.(1441-1443)CGG>TGG	p.R481W	PXN_uc001txu.2_Missense_Mutation_p.R293W|PXN_uc001txv.2_Missense_Mutation_p.R362W|PXN_uc001txx.2_Missense_Mutation_p.R314W|PXN_uc001txy.2_Missense_Mutation_p.R447W|PXN_uc001txz.2_RNA	NM_001080855	NP_001074324	P49023	PAXI_HUMAN	paxillin isoform 1	481	LIM zinc-binding 3.				cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)|breast(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
OASL	8638	broad.mit.edu	37	12	121458651	121458651	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121458651A>C	uc001tzj.1	-	6	1264	c.1258T>G	c.(1258-1260)TCC>GCC	p.S420A	OASL_uc001tzk.1_3'UTR	NM_003733	NP_003724	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like isoform a	420	Ubiquitin-like 1.				interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoplasm|nucleolus	ATP binding|DNA binding|double-stranded RNA binding|thyroid hormone receptor binding|transferase activity			skin(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	121878950	121878950	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121878950C>T	uc001uat.2	-	20	3475	c.3371G>A	c.(3370-3372)CGA>CAA	p.R1124Q	KDM2B_uc001uaq.2_Missense_Mutation_p.R564Q|KDM2B_uc010szy.1_Missense_Mutation_p.R564Q|KDM2B_uc001uar.2_Missense_Mutation_p.R715Q|KDM2B_uc001uas.2_Missense_Mutation_p.R1055Q|KDM2B_uc001uau.2_Intron|KDM2B_uc001uao.2_Missense_Mutation_p.R372Q|KDM2B_uc010szx.1_Missense_Mutation_p.R372Q|KDM2B_uc001uap.2_RNA	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform	1124					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																		---	---	---	---
CCDC62	84660	broad.mit.edu	37	12	123290847	123290847	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123290847G>A	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)														---	---	---	---
HIP1R	9026	broad.mit.edu	37	12	123344320	123344320	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123344320A>G	uc001udj.1	+	24	2467	c.2408A>G	c.(2407-2409)GAC>GGC	p.D803G	HIP1R_uc001udk.1_Missense_Mutation_p.D68G	NM_003959	NP_003950	O75146	HIP1R_HUMAN	huntingtin interacting protein-1-related	803	I/LWEQ.				receptor-mediated endocytosis	clathrin coated vesicle membrane|coated pit|perinuclear region of cytoplasm	actin binding|phosphatidylinositol binding			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)														---	---	---	---
PITPNM2	57605	broad.mit.edu	37	12	123481982	123481982	+	Silent	SNP	G	A	A	rs142848891		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123481982G>A	uc001uej.1	-	10	1501	c.1362C>T	c.(1360-1362)AAC>AAT	p.N454N	PITPNM2_uc001uek.1_Silent_p.N454N	NM_020845	NP_065896	Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein,	454					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	123687585	123687585	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123687585A>C	uc001uel.2	-	6	1018	c.911T>G	c.(910-912)ATT>AGT	p.I304S	MPHOSPH9_uc010tal.1_Intron|MPHOSPH9_uc010tam.1_RNA|MPHOSPH9_uc001uem.2_Intron	NM_022782	NP_073619	Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	304					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)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124887004	124887004	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124887004G>T	uc010tba.1	-	14	1703	c.1586C>A	c.(1585-1587)GCG>GAG	p.A529E	NCOR2_uc010tay.1_Missense_Mutation_p.A529E|NCOR2_uc010taz.1_Missense_Mutation_p.A529E|NCOR2_uc010tbb.1_Missense_Mutation_p.A529E|NCOR2_uc010tbc.1_Missense_Mutation_p.A528E|NCOR2_uc001ugj.1_Missense_Mutation_p.A529E	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2	529	Potential.				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)														---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	130184470	130184470	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130184470G>A	uc009zyl.1	-	2	1181	c.853C>T	c.(853-855)CGT>TGT	p.R285C		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	285	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)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132504627	132504627	+	Silent	SNP	C	T	T	rs113843264		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132504627C>T	uc001ujn.2	+	21	4346	c.4311C>T	c.(4309-4311)CCC>CCT	p.P1437P	EP400_uc001ujl.2_Silent_p.P1436P|EP400_uc001ujm.2_Silent_p.P1437P	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1473					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	133350862	133350862	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133350862C>T	uc001ukz.1	-	23	4747	c.4188G>A	c.(4186-4188)ACG>ACA	p.T1396T		NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	1396	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)														---	---	---	---
MPHOSPH8	54737	broad.mit.edu	37	13	20235889	20235889	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20235889G>A	uc001umh.2	+	8	1852	c.1843G>A	c.(1843-1845)GAC>AAC	p.D615N	MPHOSPH8_uc001umg.2_Missense_Mutation_p.D615N	NM_017520	NP_059990	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	615	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)														---	---	---	---
ZMYM5	9205	broad.mit.edu	37	13	20426206	20426206	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20426206C>A	uc010tcn.1	-	3	380	c.115G>T	c.(115-117)GCT>TCT	p.A39S	ZMYM5_uc001umm.1_5'UTR|ZMYM5_uc001umn.2_Missense_Mutation_p.A39S|ZMYM5_uc001umo.2_Missense_Mutation_p.A39S	NM_001142684	NP_001136156	Q9UJ78	ZMYM5_HUMAN	zinc finger protein 237 isoform 3	39						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)														---	---	---	---
ZDHHC20	253832	broad.mit.edu	37	13	21976959	21976959	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21976959C>T	uc001uob.2	-	5	530	c.417G>A	c.(415-417)GCG>GCA	p.A139A	ZDHHC20_uc001uod.2_RNA|ZDHHC20_uc001uoc.2_RNA|ZDHHC20_uc001uoe.2_RNA|ZDHHC20_uc010tcs.1_Silent_p.A76A	NM_153251	NP_694983	Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	139	DHHC-type.					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)														---	---	---	---
PARP4	143	broad.mit.edu	37	13	25020909	25020909	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25020909G>A	uc001upl.2	-							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)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26151257	26151257	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26151257G>A	uc001uqk.2	+	20	1905	c.1763G>A	c.(1762-1764)CGG>CAG	p.R588Q	ATP8A2_uc010tdi.1_Missense_Mutation_p.R548Q|ATP8A2_uc010tdj.1_RNA|ATP8A2_uc010aaj.1_Missense_Mutation_p.R98Q	NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter-like,	548	Cytoplasmic (Potential).				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)														---	---	---	---
HSPH1	10808	broad.mit.edu	37	13	31729764	31729764	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31729764A>T	uc001utj.2	-	3	591	c.193T>A	c.(193-195)TCT>ACT	p.S65T	HSPH1_uc001utk.2_Missense_Mutation_p.S65T|HSPH1_uc010aaw.2_Missense_Mutation_p.S65T|HSPH1_uc001utl.2_Missense_Mutation_p.S67T|HSPH1_uc010tds.1_Missense_Mutation_p.S67T|HSPH1_uc010tdt.1_RNA|HSPH1_uc010aax.1_Missense_Mutation_p.S67T|HSPH1_uc010aay.1_Missense_Mutation_p.S67T	NM_006644	NP_006635	Q92598	HS105_HUMAN	heat shock 105kD	65					positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein	cytoplasm|extracellular region	ATP binding				0		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)														---	---	---	---
N4BP2L2	10443	broad.mit.edu	37	13	33092117	33092117	+	Missense_Mutation	SNP	C	T	T	rs117678407	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33092117C>T	uc001uuk.3	-	6	1752	c.1574G>A	c.(1573-1575)CGA>CAA	p.R525Q	N4BP2L2_uc001uuj.2_Missense_Mutation_p.R41Q|N4BP2L2_uc010abe.1_Missense_Mutation_p.R96Q|N4BP2L2_uc010tdz.1_Missense_Mutation_p.R81Q	NM_014887	NP_055702	Q92802	N42L2_HUMAN	phosphonoformate immuno-associated protein 5	525											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)														---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33347331	33347331	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33347331G>A	uc010abf.2	+	34	4335	c.4177G>A	c.(4177-4179)GTA>ATA	p.V1393I	PDS5B_uc010abg.2_Intron	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog	1393					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)														---	---	---	---
TRPC4	7223	broad.mit.edu	37	13	38266432	38266432	+	Missense_Mutation	SNP	C	T	T	rs147415849		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38266432C>T	uc001uws.2	-	4	1173	c.938G>A	c.(937-939)CGC>CAC	p.R313H	TRPC4_uc010abv.2_Intron|TRPC4_uc001uwt.2_Missense_Mutation_p.R313H|TRPC4_uc010tey.1_Missense_Mutation_p.R313H|TRPC4_uc010abw.2_Missense_Mutation_p.R140H|TRPC4_uc010abx.2_Missense_Mutation_p.R313H|TRPC4_uc010aby.2_Missense_Mutation_p.R313H	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	313	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	39262147	39262147	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39262147C>T	uc001uwv.2	+	1	975	c.666C>T	c.(664-666)TCC>TCT	p.S222S		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	222	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	39422774	39422774	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39422774G>A	uc001uwv.2	+	8	6655	c.6346G>A	c.(6346-6348)GCC>ACC	p.A2116T	FREM2_uc001uww.2_Missense_Mutation_p.A202T	NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	2116	Extracellular (Potential).			A -> T (in Ref. 3; BAC87040).	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)														---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42277527	42277527	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42277527G>A	uc001uyj.2	-	27	3207	c.3137C>T	c.(3136-3138)ACG>ATG	p.T1046M		NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a	1046						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	42742861	42742861	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42742861G>A	uc001uyl.1	+	11	1295	c.1274G>A	c.(1273-1275)CGA>CAA	p.R425Q	DGKH_uc010tfh.1_Missense_Mutation_p.R425Q|DGKH_uc001uym.1_Missense_Mutation_p.R425Q|DGKH_uc010tfi.1_Missense_Mutation_p.R180Q|DGKH_uc010tfj.1_Missense_Mutation_p.R280Q|DGKH_uc001uyn.1_RNA|DGKH_uc001uyo.1_Missense_Mutation_p.R280Q|DGKH_uc001uyp.2_RNA	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	425	DAGKc.				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)														---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46543351	46543351	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46543351C>T	uc010tfw.1	-	13	3334	c.3328G>A	c.(3328-3330)GCC>ACC	p.A1110T	ZC3H13_uc001vaq.2_5'Flank|ZC3H13_uc001vas.1_Missense_Mutation_p.A1110T|ZC3H13_uc001vat.1_Missense_Mutation_p.A1110T	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	1110							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	46559533	46559533	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46559533C>T	uc010tfw.1	-	9	1625	c.1619G>A	c.(1618-1620)CGT>CAT	p.R540H	ZC3H13_uc001vas.1_Missense_Mutation_p.R540H|ZC3H13_uc001vat.1_Missense_Mutation_p.R540H	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	540	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	46616316	46616316	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46616316A>G	uc010tfw.1	-	3	328	c.322T>C	c.(322-324)TCA>CCA	p.S108P	ZC3H13_uc001vas.1_Missense_Mutation_p.S108P|ZC3H13_uc001vat.1_Missense_Mutation_p.S108P	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	108							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)														---	---	---	---
RCBTB1	55213	broad.mit.edu	37	13	50125518	50125518	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50125518T>C	uc001vde.1	-	8	1059	c.798A>G	c.(796-798)GGA>GGG	p.G266G		NM_018191	NP_060661	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and	266	RCC1 5.				cell cycle|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(1)	1		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|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;4.7e-09)														---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61102603	61102603	+	Missense_Mutation	SNP	G	A	A	rs140988326	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61102603G>A	uc001via.2	+	11	1753	c.965G>A	c.(964-966)CGA>CAA	p.R322Q	TDRD3_uc010aef.2_Missense_Mutation_p.R147Q|TDRD3_uc001vhz.3_Missense_Mutation_p.R322Q|TDRD3_uc010aeg.2_Missense_Mutation_p.R415Q|TDRD3_uc001vib.3_Missense_Mutation_p.R321Q	NM_030794	NP_110421	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3 isoform 2	322					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)														---	---	---	---
C13orf34	79866	broad.mit.edu	37	13	73320743	73320743	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73320743C>T	uc001viv.1	+	10	1095	c.976C>T	c.(976-978)CCA>TCA	p.P326S	C13orf34_uc010thq.1_Missense_Mutation_p.P101S|C13orf34_uc010aen.1_Missense_Mutation_p.P401S|C13orf34_uc010thr.1_Missense_Mutation_p.P256S|C13orf34_uc001viw.1_Missense_Mutation_p.P275S	NM_024808	NP_079084	Q6PGQ7	BORA_HUMAN	aurora borealis	326					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)														---	---	---	---
MIR622	693207	broad.mit.edu	37	13	90883462	90883462	+	RNA	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90883462A>G	hsa-mir-622|MI0003636	+			c.27A>G																				0																		---	---	---	---
GPR180	160897	broad.mit.edu	37	13	95279412	95279412	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95279412G>A	uc001vly.2	+	9	1388	c.1310G>A	c.(1309-1311)CGC>CAC	p.R437H	GPR180_uc001vlz.2_Missense_Mutation_p.R336H|GPR180_uc010afi.2_Missense_Mutation_p.R198H	NM_180989	NP_851320	Q86V85	GP180_HUMAN	G protein-coupled receptor 180 precursor	437						integral to membrane				breast(1)	1	all_neural(89;0.0684)|Medulloblastoma(90;0.163)																	---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	96743551	96743551	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96743551C>T	uc001vmw.2	+	1	459	c.435C>T	c.(433-435)CGC>CGT	p.R145R		NM_153456	NP_703157	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	145	Lumenal (Potential).					integral to membrane	sulfotransferase activity	p.R145C(1)		ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)																	---	---	---	---
FARP1	10160	broad.mit.edu	37	13	99092253	99092253	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99092253C>A	uc001vnj.2	+	22	2808	c.2472C>A	c.(2470-2472)TGC>TGA	p.C824*	FARP1_uc001vnh.2_Nonsense_Mutation_p.C855*	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1	824	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)															---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101710303	101710303	+	Missense_Mutation	SNP	G	A	A	rs143587652		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101710303G>A	uc001vox.1	-	43	5200	c.5011C>T	c.(5011-5013)CGT>TGT	p.R1671C		NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	1671	Cytoplasmic (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109459100	109459100	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109459100T>C	uc001vqt.1	+	7	875	c.749T>C	c.(748-750)ATA>ACA	p.I250T	MYO16_uc010agk.1_Missense_Mutation_p.I272T|MYO16_uc001vqu.1_Missense_Mutation_p.I50T	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	250	ANK 6.				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)															---	---	---	---
SOX1	6656	broad.mit.edu	37	13	112722004	112722004	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112722004A>G	uc001vsb.1	+	1	92	c.32A>G	c.(31-33)CAC>CGC	p.H11R		NM_005986	NP_005977	O00570	SOX1_HUMAN	SRY (sex determining region Y)-box 1	11					chromatin organization	nucleus	core promoter sequence-specific DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	all_lung(23;0.000652)|Lung NSC(43;0.017)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	all_cancers(25;0.000331)|Lung NSC(25;0.0496)|all_lung(25;0.0831)|all_epithelial(44;0.0868)|Breast(118;0.231)		OV - Ovarian serous cystadenocarcinoma(48;0.132)														---	---	---	---
TMCO3	55002	broad.mit.edu	37	13	114174950	114174950	+	Silent	SNP	C	T	T	rs150929637		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114174950C>T	uc001vtu.3	+	8	1606	c.1245C>T	c.(1243-1245)ACC>ACT	p.T415T	TMCO3_uc001vtt.3_Silent_p.T415T	NM_017905	NP_060375	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	415						integral to membrane	solute:hydrogen antiporter activity				0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)															---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20854765	20854765	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20854765A>C	uc001vxe.2	-	19	2742	c.2702T>G	c.(2701-2703)CTT>CGT	p.L901R	TEP1_uc010ahk.2_Missense_Mutation_p.L251R|TEP1_uc010tlf.1_RNA|TEP1_uc010tlg.1_Missense_Mutation_p.L793R	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	901					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)														---	---	---	---
OSGEP	55644	broad.mit.edu	37	14	20916315	20916315	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20916315T>C	uc001vxf.2	-	7	1008	c.652A>G	c.(652-654)ATG>GTG	p.M218V		NM_017807	NP_060277	Q9NPF4	OSGEP_HUMAN	O-sialoglycoprotein endopeptidase	218					proteolysis|tRNA processing		metal ion binding|metalloendopeptidase activity|protein binding				0	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0231)|READ - Rectum adenocarcinoma(17;0.196)														---	---	---	---
EDDM3B	64184	broad.mit.edu	37	14	21238745	21238745	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21238745G>A	uc001vyd.2	+	2	534	c.436G>A	c.(436-438)GGC>AGC	p.G146S		NM_022360	NP_071755	P56851	EP3B_HUMAN	human epididymis-specific 3 beta precursor	146					spermatid development	extracellular region				ovary(1)	1																		---	---	---	---
RAB2B	84932	broad.mit.edu	37	14	21936840	21936840	+	Silent	SNP	G	A	A	rs150391208	byFrequency;by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21936840G>A	uc010tlt.1	-	4	359	c.258C>T	c.(256-258)TAC>TAT	p.Y86Y	RAB2B_uc010tls.1_Silent_p.Y40Y|RAB2B_uc001wax.2_Silent_p.Y21Y|RAB2B_uc010ain.2_Intron	NM_032846	NP_116235	Q8WUD1	RAB2B_HUMAN	RAB2B protein isoform 1	86					protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane|plasma membrane	GTP binding			ovary(1)	1	all_cancers(95;0.000858)		Epithelial(56;1.53e-06)|all cancers(55;1.44e-05)	GBM - Glioblastoma multiforme(265;0.00391)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22434062	22434062	+	Intron	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22434062G>T	uc001wbw.2	+						uc010tmg.1_Missense_Mutation_p.A39S|uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Missense_Mutation_p.A39S					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22616582	22616582	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22616582C>T	uc001wbw.2	+						uc010aiv.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Missense_Mutation_p.A108V|uc010ajk.1_Missense_Mutation_p.A108V|uc001wdg.1_Nonsense_Mutation_p.Q24*					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
HOMEZ	57594	broad.mit.edu	37	14	23745054	23745054	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23745054C>T	uc001wja.2	-	2	1531	c.1383G>A	c.(1381-1383)CCG>CCA	p.P461P	HOMEZ_uc001wjb.2_Silent_p.P463P	NM_020834	NP_065885	Q8IX15	HOMEZ_HUMAN	homeodomain leucine zipper protein	461	Pro-rich.					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)														---	---	---	---
MYH7	4625	broad.mit.edu	37	14	23887443	23887443	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23887443C>T	uc001wjx.2	-	30	4251	c.4145G>A	c.(4144-4146)CGG>CAG	p.R1382Q	MIR208B_hsa-mir-208b|MI0005570_5'Flank	NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1382	Potential.		R -> W (in CMH1).		adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)														---	---	---	---
LRRC16B	90668	broad.mit.edu	37	14	24525864	24525864	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24525864T>C	uc001wlj.2	+	12	1056	c.899T>C	c.(898-900)TTC>TCC	p.F300S		NM_138360	NP_612369	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	300										ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
TGM1	7051	broad.mit.edu	37	14	24729876	24729876	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24729876C>T	uc001wod.2	-	4	661	c.537G>A	c.(535-537)ACG>ACA	p.T179T	TGM1_uc010tog.1_Intron	NM_000359	NP_000350	P22735	TGM1_HUMAN	transglutaminase 1	179					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)													---	---	---	---
LTB4R2	56413	broad.mit.edu	37	14	24780931	24780931	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24780931C>T	uc001woq.1	+	1	2771	c.1154C>T	c.(1153-1155)CCG>CTG	p.P385L	CIDEB_uc001woo.2_5'Flank|CIDEB_uc001wop.2_5'Flank|LTB4R2_uc001wor.2_Missense_Mutation_p.P354L|LTB4R_uc001wos.2_5'UTR|LTB4R_uc010alp.2_5'Flank|LTB4R_uc001wou.2_5'Flank	NM_019839	NP_062813	Q9NPC1	LT4R2_HUMAN	leukotriene B4 receptor 2	385	Cytoplasmic (Potential).				chemotaxis|negative regulation of adenylate cyclase activity	integral to plasma membrane					0				GBM - Glioblastoma multiforme(265;0.018)														---	---	---	---
NYNRIN	57523	broad.mit.edu	37	14	24880323	24880323	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24880323T>C	uc001wpf.3	+	5	2774	c.2456T>C	c.(2455-2457)ATG>ACG	p.M819T		NM_025081	NP_079357	Q9P2P1	NYNRI_HUMAN	hypothetical protein LOC57523	819					DNA integration	integral to membrane	DNA binding			ovary(2)|central_nervous_system(1)	3																OREG0022626	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NYNRIN	57523	broad.mit.edu	37	14	24884436	24884436	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24884436C>T	uc001wpf.3	+	9	3799	c.3481C>T	c.(3481-3483)CGC>TGC	p.R1161C		NM_025081	NP_079357	Q9P2P1	NYNRI_HUMAN	hypothetical protein LOC57523	1161					DNA integration	integral to membrane	DNA binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
COCH	1690	broad.mit.edu	37	14	31354257	31354257	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31354257A>G	uc001wqr.2	+						COCH_uc001wqp.2_Intron|COCH_uc001wqq.3_Intron|uc001wqs.2_Intron|COCH_uc001wqt.1_Intron	NM_004086	NP_004077			cochlin precursor						sensory perception of sound	proteinaceous extracellular matrix				pancreas(1)|central_nervous_system(1)|skin(1)	3	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)														---	---	---	---
STRN3	29966	broad.mit.edu	37	14	31424869	31424869	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31424869C>T	uc001wqu.2	-	3	633	c.417G>A	c.(415-417)ACG>ACA	p.T139T	STRN3_uc001wqv.2_Silent_p.T139T|STRN3_uc010tpj.1_RNA	NM_001083893	NP_001077362	Q13033	STRN3_HUMAN	nuclear autoantigen isoform 1	139					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	31575978	31575978	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31575978G>A	uc001wrc.1	-	38	7589	c.7100C>T	c.(7099-7101)GCT>GTT	p.A2367V	HECTD1_uc001wra.1_Missense_Mutation_p.A493V|HECTD1_uc001wrb.1_Missense_Mutation_p.A493V	NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	2367	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33292305	33292305	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33292305C>A	uc001wrq.2	+	13	5456	c.5286C>A	c.(5284-5286)ACC>ACA	p.T1762T		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	1762					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)														---	---	---	---
EAPP	55837	broad.mit.edu	37	14	34985626	34985626	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34985626C>T	uc001wsd.1	-	6	857	c.748G>A	c.(748-750)GTG>ATG	p.V250M		NM_018453	NP_060923	Q56P03	EAPP_HUMAN	E2F-associated phosphoprotein	250					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)														---	---	---	---
NKX2-1	7080	broad.mit.edu	37	14	36987203	36987203	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36987203C>T	uc001wtt.2	-	2	737	c.396G>A	c.(394-396)GCG>GCA	p.A132A	SFTA3_uc001wts.2_Intron|NKX2-1_uc001wtu.2_Silent_p.A162A|NKX2-1_uc001wtv.2_Silent_p.A132A|uc001wtw.1_5'Flank	NM_003317	NP_003308	P43699	NKX21_HUMAN	thyroid transcription factor 1 isoform 2	132					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								---	---	---	---
FSCB	84075	broad.mit.edu	37	14	44974717	44974717	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44974717G>A	uc001wvn.2	-	1	1783	c.1474C>T	c.(1474-1476)CGG>TGG	p.R492W		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	492	Ala-rich.					cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)														---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45478141	45478141	+	Missense_Mutation	SNP	G	A	A	rs145931350		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45478141G>A	uc001wvv.2	+	6	3139	c.2930G>A	c.(2929-2931)CGT>CAT	p.R977H	FAM179B_uc001wvw.2_Missense_Mutation_p.R977H|FAM179B_uc010anc.2_Intron	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	977	Ser-rich.						binding			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
TMX1	81542	broad.mit.edu	37	14	51710663	51710663	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51710663C>T	uc001wza.3	+	2	367	c.242C>T	c.(241-243)GCG>GTG	p.A81V	TMX1_uc010tqr.1_Missense_Mutation_p.A81V|TMX1_uc010aoa.2_5'UTR	NM_030755	NP_110382	Q9H3N1	TMX1_HUMAN	thioredoxin domain containing 1 precursor	81	Thioredoxin.|Extracellular (Potential).				anti-apoptosis|cell proliferation|cell redox homeostasis|DNA replication|electron transport chain|ER to Golgi vesicle-mediated transport|leukocyte activation|positive regulation of growth|positive regulation of transcription, DNA-dependent|response to stress|signal transduction	endoplasmic reticulum membrane|integral to membrane|membrane fraction	arsenate reductase (thioredoxin) activity|disulfide oxidoreductase activity				0																		---	---	---	---
KIAA0831	22863	broad.mit.edu	37	14	55836420	55836420	+	Missense_Mutation	SNP	C	T	T	rs144919020		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55836420C>T	uc001xbx.1	-	10	1432	c.1396G>A	c.(1396-1398)GCG>ACG	p.A466T	FBXO34_uc001xbv.2_Intron|KIAA0831_uc001xbw.1_Missense_Mutation_p.A353T	NM_014924	NP_055739	Q6ZNE5	BAKOR_HUMAN	Barkor	466					autophagic vacuole assembly|positive regulation of autophagy	autophagic vacuole|endoplasmic reticulum|pre-autophagosomal structure membrane	protein binding				0																		---	---	---	---
SYT16	83851	broad.mit.edu	37	14	62547711	62547711	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62547711G>A	uc001xfu.1	+	4	1350	c.1153G>A	c.(1153-1155)GTC>ATC	p.V385I	SYT16_uc010tsd.1_3'UTR|SYT16_uc010tse.1_5'UTR	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like	385	C2 1.									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	64634309	64634309	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64634309T>C	uc001xgm.2	+	92	17087	c.16857T>C	c.(16855-16857)GAT>GAC	p.D5619D	SYNE2_uc001xgl.2_Silent_p.D5619D|SYNE2_uc010apy.2_Silent_p.D2004D|SYNE2_uc001xgn.2_Silent_p.D581D|SYNE2_uc001xgo.2_RNA|SYNE2_uc010aqa.2_5'UTR|SYNE2_uc001xgq.2_5'UTR	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5619	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)														---	---	---	---
ZBTB25	7597	broad.mit.edu	37	14	64954065	64954065	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64954065C>T	uc001xhf.2	-	3	1067	c.884G>A	c.(883-885)CGC>CAC	p.R295H	ZBTB25_uc001xhc.2_Intron|ZBTB25_uc001xhg.2_Missense_Mutation_p.R295H	NM_006977	NP_008908	P24278	ZBT25_HUMAN	zinc finger protein 46	295						cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2				all cancers(60;0.00865)|OV - Ovarian serous cystadenocarcinoma(108;0.0102)|BRCA - Breast invasive adenocarcinoma(234;0.0469)														---	---	---	---
PLEK2	26499	broad.mit.edu	37	14	67862133	67862133	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67862133C>T	uc001xjh.1	-	3	427	c.375G>A	c.(373-375)CCG>CCA	p.P125P		NM_016445	NP_057529	Q9NYT0	PLEK2_HUMAN	pleckstrin 2	125					actin cytoskeleton organization|intracellular signal transduction	cytoplasm|cytoskeleton|lamellipodium membrane				ovary(1)|pancreas(1)	2				all cancers(60;0.000728)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.00953)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71542931	71542931	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71542931C>T	uc001xmo.2	+	28	5578	c.5132C>T	c.(5131-5133)TCG>TTG	p.S1711L	PCNX_uc010are.1_Missense_Mutation_p.S1600L|PCNX_uc010arf.1_Missense_Mutation_p.S499L	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	1711						integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	72205804	72205804	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72205804G>T	uc001xms.2	+	22	5689	c.5341G>T	c.(5341-5343)GAG>TAG	p.E1781*	SIPA1L1_uc001xmt.2_Nonsense_Mutation_p.E1760*|SIPA1L1_uc001xmu.2_Nonsense_Mutation_p.E1759*|SIPA1L1_uc001xmv.2_Nonsense_Mutation_p.E1780*|SIPA1L1_uc010ttm.1_Nonsense_Mutation_p.E1234*|SIPA1L1_uc001xmw.2_Nonsense_Mutation_p.E546*	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	1781	Potential.				actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)														---	---	---	---
PAPLN	89932	broad.mit.edu	37	14	73729153	73729153	+	Missense_Mutation	SNP	C	T	T	rs150310890	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73729153C>T	uc010ttx.1	+	18	2504	c.2341C>T	c.(2341-2343)CGC>TGC	p.R781C	PAPLN_uc001xnw.3_Missense_Mutation_p.R754C|PAPLN_uc010arl.2_Intron|PAPLN_uc010ttw.1_RNA|PAPLN_uc010tty.1_Missense_Mutation_p.R765C|PAPLN_uc010arm.2_5'UTR|PAPLN_uc010arn.2_5'UTR	NM_173462	NP_775733	O95428	PPN_HUMAN	papilin	781	BPTI/Kunitz inhibitor.					proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase inhibitor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)														---	---	---	---
FAM161B	145483	broad.mit.edu	37	14	74413287	74413287	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74413287C>T	uc001xpd.1	-	2	182	c.76G>A	c.(76-78)GCA>ACA	p.A26T		NM_152445	NP_689658			hypothetical protein LOC145483											ovary(1)	1																		---	---	---	---
YLPM1	56252	broad.mit.edu	37	14	75296006	75296006	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75296006A>G	uc001xqj.3	+	19	6378	c.6254A>G	c.(6253-6255)GAT>GGT	p.D2085G	YLPM1_uc001xql.3_RNA	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	1890					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	75367834	75367834	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75367834C>T	uc001xqv.2	+	14	1188	c.1125C>T	c.(1123-1125)GGC>GGT	p.G375G	DLST_uc001xqu.2_Silent_p.G287G|DLST_uc001xqt.2_Silent_p.G291G|DLST_uc010tuw.1_Silent_p.G289G	NM_001933	NP_001924	P36957	ODO2_HUMAN	dihydrolipoamide S-succinyltransferase (E2	375					lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|nucleus	dihydrolipoyllysine-residue succinyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00698)														---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76368503	76368503	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76368503G>A	uc001xrx.2	+	31	3964	c.3759G>A	c.(3757-3759)GGG>GGA	p.G1253G	TTLL5_uc001xsa.2_Silent_p.G327G	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	1253					protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
ESRRB	2103	broad.mit.edu	37	14	76928920	76928920	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76928920G>A	uc001xsq.1	+	3	497	c.430G>A	c.(430-432)GAG>AAG	p.E144K	ESRRB_uc001xsr.2_Missense_Mutation_p.E144K|ESRRB_uc001xso.2_RNA	NM_004452	NP_004443	A2VDJ2	A2VDJ2_HUMAN	estrogen-related receptor beta	144						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)														---	---	---	---
ISM2	145501	broad.mit.edu	37	14	77942189	77942189	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77942189C>T	uc001xtz.2	-	7	1539	c.1465G>A	c.(1465-1467)GCC>ACC	p.A489T	ISM2_uc001xua.2_3'UTR|ISM2_uc001xty.2_Missense_Mutation_p.A401T|ISM2_uc010tvl.1_Missense_Mutation_p.A408T	NM_199296	NP_954993	Q6H9L7	ISM2_HUMAN	isthmin 2 homolog isoform 1	489	AMOP.					extracellular region				skin(1)	1																		---	---	---	---
KCNK10	54207	broad.mit.edu	37	14	88729810	88729810	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88729810C>T	uc001xwo.2	-	2	580	c.123G>A	c.(121-123)CCG>CCA	p.P41P	KCNK10_uc001xwm.2_Silent_p.P46P|KCNK10_uc001xwn.2_Silent_p.P46P	NM_021161	NP_066984	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	41	Cytoplasmic (Potential).				signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|skin(2)|pancreas(1)	5																		---	---	---	---
TTC7B	145567	broad.mit.edu	37	14	91247111	91247111	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91247111C>T	uc001xyp.2	-	3	538	c.416G>A	c.(415-417)CGG>CAG	p.R139Q		NM_001010854	NP_001010854	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	139							binding			ovary(2)	2		Melanoma(154;0.222)																---	---	---	---
ITPK1	3705	broad.mit.edu	37	14	93424715	93424715	+	Intron	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93424715G>T	uc001ybg.2	-						ITPK1_uc001ybe.2_Intron|ITPK1_uc001ybf.2_Intron|ITPK1_uc001ybh.2_Intron	NM_014216	NP_055031			inositol 1,3,4-triphosphate 5/6 kinase isoform						blood coagulation|inositol trisphosphate metabolic process|signal transduction	cytosol	ATP binding|hydrolase activity|inositol tetrakisphosphate 1-kinase activity|inositol-1,3,4-trisphosphate 5/6-kinase activity|isomerase activity|ligase activity|magnesium ion binding				0		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)														---	---	---	---
KIAA1409	57578	broad.mit.edu	37	14	94087971	94087971	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94087971A>G	uc001ybv.1	+	28	4010	c.3927A>G	c.(3925-3927)GAA>GAG	p.E1309E	KIAA1409_uc001ybs.1_Silent_p.E1287E	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	1464						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)														---	---	---	---
PPP4R4	57718	broad.mit.edu	37	14	94674876	94674876	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94674876G>A	uc001ycs.1	+	3	421	c.267G>A	c.(265-267)ACG>ACA	p.T89T	PPP4R4_uc001ycr.2_Silent_p.T89T	NM_058237	NP_478144	Q6NUP7	PP4R4_HUMAN	HEAT-like repeat-containing protein isoform 1	89						cytoplasm|protein serine/threonine phosphatase complex	protein binding	p.T89M(1)		skin(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
SERPINA12	145264	broad.mit.edu	37	14	94964713	94964713	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94964713C>T	uc001ydj.2	-	3	818	c.22G>A	c.(22-24)GCC>ACC	p.A8T		NM_173850	NP_776249	Q8IW75	SPA12_HUMAN	serine (or cysteine) proteinase inhibitor, clade	8					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			central_nervous_system(2)|ovary(1)|lung(1)	4				COAD - Colon adenocarcinoma(157;0.235)														---	---	---	---
SERPINA5	5104	broad.mit.edu	37	14	95053815	95053815	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95053815C>T	uc001ydm.2	+	3	326	c.116C>T	c.(115-117)ACG>ATG	p.T39M	SERPINA5_uc010ave.2_Missense_Mutation_p.T39M|SERPINA5_uc001ydn.1_Missense_Mutation_p.T39M	NM_000624	NP_000615	P05154	IPSP_HUMAN	serine (or cysteine) proteinase inhibitor, clade	39					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)													---	---	---	---
DYNC1H1	1778	broad.mit.edu	37	14	102449771	102449771	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102449771A>G	uc001yks.2	+	7	1450	c.1286A>G	c.(1285-1287)AAA>AGA	p.K429R		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	429	Stem (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10																		---	---	---	---
KIAA0284	283638	broad.mit.edu	37	14	105346747	105346747	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105346747C>T	uc010axb.2	+	6	681	c.457C>T	c.(457-459)CGG>TGG	p.R153W	INF2_uc010tyi.1_Intron|KIAA0284_uc001ypr.2_Missense_Mutation_p.R83W|KIAA0284_uc001yps.2_Missense_Mutation_p.R59W	NM_001112726	NP_001106197	Q9Y4F5	K0284_HUMAN	hypothetical protein LOC283638 isoform 1	153						cytoplasm|microtubule				breast(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000472)|OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0149)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.178)														---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105406444	105406444	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105406444T>C	uc010axc.1	-	7	15464	c.15344A>G	c.(15343-15345)CAG>CGG	p.Q5115R	AHNAK2_uc001ypx.2_Missense_Mutation_p.Q5015R	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5115						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)															---	---	---	---
SNORD116-4	100033416	broad.mit.edu	37	15	25315626	25315626	+	Intron	SNP	C	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25315626C>G	uc001yxh.1	+						SNORD116-4_uc001yxm.1_Intron|IPW_uc001yxn.3_Intron|SNORD116-8_uc001yxr.2_RNA|SNORD116-3_uc001yxs.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0																		---	---	---	---
SNORD115-20	100033460	broad.mit.edu	37	15	25463851	25463851	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25463851G>A	uc001yzq.1	+						uc001yzt.1_Intron|SNORD115-26_uc001yzw.1_RNA|HBII-52-27_uc010ayq.1_5'Flank	NR_003313				Homo sapiens small nucleolar RNA, C/D box 115-15 (SNORD115-15), non-coding RNA.												0																		---	---	---	---
SNORD115-20	100033460	broad.mit.edu	37	15	25468399	25468399	+	Intron	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25468399A>G	uc001yzq.1	+						SNORD115-26_uc001yzw.1_Intron|SNORD115-11_uc001yzx.1_RNA|SNORD115-30_uc001yzy.1_5'Flank	NR_003313				Homo sapiens small nucleolar RNA, C/D box 115-15 (SNORD115-15), non-coding RNA.												0																		---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28467371	28467371	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28467371C>T	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)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	34113561	34113561	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34113561G>A	uc001zhi.2	+	79	10976	c.10906G>A	c.(10906-10908)GCT>ACT	p.A3636T	RYR3_uc010bar.2_Missense_Mutation_p.A3631T	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3636					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	34145278	34145278	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34145278T>C	uc001zhi.2	+	95	13731	c.13661T>C	c.(13660-13662)GTA>GCA	p.V4554A	RYR3_uc010bar.2_Missense_Mutation_p.V4549A	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	4554					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
C15orf55	256646	broad.mit.edu	37	15	34649679	34649679	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34649679G>A	uc001zif.2	+	7	3541	c.3386G>A	c.(3385-3387)CGT>CAT	p.R1129H	C15orf55_uc010ucc.1_Missense_Mutation_p.R1157H|C15orf55_uc010ucd.1_Missense_Mutation_p.R1147H	NM_175741	NP_786883	Q86Y26	NUT_HUMAN	nuclear protein in testis	1129						cytoplasm|nucleus			BRD4_ENST00000263377/C15orf55(24)|BRD3/C15orf55(3)	midline_organs(25)|ovary(2)|lung(2)|skin(1)	30		all_lung(180;2.78e-08)		all cancers(64;4.53e-18)|GBM - Glioblastoma multiforme(113;8.29e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0249)				T	BRD3|BRD4	lethal midline carcinoma								---	---	---	---
LPCAT4	254531	broad.mit.edu	37	15	34655878	34655878	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34655878C>T	uc001zig.2	-	6	789	c.695G>A	c.(694-696)CGC>CAC	p.R232H		NM_153613	NP_705841	Q643R3	LPCT4_HUMAN	lysophosphatidylcholine acyltransferase 4	232					phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity|calcium ion binding				0																		---	---	---	---
INO80	54617	broad.mit.edu	37	15	41366688	41366688	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41366688G>A	uc001zni.2	-	10	1420	c.1207C>T	c.(1207-1209)CGA>TGA	p.R403*	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	403	Assembles INO80 complex module consisting of conserved components ACTR8, ACTL6A and YY1.|DBINO.				cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
LTK	4058	broad.mit.edu	37	15	41800405	41800405	+	Nonsense_Mutation	SNP	C	A	A	rs141049740		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41800405C>A	uc001zoa.3	-	9	1289	c.1111G>T	c.(1111-1113)GGA>TGA	p.G371*	LTK_uc001zob.3_Nonsense_Mutation_p.G310*|LTK_uc010ucx.1_Nonsense_Mutation_p.G310*|LTK_uc010bcg.2_Nonsense_Mutation_p.G53*	NM_002344	NP_002335	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase isoform 1	371	Extracellular (Potential).				apoptosis|cell proliferation|phosphatidylinositol 3-kinase cascade|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|central_nervous_system(1)	7		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)											TSP Lung(18;0.14)			---	---	---	---
LTK	4058	broad.mit.edu	37	15	41804949	41804949	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41804949C>T	uc001zoa.3	-	3	493	c.315G>A	c.(313-315)CTG>CTA	p.L105L	LTK_uc001zob.3_Silent_p.L105L|LTK_uc010ucx.1_Silent_p.L105L|LTK_uc010bcg.2_Intron	NM_002344	NP_002335	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase isoform 1	105	Extracellular (Potential).				apoptosis|cell proliferation|phosphatidylinositol 3-kinase cascade|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|central_nervous_system(1)	7		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)											TSP Lung(18;0.14)			---	---	---	---
MAPKBP1	23005	broad.mit.edu	37	15	42105236	42105236	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42105236G>A	uc001zok.3	+	8	1042	c.756G>A	c.(754-756)ACG>ACA	p.T252T	MAPKBP1_uc001zoj.3_Silent_p.T252T|MAPKBP1_uc010bcj.2_5'UTR|MAPKBP1_uc010bci.2_Silent_p.T252T|MAPKBP1_uc010udb.1_Silent_p.T140T|MAPKBP1_uc010bck.2_5'UTR|MAPKBP1_uc010bcl.2_5'UTR	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein	252										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)														---	---	---	---
CDAN1	146059	broad.mit.edu	37	15	43021275	43021275	+	Missense_Mutation	SNP	C	A	A	rs145082607		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43021275C>A	uc001zql.2	-	19	2708	c.2591G>T	c.(2590-2592)CGG>CTG	p.R864L	CDAN1_uc001zqj.2_RNA|CDAN1_uc001zqk.2_Missense_Mutation_p.R190L	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	864						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)														---	---	---	---
LCMT2	9836	broad.mit.edu	37	15	43622232	43622232	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43622232G>T	uc001zrg.2	-	1	660	c.456C>A	c.(454-456)AGC>AGA	p.S152R	LCMT2_uc010udn.1_Intron|ADAL_uc001zrh.2_5'Flank|ADAL_uc010udo.1_5'Flank	NM_014793	NP_055608	O60294	LCMT2_HUMAN	leucine carboxyl methyltransferase 2	152					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)													---	---	---	---
CKMT1B	1159	broad.mit.edu	37	15	43891410	43891410	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43891410G>A	uc001zsc.2	+	10	1585	c.1193G>A	c.(1192-1194)CGG>CAG	p.R398Q	CKMT1B_uc010uds.1_Missense_Mutation_p.R429Q|CKMT1B_uc001zsd.3_Missense_Mutation_p.R398Q|CKMT1B_uc010bdj.2_RNA	NM_020990	NP_066270	P12532	KCRU_HUMAN	creatine kinase, mitochondrial 1B precursor	398	Phosphagen kinase C-terminal.				creatine metabolic process	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)	Creatine(DB00148)													---	---	---	---
WDR76	79968	broad.mit.edu	37	15	44131849	44131849	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44131849C>T	uc001zti.1	+	5	678	c.655C>T	c.(655-657)CGA>TGA	p.R219*		NM_024908	NP_079184	Q9H967	WDR76_HUMAN	WD repeat domain 76	219											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)														---	---	---	---
USP8	9101	broad.mit.edu	37	15	50774185	50774185	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50774185C>A	uc001zym.3	+	12	2226	c.1726C>A	c.(1726-1728)CCA>ACA	p.P576T	USP8_uc001zyk.1_Missense_Mutation_p.P277T|USP8_uc001zyl.3_Missense_Mutation_p.P576T|USP8_uc001zyn.3_Missense_Mutation_p.P576T|USP8_uc010ufh.1_Missense_Mutation_p.P499T|USP8_uc010bev.1_Missense_Mutation_p.P205T	NM_001128611	NP_001122083	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	576					cell cycle|cell proliferation|endosome organization|protein K48-linked deubiquitination|protein K63-linked deubiquitination|ubiquitin-dependent protein catabolic process	cytosol|early endosome|extrinsic to plasma membrane|nucleus	cysteine-type endopeptidase activity|SH3 domain binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(1)|central_nervous_system(1)	2				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)														---	---	---	---
TRPM7	54822	broad.mit.edu	37	15	50901830	50901830	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50901830C>T	uc001zyt.3	-	19	2792	c.2528G>A	c.(2527-2529)CGA>CAA	p.R843Q	TRPM7_uc010bew.1_Missense_Mutation_p.R843Q|TRPM7_uc001zyu.2_Missense_Mutation_p.R401Q	NM_017672	NP_060142	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel,	843	Extracellular (Potential).				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)														---	---	---	---
GLDN	342035	broad.mit.edu	37	15	51634199	51634199	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51634199C>T	uc002aba.2	+	1	487	c.318C>T	c.(316-318)GCC>GCT	p.A106A	GLDN_uc010bez.1_Silent_p.A106A	NM_181789	NP_861454	Q6ZMI3	GLDN_HUMAN	gliomedin	106	Extracellular (Potential).				cell differentiation|nervous system development	collagen|integral to membrane|plasma membrane				ovary(2)	2				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)														---	---	---	---
MYO5C	55930	broad.mit.edu	37	15	52510876	52510876	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52510876T>C	uc010bff.2	-	32	3931	c.3794A>G	c.(3793-3795)GAA>GGA	p.E1265G	MYO5C_uc010uga.1_RNA	NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC	1265	Potential.					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	54793039	54793039	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54793039C>T	uc002ack.2	+	20	5164	c.5164C>T	c.(5164-5166)CAG>TAG	p.Q1722*		NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	1722	MHD1.				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)														---	---	---	---
PIGB	9488	broad.mit.edu	37	15	55626105	55626105	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55626105C>T	uc002act.2	+	6	1010	c.694C>T	c.(694-696)CGT>TGT	p.R232C	PIGB_uc010ugg.1_Missense_Mutation_p.R37C	NM_004855	NP_004846	Q92521	PIGB_HUMAN	phosphatidylinositol glycan, class B	232	Helical; (Potential).				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)														---	---	---	---
CGNL1	84952	broad.mit.edu	37	15	57810601	57810601	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57810601G>A	uc002aeg.2	+	10	2697	c.2621G>A	c.(2620-2622)CGA>CAA	p.R874Q	CGNL1_uc010bfw.2_Missense_Mutation_p.R874Q	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1	874	Potential.					myosin complex|tight junction	motor activity	p.R874R(1)		skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)														---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62148607	62148607	+	Nonsense_Mutation	SNP	G	A	A	rs138846118		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62148607G>A	uc002agz.2	-	83	11028	c.10954C>T	c.(10954-10956)CGA>TGA	p.R3652*	VPS13C_uc002aha.2_Nonsense_Mutation_p.R3609*	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	3652					protein localization					ovary(2)	2																		---	---	---	---
TLN2	83660	broad.mit.edu	37	15	63054564	63054564	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63054564A>G	uc002alb.3	+	36	4873	c.4873A>G	c.(4873-4875)AAC>GAC	p.N1625D	TLN2_uc002alc.3_Missense_Mutation_p.N18D|TLN2_uc002ald.2_Missense_Mutation_p.N18D	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	1625					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																		---	---	---	---
ZNF609	23060	broad.mit.edu	37	15	64966762	64966762	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64966762G>A	uc002ann.2	+	4	1709	c.1709G>A	c.(1708-1710)CGA>CAA	p.R570Q		NM_015042	NP_055857	O15014	ZN609_HUMAN	zinc finger protein 609	570						nucleus	zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
ITGA11	22801	broad.mit.edu	37	15	68623337	68623337	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68623337C>A	uc002ari.2	-	15	1970	c.1883G>T	c.(1882-1884)GGC>GTC	p.G628V	ITGA11_uc010bib.2_Missense_Mutation_p.G628V	NM_001004439	NP_001004439	Q9UKX5	ITA11_HUMAN	integrin, alpha 11 precursor	628	FG-GAP 7.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)													---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72170488	72170488	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72170488G>A	uc002atl.3	-	31	6297	c.5824C>T	c.(5824-5826)CGT>TGT	p.R1942C	MYO9A_uc002atk.2_Missense_Mutation_p.R737C|MYO9A_uc002atm.1_Missense_Mutation_p.R738C	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA	1942	Tail.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
PKM2	5315	broad.mit.edu	37	15	72502148	72502148	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72502148A>G	uc002atx.1	-	5	672	c.431T>C	c.(430-432)CTG>CCG	p.L144P	PKM2_uc002ats.1_5'Flank|PKM2_uc002att.1_5'Flank|PKM2_uc002atu.1_5'UTR|PKM2_uc010bit.1_Missense_Mutation_p.L149P|PKM2_uc010uki.1_Missense_Mutation_p.L218P|PKM2_uc002atv.1_Missense_Mutation_p.L179P|PKM2_uc002atw.1_Missense_Mutation_p.L144P|PKM2_uc002aty.1_Missense_Mutation_p.L144P|PKM2_uc010ukj.1_Missense_Mutation_p.L129P|PKM2_uc010ukk.1_Missense_Mutation_p.L70P|PKM2_uc010biu.1_Missense_Mutation_p.L165P|PKM2_uc002atz.1_RNA	NM_182471	NP_872271	P14618	KPYM_HUMAN	pyruvate kinase, muscle isoform M1	144					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)													---	---	---	---
PML	5371	broad.mit.edu	37	15	74315711	74315711	+	Missense_Mutation	SNP	G	A	A	rs149871195		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74315711G>A	uc002awv.2	+	3	1285	c.1145G>A	c.(1144-1146)CGC>CAC	p.R382H	PML_uc002awm.2_Missense_Mutation_p.R382H|PML_uc002awl.2_Missense_Mutation_p.R382H|PML_uc002awj.1_Missense_Mutation_p.R382H|PML_uc002awk.2_Missense_Mutation_p.R382H|PML_uc002awn.2_Missense_Mutation_p.R382H|PML_uc002awo.2_Missense_Mutation_p.R382H|PML_uc002awp.2_Missense_Mutation_p.R382H|PML_uc002awq.2_Missense_Mutation_p.R382H|PML_uc002awr.2_Missense_Mutation_p.R382H|PML_uc002aws.2_Missense_Mutation_p.R382H|PML_uc002awt.2_Missense_Mutation_p.R382H|PML_uc002awu.2_Missense_Mutation_p.R382H|PML_uc010ule.1_Intron|PML_uc002aww.1_Missense_Mutation_p.R297H|PML_uc002awx.2_Missense_Mutation_p.R140H|PML_uc002awy.2_5'Flank	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1	382					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	74425791	74425791	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74425791G>A	uc002axd.2	+	4	1465	c.696G>A	c.(694-696)CCG>CCA	p.P232P	ISLR2_uc002axe.2_Silent_p.P232P|ISLR2_uc010bjg.2_Silent_p.P232P|ISLR2_uc010bjf.2_Silent_p.P232P	NM_001130136	NP_001123608	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing	232	Extracellular (Potential).|LRRCT.				positive regulation of axon extension	cell surface|integral to membrane|plasma membrane					0																		---	---	---	---
SIN3A	25942	broad.mit.edu	37	15	75692403	75692403	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75692403C>T	uc002bai.2	-	12	2091	c.1832G>A	c.(1831-1833)CGT>CAT	p.R611H	SIN3A_uc002baj.2_Missense_Mutation_p.R611H|SIN3A_uc010uml.1_Missense_Mutation_p.R611H	NM_015477	NP_056292	Q96ST3	SIN3A_HUMAN	transcriptional co-repressor Sin3A	611	Interactions with SUDS3 and SAP130.|Interaction with NCOR1 (By similarity).				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																		---	---	---	---
IREB2	3658	broad.mit.edu	37	15	78780136	78780136	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78780136G>A	uc002bdr.2	+	14	1933	c.1771G>A	c.(1771-1773)GCA>ACA	p.A591T	IREB2_uc010unb.1_Missense_Mutation_p.A341T	NM_004136	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	591							4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)														---	---	---	---
RASGRF1	5923	broad.mit.edu	37	15	79356791	79356791	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79356791G>A	uc002beq.2	-	2	729	c.354C>T	c.(352-354)GAC>GAT	p.D118D	RASGRF1_uc002bep.2_Silent_p.D118D|RASGRF1_uc010blm.1_Silent_p.D40D|RASGRF1_uc002ber.3_Silent_p.D118D	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine	118	PH 1.				activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6																		---	---	---	---
FAH	2184	broad.mit.edu	37	15	80452206	80452206	+	Missense_Mutation	SNP	G	A	A	rs11555097		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80452206G>A	uc002bfj.2	+	4	383	c.301G>A	c.(301-303)GAA>AAA	p.E101K	FAH_uc002bfk.1_Missense_Mutation_p.E101K|FAH_uc002bfm.1_Missense_Mutation_p.E101K|FAH_uc002bfn.1_Missense_Mutation_p.E31K|FAH_uc010unl.1_Missense_Mutation_p.E101K|FAH_uc002bfl.1_Missense_Mutation_p.E101K	NM_000137	NP_000128	P16930	FAAA_HUMAN	fumarylacetoacetase	101					L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	fumarylacetoacetase activity|metal ion binding				0														Tyrosinemia_type_1				---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84611672	84611672	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84611672C>T	uc002bjz.3	+	19	2552	c.2328C>T	c.(2326-2328)GGC>GGT	p.G776G	ADAMTSL3_uc010bmt.1_Silent_p.G776G|ADAMTSL3_uc010bmu.1_Silent_p.G776G	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor	776	TSP type-1 6.					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
ALPK3	57538	broad.mit.edu	37	15	85410563	85410563	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85410563T>A	uc002ble.2	+	13	5512	c.5345T>A	c.(5344-5346)ATG>AAG	p.M1782K	ALPK3_uc010upc.1_Missense_Mutation_p.M83K	NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1782	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	86189060	86189060	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86189060T>C	uc002blv.1	+	10	4419	c.4249T>C	c.(4249-4251)TTC>CTC	p.F1417L	AKAP13_uc002blt.1_Missense_Mutation_p.F1417L|AKAP13_uc002blu.1_Missense_Mutation_p.F1417L|AKAP13_uc010bnf.1_Missense_Mutation_p.F57L|AKAP13_uc010bne.1_Missense_Mutation_p.F70L	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	1417					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																		---	---	---	---
FES	2242	broad.mit.edu	37	15	91428314	91428314	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91428314C>T	uc002bpv.2	+	2	135	c.39C>T	c.(37-39)CAC>CAT	p.H13H	FES_uc010uqj.1_Silent_p.H13H|FES_uc010uqk.1_Silent_p.H13H|FES_uc002bpw.2_RNA|FES_uc010bny.2_Silent_p.H13H|FES_uc002bpx.2_Silent_p.H13H|FES_uc002bpy.2_Silent_p.H13H	NM_002005	NP_001996	P07332	FES_HUMAN	feline sarcoma oncogene isoform 1	13	FCH.|Important for interaction with membranes containing phosphoinositides.				axon guidance|cell proliferation|peptidyl-tyrosine phosphorylation	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(2)	2	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)															---	---	---	---
C15orf51	196968	broad.mit.edu	37	15	100331866	100331866	+	RNA	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100331866T>C	uc010urx.1	-	5		c.2326A>G			C15orf51_uc010ury.1_RNA	NR_003260				Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288.												0																		---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100695507	100695507	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100695507G>A	uc002bvv.1	-	9	1279	c.1200C>T	c.(1198-1200)GAC>GAT	p.D400D	ADAMTS17_uc002bvx.1_Silent_p.D157D	NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1	400	Peptidase M12B.				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)														---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100821466	100821466	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100821466C>T	uc002bvv.1	-	4	836	c.757G>A	c.(757-759)GCC>ACC	p.A253T	ADAMTS17_uc002bvx.1_Missense_Mutation_p.A10T	NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1	253	Peptidase M12B.				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)														---	---	---	---
LRRK1	79705	broad.mit.edu	37	15	101588759	101588759	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101588759A>C	uc002bwr.2	+	22	3515	c.3196A>C	c.(3196-3198)ACA>CCA	p.T1066P	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_Intron	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	1066					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)															---	---	---	---
LUC7L	55692	broad.mit.edu	37	16	239997	239997	+	Missense_Mutation	SNP	C	T	T	rs146490197		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:239997C>T	uc002cgc.1	-	9	1055	c.944G>A	c.(943-945)CGG>CAG	p.R315Q	LUC7L_uc002cga.1_Missense_Mutation_p.R315Q|LUC7L_uc002cgd.1_RNA|LUC7L_uc002cge.1_Missense_Mutation_p.R315Q|LUC7L_uc002cgb.1_Missense_Mutation_p.R229Q	NM_201412	NP_958815	Q9NQ29	LUC7L_HUMAN	LUC7-like isoform b	315	Arg/Ser-rich.						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)																---	---	---	---
UBE2I	7329	broad.mit.edu	37	16	1370217	1370217	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1370217C>T	uc002clc.1	+	5	370	c.266C>T	c.(265-267)TCG>TTG	p.S89L	UBE2I_uc002cld.1_Missense_Mutation_p.S89L|UBE2I_uc002clf.1_Missense_Mutation_p.S89L|UBE2I_uc002clg.1_Missense_Mutation_p.S89L|UBE2I_uc002clh.1_Missense_Mutation_p.S89L|UBE2I_uc002cli.1_Missense_Mutation_p.S89L	NM_194261	NP_919237	P63279	UBC9_HUMAN	ubiquitin-conjugating enzyme E2I	89				VYPS -> GVPF (in Ref. 6; AAC50603).	cell division|chromosome segregation|interspecies interaction between organisms|mitosis|negative regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|protein sumoylation	cytoplasm|PML body|synaptonemal complex	ATP binding|enzyme binding|ubiquitin-protein ligase activity			breast(1)|skin(1)	2		Hepatocellular(780;0.00369)																---	---	---	---
GNPTG	84572	broad.mit.edu	37	16	1412640	1412640	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1412640T>G	uc002clm.2	+	9	673	c.638T>G	c.(637-639)TTT>TGT	p.F213C		NM_032520	NP_115909	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphotransferase, gamma	213						extracellular region|Golgi apparatus	protein binding			central_nervous_system(1)	1		Hepatocellular(780;0.0893)																---	---	---	---
IFT140	9742	broad.mit.edu	37	16	1574907	1574907	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1574907G>A	uc002cmb.2	-	23	3237	c.2875C>T	c.(2875-2877)CGG>TGG	p.R959W	IFT140_uc002clz.2_Missense_Mutation_p.R572W	NM_014714	NP_055529	Q96RY7	IF140_HUMAN	intraflagellar transport 140	959	TPR 4.									ovary(3)|pancreas(1)|skin(1)	5		Hepatocellular(780;0.219)																---	---	---	---
NUBP2	10101	broad.mit.edu	37	16	1837726	1837726	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1837726A>G	uc002cmw.3	+	4	472	c.383A>G	c.(382-384)TAC>TGC	p.Y128C	NUBP2_uc002cmx.3_5'UTR|NUBP2_uc010brx.2_Missense_Mutation_p.Y68C	NM_012225	NP_036357	Q9Y5Y2	NUBP2_HUMAN	nucleotide binding protein 2 (MinD homolog, E.	128						microtubule organizing center|nucleus	4 iron, 4 sulfur cluster binding|ATP binding|metal ion binding|protein binding				0																		---	---	---	---
SLC9A3R2	9351	broad.mit.edu	37	16	2086453	2086453	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2086453G>A	uc002coi.2	+	3	662	c.543G>A	c.(541-543)CCG>CCA	p.P181P	SLC9A3R2_uc002coj.2_Silent_p.P181P|SLC9A3R2_uc002cok.2_Silent_p.P70P	NM_001130012	NP_001123484	Q15599	NHRF2_HUMAN	solute carrier family 9 isoform 3 regulator 2	181	PDZ 2.				protein complex assembly	apical plasma membrane|endomembrane system|nucleus	beta-catenin binding|phosphatase binding|protein C-terminus binding|receptor binding			central_nervous_system(1)	1																		---	---	---	---
DNASE1	1773	broad.mit.edu	37	16	3706167	3706167	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3706167C>T	uc002cvr.2	+	4	2408	c.301C>T	c.(301-303)CGC>TGC	p.R101C		NM_005223	NP_005214	P24855	DNAS1_HUMAN	deoxyribonuclease I precursor	101					apoptosis|DNA catabolic process	extracellular region|nuclear envelope	actin binding|deoxyribonuclease I activity				0		Ovarian(90;0.0261)		Kidney(780;0.0556)	Dornase Alfa(DB00003)								Direct_reversal_of_damage					---	---	---	---
GLIS2	84662	broad.mit.edu	37	16	4384878	4384878	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4384878C>G	uc002cwc.1	+	3	479	c.422C>G	c.(421-423)GCC>GGC	p.A141G		NM_032575	NP_115964	Q9BZE0	GLIS2_HUMAN	GLIS family zinc finger 2	141	Interaction with CTNND1 (By similarity).				cell differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development	cytoplasm|nuclear speck	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|transcription regulatory region DNA binding|zinc ion binding				0																		---	---	---	---
CORO7	79585	broad.mit.edu	37	16	4409582	4409582	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4409582G>T	uc002cwh.3	-	22	2269	c.2149C>A	c.(2149-2151)CTG>ATG	p.L717M	CORO7_uc002cwe.2_RNA|CORO7_uc002cwf.2_Missense_Mutation_p.L717M|CORO7_uc002cwg.3_Missense_Mutation_p.L497M|CORO7_uc010uxh.1_Missense_Mutation_p.L699M|CORO7_uc010uxi.1_Missense_Mutation_p.L632M|CORO7_uc002cwi.1_Missense_Mutation_p.L497M	NM_024535	NP_078811	P57737	CORO7_HUMAN	coronin 7	717						cytoplasmic membrane-bounded vesicle|cytosol|Golgi membrane|integral to membrane of membrane fraction|soluble fraction					0																OREG0023580	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PPL	5493	broad.mit.edu	37	16	4933690	4933690	+	Missense_Mutation	SNP	G	A	A	rs140094738	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4933690G>A	uc002cyd.1	-	22	5056	c.4966C>T	c.(4966-4968)CGC>TGC	p.R1656C		NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin	1656	Plectin 1.				keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
ALG1	56052	broad.mit.edu	37	16	5129739	5129739	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5129739C>T	uc002cym.2	+						ALG1_uc002cyj.2_Intron|ALG1_uc002cyn.2_Intron|ALG1_uc010bue.2_Intron|ALG1_uc010uxy.1_Intron	NM_019109	NP_061982			beta-1,4-mannosyltransferase						dolichol-linked oligosaccharide biosynthetic process|lipopolysaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	chitobiosyldiphosphodolichol beta-mannosyltransferase activity			upper_aerodigestive_tract(1)|ovary(1)	2		Ovarian(90;0.0164)																---	---	---	---
ATF7IP2	80063	broad.mit.edu	37	16	10575765	10575765	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10575765A>C	uc002czu.2	+	12	1935	c.1708A>C	c.(1708-1710)ACC>CCC	p.T570P	ATF7IP2_uc002czv.2_3'UTR|ATF7IP2_uc010uyo.1_RNA|ATF7IP2_uc010uyp.1_Missense_Mutation_p.T114P|ATF7IP2_uc002czw.2_Missense_Mutation_p.T570P|ATF7IP2_uc010uyq.1_RNA	NM_024997	NP_079273	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting	570					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0																		---	---	---	---
ZC3H7A	29066	broad.mit.edu	37	16	11868230	11868230	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11868230C>T	uc002dbk.2	-	8	963	c.765G>A	c.(763-765)CTG>CTA	p.L255L	ZC3H7A_uc002dbl.2_Silent_p.L255L|ZC3H7A_uc002dbm.1_Silent_p.L255L	NM_014153	NP_054872	Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	255						nucleus	nucleic acid binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
MKL2	57496	broad.mit.edu	37	16	14234605	14234605	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14234605G>A	uc010uza.1	+	3	297	c.142G>A	c.(142-144)GAA>AAA	p.E48K	MKL2_uc002dcg.2_Missense_Mutation_p.E48K	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein	Error:Variant_position_missing_in_Q9ULH7_after_alignment					cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
PARN	5073	broad.mit.edu	37	16	14540788	14540788	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14540788C>A	uc010uzd.1	-	23	1963	c.1821G>T	c.(1819-1821)AAG>AAT	p.K607N	PARN_uc010uzc.1_Missense_Mutation_p.K546N|PARN_uc010uze.1_Missense_Mutation_p.K561N|PARN_uc010uzf.1_Missense_Mutation_p.K432N	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation	607					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																		---	---	---	---
ABCC1	4363	broad.mit.edu	37	16	16235147	16235147	+	3'UTR	SNP	G	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16235147G>C	uc010bvi.2	+	31					ABCC1_uc010bvj.2_3'UTR|ABCC1_uc010bvk.2_3'UTR|ABCC1_uc010bvl.2_3'UTR|ABCC1_uc010bvm.2_3'UTR|ABCC1_uc002del.3_3'UTR	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)													---	---	---	---
C16orf62	57020	broad.mit.edu	37	16	19710946	19710946	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19710946C>T	uc002dgn.1	+	30	2781	c.2769C>T	c.(2767-2769)CAC>CAT	p.H923H	C16orf62_uc002dgo.1_Silent_p.H830H|C16orf62_uc002dgp.1_Silent_p.H672H	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020	923						integral to membrane				ovary(1)	1																		---	---	---	---
PDILT	204474	broad.mit.edu	37	16	20373737	20373737	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20373737C>T	uc002dhc.1	-	10	1628	c.1405G>A	c.(1405-1407)GGC>AGC	p.G469S		NM_174924	NP_777584	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis	469					cell differentiation|cell redox homeostasis|multicellular organismal development|spermatogenesis	endoplasmic reticulum	isomerase activity			large_intestine(1)	1																		---	---	---	---
IGSF6	10261	broad.mit.edu	37	16	21663892	21663892	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21663892C>T	uc002djg.1	-	1	81	c.28G>A	c.(28-30)GCT>ACT	p.A10T	uc002diq.3_Intron|METTL9_uc002dje.2_Intron|METTL9_uc002djf.2_Intron|IGSF6_uc010vbi.1_Missense_Mutation_p.A10T	NM_005849	NP_005840	O95976	IGSF6_HUMAN	immunoglobulin superfamily, member 6 precursor	10					cell surface receptor linked signaling pathway|immune response	integral to plasma membrane	transmembrane receptor activity				0				GBM - Glioblastoma multiforme(48;0.066)														---	---	---	---
EEF2K	29904	broad.mit.edu	37	16	22268710	22268710	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22268710C>T	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)														---	---	---	---
TNRC6A	27327	broad.mit.edu	37	16	24817959	24817959	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24817959T>C	uc002dmm.2	+	17	4508	c.4394T>C	c.(4393-4395)TTG>TCG	p.L1465S	TNRC6A_uc010bxs.2_Missense_Mutation_p.L1212S|TNRC6A_uc002dmn.2_Missense_Mutation_p.L1163S|TNRC6A_uc002dmo.2_Missense_Mutation_p.L1104S|TNRC6A_uc002dmp.2_Missense_Mutation_p.L66S|TNRC6A_uc002dmq.2_Missense_Mutation_p.L132S	NM_014494	NP_055309	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1465					negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|micro-ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0394)														---	---	---	---
GTF3C1	2975	broad.mit.edu	37	16	27475926	27475926	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27475926G>A	uc002dov.1	-	34	5627	c.5587C>T	c.(5587-5589)CGC>TGC	p.R1863C	GTF3C1_uc002dou.2_Missense_Mutation_p.R1863C	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	1863						transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5																		---	---	---	---
ATXN2L	11273	broad.mit.edu	37	16	28846629	28846629	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28846629C>G	uc002drc.2	+	20	2762	c.2594C>G	c.(2593-2595)GCC>GGC	p.A865G	uc010vct.1_Intron|ATXN2L_uc002drb.2_Missense_Mutation_p.A865G|ATXN2L_uc002dqy.2_Missense_Mutation_p.A865G|ATXN2L_uc002dra.2_Missense_Mutation_p.A865G|ATXN2L_uc002dqz.2_Missense_Mutation_p.A865G|ATXN2L_uc010vdb.1_Missense_Mutation_p.A871G|ATXN2L_uc002dre.2_Missense_Mutation_p.A865G|ATXN2L_uc002drf.2_Missense_Mutation_p.A274G|ATXN2L_uc002drg.2_Missense_Mutation_p.A147G	NM_007245	NP_009176	Q8WWM7	ATX2L_HUMAN	ataxin 2 related protein isoform A	865						membrane				upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
SH2B1	25970	broad.mit.edu	37	16	28878130	28878130	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28878130G>A	uc002dri.2	+	4	1154	c.715G>A	c.(715-717)GCC>ACC	p.A239T	uc010vct.1_Intron|SH2B1_uc010vdc.1_Intron|SH2B1_uc002drj.2_Missense_Mutation_p.A239T|SH2B1_uc002drk.2_Missense_Mutation_p.A239T|SH2B1_uc002drl.2_Missense_Mutation_p.A239T|SH2B1_uc010vdd.1_Intron|SH2B1_uc010vde.1_Missense_Mutation_p.A239T|SH2B1_uc002drm.2_Missense_Mutation_p.A239T	NM_001145795	NP_001139267	Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1 isoform 1	239	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation) (By similarity).|Required for NGF signaling (By similarity).				blood coagulation|intracellular signal transduction	cytosol|membrane|nucleus	signal transducer activity			ovary(2)	2																		---	---	---	---
RABEP2	79874	broad.mit.edu	37	16	28925566	28925566	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28925566C>T	uc002drq.2	-	5	933	c.885G>A	c.(883-885)CTG>CTA	p.L295L	uc010vct.1_Intron|RABEP2_uc010vdf.1_Silent_p.L224L|RABEP2_uc010byn.2_Silent_p.L295L|RABEP2_uc002drr.2_Silent_p.L295L	NM_024816	NP_079092	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	295	Potential.				endocytosis|protein transport	early endosome	growth factor activity|GTPase activator activity			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
NFATC2IP	84901	broad.mit.edu	37	16	28970351	28970351	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28970351C>T	uc002dru.2	+	7	1046	c.1031C>T	c.(1030-1032)ACG>ATG	p.T344M	uc010vct.1_Intron|NFATC2IP_uc002drt.2_Missense_Mutation_p.T65M|NFATC2IP_uc002drv.2_Missense_Mutation_p.T63M|NFATC2IP_uc010vdh.1_Missense_Mutation_p.T52M	NM_032815	NP_116204	Q8NCF5	NF2IP_HUMAN	nuclear factor of activated T-cells,	344						cytoplasm|nucleus				ovary(1)	1																		---	---	---	---
ITGAL	3683	broad.mit.edu	37	16	30507880	30507880	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30507880G>A	uc002dyi.3	+	15	2001	c.1825G>A	c.(1825-1827)GTG>ATG	p.V609M	ITGAL_uc002dyj.3_Missense_Mutation_p.V526M|ITGAL_uc010vev.1_Intron	NM_002209	NP_002200	P20701	ITAL_HUMAN	integrin alpha L isoform a precursor	609	FG-GAP 7.|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)													---	---	---	---
SRCAP	10847	broad.mit.edu	37	16	30732518	30732518	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30732518T>C	uc002dze.1	+	21	3647	c.3262T>C	c.(3262-3264)TCC>CCC	p.S1088P	SRCAP_uc002dzf.2_Intron|SRCAP_uc002dzg.1_Missense_Mutation_p.S945P|SRCAP_uc010bzz.1_Missense_Mutation_p.S658P	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	1088	Pro-rich.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)															---	---	---	---
SRCAP	10847	broad.mit.edu	37	16	30744953	30744953	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30744953C>T	uc002dze.1	+	29	6713	c.6328C>T	c.(6328-6330)CGC>TGC	p.R2110C	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Missense_Mutation_p.R1905C	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	2110	Helicase C-terminal.				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	31088883	31088883	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31088883C>T	uc002eap.2	+	2	1527	c.1238C>T	c.(1237-1239)GCG>GTG	p.A413V		NM_014699	NP_055514	O15015	ZN646_HUMAN	zinc finger protein 646	413	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(2)	2																		---	---	---	---
ITGAX	3687	broad.mit.edu	37	16	31371765	31371765	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31371765T>C	uc002ebu.1	+	8	909	c.842T>C	c.(841-843)ATC>ACC	p.I281T	ITGAX_uc002ebt.2_Missense_Mutation_p.I281T|ITGAX_uc010vfk.1_5'Flank	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	281	VWFA.|Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ITGAX	3687	broad.mit.edu	37	16	31391664	31391664	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31391664C>A	uc002ebu.1	+	27	3205	c.3138C>A	c.(3136-3138)ACC>ACA	p.T1046T	ITGAX_uc002ebt.2_Silent_p.T1046T	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	1046	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ORC6L	23594	broad.mit.edu	37	16	46731427	46731427	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46731427A>G	uc002eeh.2	+	7	749	c.689A>G	c.(688-690)CAG>CGG	p.Q230R		NM_014321	NP_055136	Q9Y5N6	ORC6_HUMAN	origin recognition complex subunit 6	230					cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA binding|protein binding				0		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)																---	---	---	---
ABCC12	94160	broad.mit.edu	37	16	48119514	48119514	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48119514C>T	uc002efc.1	-	27	4164	c.3818G>A	c.(3817-3819)CGT>CAT	p.R1273H	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_RNA|ABCC12_uc002efa.1_RNA|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_RNA	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	1273	ABC transporter 2.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)																---	---	---	---
ABCC12	94160	broad.mit.edu	37	16	48120729	48120729	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48120729A>G	uc002efc.1	-	26	3983	c.3637T>C	c.(3637-3639)TAC>CAC	p.Y1213H	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_Intron|ABCC12_uc002efa.1_Intron|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_Intron	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	1213	ABC transporter 2.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)																---	---	---	---
CBLN1	869	broad.mit.edu	37	16	49315194	49315194	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49315194C>A	uc002efq.2	-	1	522	c.183G>T	c.(181-183)AAG>AAT	p.K61N		NM_004352	NP_004343	P23435	CBLN1_HUMAN	cerebellin 1 precursor	61	C1q.				nervous system development|synaptic transmission	cell junction|extracellular region|synapse					0		all_cancers(37;0.0766)|all_lung(18;0.24)																---	---	---	---
CYLD	1540	broad.mit.edu	37	16	50815288	50815288	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50815288G>A	uc002egp.1	+	10	2065	c.1650G>A	c.(1648-1650)CCG>CCA	p.P550P	CYLD_uc002ego.2_Silent_p.P547P|CYLD_uc010cbs.1_Silent_p.P547P|CYLD_uc002egq.1_Silent_p.P547P|CYLD_uc002egr.1_Silent_p.P547P|CYLD_uc002egs.1_Silent_p.P547P	NM_015247	NP_056062	Q9NQC7	CYLD_HUMAN	ubiquitin carboxyl-terminal hydrolase CYLD	550	Interaction with TRIP.|Interaction with IKBKG/NEMO.				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				---	---	---	---
RPGRIP1L	23322	broad.mit.edu	37	16	53682940	53682940	+	Missense_Mutation	SNP	C	T	T	rs142349647	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53682940C>T	uc002ehp.2	-	16	2304	c.2240G>A	c.(2239-2241)CGA>CAA	p.R747Q	RPGRIP1L_uc002eho.3_Missense_Mutation_p.R747Q|RPGRIP1L_uc010vgy.1_Missense_Mutation_p.R747Q|RPGRIP1L_uc010cbx.2_Missense_Mutation_p.R747Q|RPGRIP1L_uc010vgz.1_Missense_Mutation_p.R747Q	NM_015272	NP_056087	Q68CZ1	FTM_HUMAN	RPGRIP1-like isoform a	747					negative regulation of G-protein coupled receptor protein signaling pathway	cell-cell junction|centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)																---	---	---	---
IRX3	79191	broad.mit.edu	37	16	54318212	54318212	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54318212G>A	uc002eht.1	-	3	1813	c.1397C>T	c.(1396-1398)GCC>GTC	p.A466V		NM_024336	NP_077312	P78415	IRX3_HUMAN	iroquois homeobox 3	466					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
NLRC5	84166	broad.mit.edu	37	16	57060011	57060011	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57060011C>T	uc002ekk.1	+	6	1381	c.1156C>T	c.(1156-1158)CGG>TGG	p.R386W	NLRC5_uc010ccq.1_RNA|NLRC5_uc002ekn.2_Missense_Mutation_p.R191W|NLRC5_uc002ekl.2_Missense_Mutation_p.R191W|NLRC5_uc002ekm.2_Missense_Mutation_p.R191W|NLRC5_uc010ccr.1_RNA	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27	386	NACHT.				defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)																---	---	---	---
NLRC5	84166	broad.mit.edu	37	16	57060522	57060522	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57060522G>A	uc002ekk.1	+	6	1892	c.1667G>A	c.(1666-1668)GGC>GAC	p.G556D	NLRC5_uc010ccq.1_RNA|NLRC5_uc002ekn.2_Missense_Mutation_p.G361D|NLRC5_uc002ekl.2_Missense_Mutation_p.G361D|NLRC5_uc002ekm.2_Missense_Mutation_p.G361D|NLRC5_uc010ccr.1_RNA	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27	556					defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)																---	---	---	---
CPNE2	221184	broad.mit.edu	37	16	57181521	57181521	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57181521A>G	uc002eks.1	+	16	1827	c.1598A>G	c.(1597-1599)CAG>CGG	p.Q533R	CPNE2_uc010cct.1_Missense_Mutation_p.Q559R|CPNE2_uc010ccu.1_Missense_Mutation_p.Q533R|CPNE2_uc002ekt.1_3'UTR	NM_152727	NP_689940	Q96FN4	CPNE2_HUMAN	copine II	533										central_nervous_system(1)|skin(1)	2		all_neural(199;0.224)																---	---	---	---
CCDC135	84229	broad.mit.edu	37	16	57760011	57760011	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57760011C>T	uc002emi.2	+	13	1879	c.1790C>T	c.(1789-1791)GCG>GTG	p.A597V	CCDC135_uc002emj.2_Missense_Mutation_p.A597V|CCDC135_uc002emk.2_Missense_Mutation_p.A532V	NM_032269	NP_115645	Q8IY82	CC135_HUMAN	coiled-coil domain containing 135	597						cytoplasm				central_nervous_system(1)	1																		---	---	---	---
PRSS54	221191	broad.mit.edu	37	16	58324964	58324964	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58324964C>T	uc002enf.2	-	4	557	c.162G>A	c.(160-162)CCG>CCA	p.P54P	PRSS54_uc002eng.2_Silent_p.P54P|PRSS54_uc010vie.1_Intron	NM_001080492	NP_001073961	Q6PEW0	PRS54_HUMAN	plasma kallikrein-like protein 4 precursor	54	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58581500	58581500	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58581500T>C	uc002env.2	-	26	3902	c.3609A>G	c.(3607-3609)ACA>ACG	p.T1203T	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Silent_p.T1198T|CNOT1_uc002enx.2_Silent_p.T1203T|CNOT1_uc010vik.1_Intron	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1203					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	58581512	58581512	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58581512T>C	uc002env.2	-	26	3890	c.3597A>G	c.(3595-3597)CTA>CTG	p.L1199L	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Silent_p.L1194L|CNOT1_uc002enx.2_Silent_p.L1199L|CNOT1_uc010vik.1_Intron	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1199					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)														---	---	---	---
CDH5	1003	broad.mit.edu	37	16	66436800	66436800	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66436800G>A	uc002eom.3	+	12	2239	c.2083G>A	c.(2083-2085)GCG>ACG	p.A695T		NM_001795	NP_001786	P33151	CADH5_HUMAN	cadherin 5, type 2 preproprotein	695	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|regulation of establishment of cell polarity	integral to membrane|membrane fraction	beta-catenin binding|calcium ion binding|ion channel binding|receptor binding			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)														---	---	---	---
NAE1	8883	broad.mit.edu	37	16	66847501	66847501	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66847501C>T	uc002eqf.2	-	13	1077	c.1000G>A	c.(1000-1002)GCA>ACA	p.A334T	NAE1_uc002eqe.2_Missense_Mutation_p.A328T|NAE1_uc002eqg.2_Missense_Mutation_p.A245T|NAE1_uc010cdv.2_Missense_Mutation_p.A337T	NM_003905	NP_003896	Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1 isoform a	334	Interaction with UBA3.				apoptosis|cell cycle|DNA replication|mitotic cell cycle DNA replication checkpoint|protein neddylation|signal transduction	cytoplasm|insoluble fraction|plasma membrane	catalytic activity|protein heterodimerization activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)													---	---	---	---
FHOD1	29109	broad.mit.edu	37	16	67268086	67268086	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67268086G>A	uc002esl.2	-	13	1632	c.1520C>T	c.(1519-1521)GCC>GTC	p.A507V	FHOD1_uc010ced.2_Missense_Mutation_p.A314V|FHOD1_uc010vjh.1_Missense_Mutation_p.A167V	NM_013241	NP_037373	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	507	FH1.				actin cytoskeleton organization	cytoplasm|cytoskeleton|nucleus	actin binding			breast(2)|ovary(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)														---	---	---	---
CDH1	999	broad.mit.edu	37	16	68835713	68835713	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68835713G>A	uc002ewg.1	+	3	428	c.304G>A	c.(304-306)GCC>ACC	p.A102T	CDH1_uc010vlj.1_RNA|CDH1_uc010cfg.1_Missense_Mutation_p.A102T	NM_004360	NP_004351	P12830	CADH1_HUMAN	cadherin 1, type 1 preproprotein	102					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				---	---	---	---
MTSS1L	92154	broad.mit.edu	37	16	70714936	70714936	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70714936G>A	uc002ezj.2	-						MTSS1L_uc002ezk.1_5'Flank	NM_138383	NP_612392			metastasis suppressor 1-like						filopodium assembly|signal transduction		actin binding|cytoskeletal adaptor activity|SH3 domain binding			central_nervous_system(1)	1																		---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	70977708	70977708	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70977708G>A	uc002ezr.2	-							NM_032821	NP_116210			hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
ZNF19	7567	broad.mit.edu	37	16	71509780	71509780	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71509780G>A	uc010cgc.1	-	6	1176	c.670C>T	c.(670-672)CGA>TGA	p.R224*	ZNF23_uc002fai.2_Intron|ZNF19_uc002fak.1_Nonsense_Mutation_p.R212*|ZNF19_uc002fal.1_Nonsense_Mutation_p.R212*|ZNF19_uc002fam.1_Nonsense_Mutation_p.R224*	NM_006961	NP_008892	P17023	ZNF19_HUMAN	zinc finger protein 19	224	C2H2-type 3.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)														---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72830135	72830135	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72830135C>T	uc002fck.2	-	9	7119	c.6446G>A	c.(6445-6447)CGC>CAC	p.R2149H	ZFHX3_uc002fcl.2_Missense_Mutation_p.R1235H	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	2149	Homeobox 1.				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	72984509	72984509	+	Silent	SNP	G	A	A	rs137984545	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72984509G>A	uc002fck.2	-	3	3748	c.3075C>T	c.(3073-3075)AAC>AAT	p.N1025N	ZFHX3_uc002fcl.2_Silent_p.N111N	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	1025					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	72993351	72993351	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72993351G>A	uc002fck.2	-	2	1367	c.694C>T	c.(694-696)CGC>TGC	p.R232C	ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	232					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)																---	---	---	---
CHST5	23563	broad.mit.edu	37	16	75563418	75563418	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75563418G>A	uc002fei.2	-	3	2260	c.865C>T	c.(865-867)CGC>TGC	p.R289C	CHST5_uc002fej.1_Missense_Mutation_p.R295C	NM_024533	NP_078809	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	289	Lumenal (Potential).				N-acetylglucosamine metabolic process|protein sulfation	integral to membrane|intrinsic to Golgi membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0																		---	---	---	---
KARS	3735	broad.mit.edu	37	16	75669691	75669691	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75669691G>A	uc002feq.2	-	6	730	c.682C>T	c.(682-684)CGC>TGC	p.R228C	KARS_uc002fer.2_Missense_Mutation_p.R256C|KARS_uc002fes.2_Missense_Mutation_p.R72C|KARS_uc010cgz.2_Missense_Mutation_p.R72C	NM_005548	NP_005539	Q15046	SYK_HUMAN	lysyl-tRNA synthetase isoform 2	228					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)													---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77369762	77369762	+	Missense_Mutation	SNP	C	T	T	rs149189203	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77369762C>T	uc002ffc.3	-	12	2169	c.1750G>A	c.(1750-1752)GGG>AGG	p.G584R	ADAMTS18_uc010chc.1_Missense_Mutation_p.G172R|ADAMTS18_uc002ffe.1_Missense_Mutation_p.G280R	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	584					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																		---	---	---	---
OSGIN1	29948	broad.mit.edu	37	16	83994222	83994222	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83994222G>A	uc002fha.2	+	5	885	c.502G>A	c.(502-504)GTG>ATG	p.V168M	OSGIN1_uc002fhb.2_Missense_Mutation_p.V85M|OSGIN1_uc002fhc.2_Missense_Mutation_p.V85M	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	168					cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0																		---	---	---	---
MBTPS1	8720	broad.mit.edu	37	16	84088130	84088130	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84088130G>A	uc002fhi.2	-	23	3585	c.3083C>T	c.(3082-3084)CCG>CTG	p.P1028L	MBTPS1_uc002fhh.2_Missense_Mutation_p.P532L	NM_003791	NP_003782	Q14703	MBTP1_HUMAN	membrane-bound transcription factor site-1	1028	Arg/Lys/Pro-rich (basic).|Cytoplasmic (Potential).				cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
MBTPS1	8720	broad.mit.edu	37	16	84100196	84100196	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84100196C>T	uc002fhi.2	-	17	2753	c.2251G>A	c.(2251-2253)GGA>AGA	p.G751R	MBTPS1_uc002fhh.2_Missense_Mutation_p.G255R	NM_003791	NP_003782	Q14703	MBTP1_HUMAN	membrane-bound transcription factor site-1	751	Lumenal (Potential).				cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
TAF1C	9013	broad.mit.edu	37	16	84216839	84216839	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84216839G>A	uc002fhn.2	-						TAF1C_uc002fhm.2_Intron|TAF1C_uc010vnx.1_Intron|TAF1C_uc010vny.1_Intron|TAF1C_uc010vnz.1_Intron|TAF1C_uc002fho.2_Intron|TAF1C_uc010voa.1_Intron|TAF1C_uc002fhp.1_Intron|TAF1C_uc010vob.1_Intron	NM_005679	NP_005670			TBP-associated factor 1C isoform 1						regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding			ovary(1)	1																		---	---	---	---
FAM92B	339145	broad.mit.edu	37	16	85132790	85132790	+	3'UTR	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85132790G>A	uc010vok.1	-	8						NM_198491	NP_940893			hypothetical protein LOC339145											central_nervous_system(1)	1																		---	---	---	---
FOXF1	2294	broad.mit.edu	37	16	86544392	86544392	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86544392G>A	uc002fjl.2	+	1	260	c.217G>A	c.(217-219)GAG>AAG	p.E73K	uc002fjk.1_5'Flank	NM_001451	NP_001442	Q12946	FOXF1_HUMAN	forkhead box F1	73	Fork-head.				branching involved in open tracheal system development|cardiac left ventricle morphogenesis|embryonic ectodermal digestive tract morphogenesis|endocardial cushion development|in utero embryonic development|lung vasculature development|midgut development|pancreas development|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|ureter development|venous blood vessel development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding				0																		---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89351372	89351372	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89351372G>A	uc002fmx.1	-	9	2039	c.1578C>T	c.(1576-1578)CAC>CAT	p.H526H	ANKRD11_uc002fmy.1_Silent_p.H526H|ANKRD11_uc002fnc.1_Silent_p.H526H|ANKRD11_uc002fnb.1_Silent_p.H483H	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	526	Ser-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)														---	---	---	---
GAS8	2622	broad.mit.edu	37	16	90094141	90094141	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90094141C>T	uc002fqi.1	+						GAS8_uc010vps.1_Intron|GAS8_uc002fqh.2_Intron|GAS8_uc010vpt.1_Intron|GAS8_uc010vpu.1_Intron|GAS8_uc010vpv.1_Intron|GAS8_uc010cjc.1_Intron|GAS8_uc010vpw.1_Intron|GAS8_uc002fqj.1_Intron	NM_001481	NP_001472			growth arrest-specific 8						negative regulation of cell proliferation|sperm motility	cilium|Golgi apparatus|microtubule|microtubule basal body|microtubule-based flagellum	protein 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;0.029)														---	---	---	---
TRPV3	162514	broad.mit.edu	37	17	3431412	3431412	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3431412C>T	uc002fvt.1	-	11	1732	c.1410G>A	c.(1408-1410)CCG>CCA	p.P470P	TRPV3_uc002fvs.1_RNA|TRPV3_uc010vrh.1_Silent_p.P454P|TRPV3_uc010vri.1_Silent_p.P425P|TRPV3_uc010vrj.1_Silent_p.P454P|TRPV3_uc010vrk.1_RNA|TRPV3_uc010vrl.1_Silent_p.P454P|TRPV3_uc010vrm.1_RNA|TRPV3_uc002fvr.2_Silent_p.P470P|TRPV3_uc002fvu.2_Silent_p.P470P|TRPV3_uc010vrn.1_Silent_p.P52P	NM_145068	NP_659505	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel,	470	Extracellular (Potential).					integral to membrane	calcium channel activity			ovary(4)	4					Menthol(DB00825)													---	---	---	---
CAMKK1	84254	broad.mit.edu	37	17	3786397	3786397	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3786397A>G	uc002fwt.2	-	6	681	c.587T>C	c.(586-588)GTG>GCG	p.V196A	CAMKK1_uc002fwu.2_Missense_Mutation_p.V196A|CAMKK1_uc002fwv.2_Missense_Mutation_p.V196A	NM_172206	NP_757343	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase 1	196	Protein kinase.				synaptic transmission	cytosol|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)														---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3926101	3926101	+	Missense_Mutation	SNP	G	A	A	rs149535137		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3926101G>A	uc002fxe.2	-	44	7178	c.7114C>T	c.(7114-7116)CGT>TGT	p.R2372C	ZZEF1_uc002fxh.2_Missense_Mutation_p.R686C|ZZEF1_uc002fxi.2_Missense_Mutation_p.R607C	NM_015113	NP_055928	O43149	ZZEF1_HUMAN	zinc finger, ZZ type with EF hand domain 1	2372							calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	4020254	4020254	+	Intron	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4020254A>C	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																		---	---	---	---
MYBBP1A	10514	broad.mit.edu	37	17	4448573	4448573	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4448573C>T	uc002fyb.3	-	16	2203	c.2141G>A	c.(2140-2142)CGG>CAG	p.R714Q	MYBBP1A_uc002fxz.3_Missense_Mutation_p.R714Q|MYBBP1A_uc002fya.3_5'Flank|MYBBP1A_uc010vsa.1_5'Flank	NM_014520	NP_055335	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 2	714					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																		---	---	---	---
USP6	9098	broad.mit.edu	37	17	5041042	5041042	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5041042C>T	uc002gau.1	+	20	3152	c.922C>T	c.(922-924)CAG>TAG	p.Q308*	USP6_uc002gav.1_Nonsense_Mutation_p.Q308*|USP6_uc010ckz.1_5'UTR|uc002gbd.2_5'Flank	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6	308					protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5								T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								---	---	---	---
CLEC10A	10462	broad.mit.edu	37	17	6978516	6978516	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6978516C>T	uc002gek.2	-	9	1111	c.808G>A	c.(808-810)GAC>AAC	p.D270N	CLEC10A_uc002gej.2_Missense_Mutation_p.D246N|CLEC10A_uc002gel.2_Missense_Mutation_p.D243N|CLEC10A_uc010clv.1_3'UTR	NM_182906	NP_878910	Q8IUN9	CLC10_HUMAN	C-type lectin, superfamily member 14 isoform 1	270	C-type lectin.|Extracellular (Potential).				endocytosis|innate immune response	integral to membrane|plasma membrane	sugar binding				0																		---	---	---	---
DLG4	1742	broad.mit.edu	37	17	7106649	7106649	+	Splice_Site	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7106649C>T	uc002get.3	-	9	1836	c.635_splice	c.e9-1	p.G212_splice	DLG4_uc010vtm.1_Splice_Site|DLG4_uc010vtn.1_Splice_Site_p.G109_splice|DLG4_uc010cly.2_Splice_Site_p.G166_splice|DLG4_uc010vto.1_Splice_Site_p.G209_splice|DLG4_uc002geu.2_Splice_Site_p.G166_splice	NM_001365	NP_001356			post-synaptic density protein 95 isoform 1						axon guidance|learning|protein complex assembly|protein localization to synapse|signal transduction|synaptic transmission	cell junction|cortical cytoskeleton|endocytic vesicle membrane|neuron spine|postsynaptic density|postsynaptic membrane|synaptosome	protein binding|protein C-terminus binding			ovary(1)|breast(1)	2																		---	---	---	---
AMAC1L3	643664	broad.mit.edu	37	17	7386241	7386241	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7386241C>T	uc010cmj.1	+	2	1053	c.938C>T	c.(937-939)GCA>GTA	p.A313V	ZBTB4_uc002ghd.3_Intron|POLR2A_uc002ghe.2_5'Flank|POLR2A_uc002ghf.3_5'Flank	NM_001102614	NP_001096084	P0C7Q6	AMCL3_HUMAN	acyl-malonyl condensing enzyme 1-like 3	313	DUF6 2.|Helical; (Potential).					integral to membrane					0		Prostate(122;0.173)																---	---	---	---
TP53	7157	broad.mit.edu	37	17	7577121	7577121	+	Missense_Mutation	SNP	G	A	A	rs121913343		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577121G>A	uc002gim.2	-	8	1011	c.817C>T	c.(817-819)CGT>TGT	p.R273C	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.R273C|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R141C|TP53_uc010cng.1_Missense_Mutation_p.R141C|TP53_uc002gii.1_Missense_Mutation_p.R141C|TP53_uc010cnh.1_Missense_Mutation_p.R273C|TP53_uc010cni.1_Missense_Mutation_p.R273C|TP53_uc002gij.2_Missense_Mutation_p.R273C	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	273	Interaction with DNA.||Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (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.R273H(467)|p.R273C(396)|p.R273L(83)|p.R273P(24)|p.R273S(11)|p.R273G(9)|p.0?(7)|p.R273fs*72(3)|p.?(2)|p.R273fs*33(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273R(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(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)		R273C(SH10TC_STOMACH)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(RH30_SOFT_TISSUE)|R273C(PANC0213_PANCREAS)|R273C(SJRH30_SOFT_TISSUE)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(TT2609C02_THYROID)|R273C(MFE319_ENDOMETRIUM)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(NCIH1048_LUNG)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	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)			---	---	---	---
CHD3	1107	broad.mit.edu	37	17	7810789	7810789	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7810789G>T	uc002gje.2	+	32	5057	c.4907G>T	c.(4906-4908)GGG>GTG	p.G1636V	CHD3_uc002gjd.2_Missense_Mutation_p.G1695V|CHD3_uc002gjf.2_Missense_Mutation_p.G1636V|CHD3_uc002gjh.2_Missense_Mutation_p.G212V|CHD3_uc002gjj.2_5'Flank	NM_001005273	NP_001005273	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1636	Required for interaction with PCNT.				chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)																---	---	---	---
ALOX12B	242	broad.mit.edu	37	17	7978911	7978911	+	Splice_Site	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7978911A>G	uc002gjy.1	-	12	1915	c.1654_splice	c.e12+1	p.G552_splice		NM_001139	NP_001130			arachidonate 12-lipoxygenase, 12R type						epidermis development|leukotriene biosynthetic process		arachidonate 12-lipoxygenase activity|iron ion binding|lipoxygenase activity				0															Multiple Myeloma(8;0.094)			---	---	---	---
TMEM107	84314	broad.mit.edu	37	17	8077915	8077915	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8077915A>G	uc002gkg.3	-	4	386	c.276T>C	c.(274-276)AGT>AGC	p.S92S	TMEM107_uc002gkh.3_Silent_p.S98S|TMEM107_uc002gki.3_Silent_p.S98S|TMEM107_uc002gkj.3_Intron|TMEM107_uc002gkk.2_3'UTR	NM_183065	NP_898888	Q6UX40	TM107_HUMAN	transmembrane protein 107 isoform 2	92	Helical; (Potential).					integral to membrane					0																		---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8393780	8393780	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8393780C>T	uc002gll.2	-	33	4765	c.4669G>A	c.(4669-4671)GCC>ACC	p.A1557T	MYH10_uc002glm.2_Missense_Mutation_p.A1588T|MYH10_uc010cnx.2_Missense_Mutation_p.A1566T	NM_005964	NP_005955	P35580	MYH10_HUMAN	myosin, heavy polypeptide 10, non-muscle	1557	Potential.				actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
WDR16	146845	broad.mit.edu	37	17	9515631	9515631	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9515631T>A	uc002gly.2	+	8	929	c.860T>A	c.(859-861)ATT>AAT	p.I287N	WDR16_uc002glz.2_Missense_Mutation_p.I219N|WDR16_uc010coc.2_Missense_Mutation_p.I297N	NM_145054	NP_659491	Q8N1V2	WDR16_HUMAN	WD40-repeat protein upregulated in HCC isoform	287						cytoplasm|intracellular membrane-bounded organelle	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
MYH8	4626	broad.mit.edu	37	17	10303844	10303844	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10303844C>T	uc002gmm.2	-	27	3693	c.3598G>A	c.(3598-3600)GCA>ACA	p.A1200T	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1200	Potential.				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	10355428	10355428	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10355428C>T	uc002gmn.2	-	27	3679	c.3568G>A	c.(3568-3570)GAA>AAA	p.E1190K	uc002gml.1_Intron	NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	1190	Potential.				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																		---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11713626	11713626	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11713626A>G	uc002gne.2	+	45	8715	c.8647A>G	c.(8647-8649)ACT>GCT	p.T2883A	DNAH9_uc010coo.2_Missense_Mutation_p.T2177A	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	2883	AAA 4 (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)														---	---	---	---
LRRC48	83450	broad.mit.edu	37	17	17897742	17897742	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17897742C>T	uc010vxd.1	+						LRRC48_uc002gsa.2_Intron|LRRC48_uc010vxc.1_Intron|LRRC48_uc002gsb.2_Intron	NM_001130090	NP_001123562			leucine rich repeat containing 48 isoform a							cytoplasm				pancreas(1)	1	all_neural(463;0.228)															OREG0024221	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
LLGL1	3996	broad.mit.edu	37	17	18140896	18140896	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18140896C>T	uc002gsp.2	+	14	1774	c.1713C>T	c.(1711-1713)CAC>CAT	p.H571H		NM_004140	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1	571	WD 9.				cortical actin cytoskeleton organization|exocytosis|protein complex assembly	cortical actin cytoskeleton	protein kinase binding|structural molecule activity			breast(2)|skin(2)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)	6	all_neural(463;0.228)																	---	---	---	---
LLGL1	3996	broad.mit.edu	37	17	18140961	18140961	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18140961T>C	uc002gsp.2	+	14	1839	c.1778T>C	c.(1777-1779)GTG>GCG	p.V593A		NM_004140	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1	593	WD 9.				cortical actin cytoskeleton organization|exocytosis|protein complex assembly	cortical actin cytoskeleton	protein kinase binding|structural molecule activity			breast(2)|skin(2)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)	6	all_neural(463;0.228)																	---	---	---	---
FBXW10	10517	broad.mit.edu	37	17	18675757	18675757	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18675757T>C	uc002guk.2	+	12	2271	c.2039T>C	c.(2038-2040)ATG>ACG	p.M680T	FBXW10_uc002guj.2_Missense_Mutation_p.M680T|FBXW10_uc002gul.2_Missense_Mutation_p.M709T|FBXW10_uc010cqh.1_Missense_Mutation_p.M627T	NM_031456	NP_113644	Q5XX13	FBW10_HUMAN	F-box and WD-40 domain protein 10	680										ovary(1)	1																		---	---	---	---
NOS2	4843	broad.mit.edu	37	17	26125843	26125843	+	5'UTR	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26125843G>T	uc002gzu.2	-	2					NOS2_uc010crh.1_5'UTR|NOS2_uc010wab.1_5'UTR	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)													---	---	---	---
ALDOC	230	broad.mit.edu	37	17	26902512	26902512	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26902512C>T	uc002hbp.2	-	2	184	c.39G>A	c.(37-39)AAG>AAA	p.K13K	ALDOC_uc010cro.2_Silent_p.K13K	NM_005165	NP_005156	P09972	ALDOC_HUMAN	fructose-bisphosphate aldolase C	13					fructose 1,6-bisphosphate metabolic process|gluconeogenesis|glycolysis	cytosol	cytoskeletal protein binding|fructose-bisphosphate aldolase activity			ovary(1)	1	Lung NSC(42;0.00431)															OREG0024278	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26958520	26958520	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26958520G>A	uc002hbu.2	-	23	4375	c.4276C>T	c.(4276-4278)CAT>TAT	p.H1426Y		NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor	1426						extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
FLOT2	2319	broad.mit.edu	37	17	27209367	27209367	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27209367G>A	uc002hdc.2	-	6	690	c.567C>T	c.(565-567)GAC>GAT	p.D189D		NM_004475	NP_004466	Q14254	FLOT2_HUMAN	flotillin 2	189					cell adhesion|epidermis development	cell surface|endocytic vesicle|endosome|membrane fraction					0	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;3.26e-06)|all cancers(11;1.76e-05)|BRCA - Breast invasive adenocarcinoma(11;0.00015)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)															---	---	---	---
NF1	4763	broad.mit.edu	37	17	29556992	29556992	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29556992G>T	uc002hgg.2	+	22	3323	c.2990G>T	c.(2989-2991)AGG>ATG	p.R997M	NF1_uc002hgh.2_Missense_Mutation_p.R997M|NF1_uc010csn.1_Missense_Mutation_p.R857M|NF1_uc002hgi.1_Missense_Mutation_p.R30M	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	997					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)|p.R997fs*16(1)|p.R997K(1)		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)			---	---	---	---
TMEM132E	124842	broad.mit.edu	37	17	32956140	32956140	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32956140G>T	uc002hif.2	+	5	1313	c.985G>T	c.(985-987)GGC>TGC	p.G329C		NM_207313	NP_997196	Q6IEE7	T132E_HUMAN	transmembrane protein 132E precursor	329	Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(366;0.231)														---	---	---	---
SLFN5	162394	broad.mit.edu	37	17	33586176	33586176	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33586176A>C	uc002hjf.3	+	2	584	c.467A>C	c.(466-468)CAG>CCG	p.Q156P	SLFN5_uc002hje.2_Missense_Mutation_p.Q156P|SLFN5_uc010wcg.1_Missense_Mutation_p.Q156P	NM_144975	NP_659412	Q08AF3	SLFN5_HUMAN	schlafen family member 5	156					cell differentiation		ATP binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)														---	---	---	---
CCL15	6359	broad.mit.edu	37	17	34324855	34324855	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34324855C>A	uc010wcu.1	-	4	859	c.290G>T	c.(289-291)AGT>ATT	p.S97I	CCL14-CCL15_uc010wcs.1_RNA|CCL14-CCL15_uc010wct.1_RNA	NM_032965	NP_116741	Q16663	CCL15_HUMAN	chemokine (C-C motif) ligand 15 precursor	97					cell-cell signaling|cellular calcium ion homeostasis|immune response	extracellular space	chemoattractant activity|chemokine activity|heparin binding|signal transducer activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
SYNRG	11276	broad.mit.edu	37	17	35902366	35902366	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35902366C>T	uc002hoa.2	-	15	2993	c.2910G>A	c.(2908-2910)ACG>ACA	p.T970T	SYNRG_uc010wde.1_Silent_p.T892T|SYNRG_uc010wdf.1_Silent_p.T892T|SYNRG_uc002hoc.2_Silent_p.T891T|SYNRG_uc002hoe.2_Silent_p.T892T|SYNRG_uc002hod.2_Silent_p.T847T|SYNRG_uc010wdg.1_Silent_p.T764T|SYNRG_uc002hob.2_Silent_p.T970T|SYNRG_uc002hof.2_Silent_p.T636T	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1	970					endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2																		---	---	---	---
C17orf98	388381	broad.mit.edu	37	17	36997563	36997563	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36997563C>T	uc002hqv.2	-	1	80	c.80G>A	c.(79-81)CGC>CAC	p.R27H		NM_001080465	NP_001073934	A8MV24	CQ098_HUMAN	hypothetical protein LOC388381	27											0																		---	---	---	---
NR1D1	9572	broad.mit.edu	37	17	38253490	38253490	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38253490G>A	uc002htz.1	-	2	824	c.198C>T	c.(196-198)CGC>CGT	p.R66R	NR1D1_uc010cwq.1_RNA|NR1D1_uc010cwr.1_5'Flank	NM_021724	NP_068370	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	66					cellular response to lipopolysaccharide|negative regulation of receptor biosynthetic process|negative regulation of toll-like receptor 4 signaling pathway|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin|nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding			skin(1)	1	Colorectal(19;0.000442)																	---	---	---	---
KRT27	342574	broad.mit.edu	37	17	38936090	38936090	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38936090C>A	uc002hvg.2	-	4	749	c.708G>T	c.(706-708)GCG>GCT	p.A236A		NM_181537	NP_853515	Q7Z3Y8	K1C27_HUMAN	keratin 27	236	Rod.|Linker 12.					cytoplasm|intermediate filament	structural molecule activity				0		Breast(137;0.000812)																---	---	---	---
KRT12	3859	broad.mit.edu	37	17	39021080	39021080	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39021080T>C	uc002hvk.2	-	3	809	c.785A>G	c.(784-786)TAC>TGC	p.Y262C		NM_000223	NP_000214	Q99456	K1C12_HUMAN	keratin 12	262	Rod.|Coil 1B.				visual perception	intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)																---	---	---	---
KRT17	3872	broad.mit.edu	37	17	39776936	39776936	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39776936G>A	uc002hxh.2	-	6	1277	c.1156C>T	c.(1156-1158)CGC>TGC	p.R386C	JUP_uc010wfs.1_Intron	NM_000422	NP_000413	Q04695	K1C17_HUMAN	keratin 17	386	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				---	---	---	---
NAGLU	4669	broad.mit.edu	37	17	40695811	40695811	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40695811G>A	uc002hzv.2	+	6	2127	c.1787G>A	c.(1786-1788)GGC>GAC	p.G596D		NM_000263	NP_000254	P54802	ANAG_HUMAN	alpha-N-acetylglucosaminidase precursor	596						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)													---	---	---	---
HSD17B1	3292	broad.mit.edu	37	17	40706500	40706500	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40706500A>C	uc002hzw.2	+	5	1585	c.617A>C	c.(616-618)GAC>GCC	p.D206A	HSD17B1_uc002hzx.2_Missense_Mutation_p.D207A|HSD17B1_uc010wgm.1_RNA|uc002hzy.2_5'UTR|HSD17B1_uc010cyi.2_Missense_Mutation_p.D237A	NM_000413	NP_000404	P14061	DHB1_HUMAN	hydroxysteroid (17-beta) dehydrogenase 1	206					estrogen biosynthetic process	cytosol	binding|estradiol 17-beta-dehydrogenase activity				0		all_cancers(22;5.59e-08)|all_epithelial(22;7e-07)|Ovarian(249;0.0261)		BRCA - Breast invasive adenocarcinoma(366;0.129)	NADH(DB00157)													---	---	---	---
PSMC3IP	29893	broad.mit.edu	37	17	40725006	40725006	+	Missense_Mutation	SNP	C	T	T	rs149230650		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40725006C>T	uc002iai.2	-	8	677	c.634G>A	c.(634-636)GTC>ATC	p.V212I	MLX_uc002iaf.2_3'UTR|MLX_uc002iag.2_3'UTR|MLX_uc002iah.2_3'UTR|PSMC3IP_uc002iaj.2_Missense_Mutation_p.V149I|PSMC3IP_uc002iak.2_Missense_Mutation_p.V200I|PSMC3IP_uc010wgn.1_Missense_Mutation_p.V133I|PSMC3IP_uc010wgo.1_RNA|PSMC3IP_uc010wgp.1_RNA	NM_016556	NP_057640	Q9P2W1	HOP2_HUMAN	PSMC3 interacting protein isoform 2	212					DNA recombination|meiosis	nucleus	DNA binding			upper_aerodigestive_tract(1)|skin(1)	2		all_cancers(22;0.00426)|Breast(137;0.00116)|all_epithelial(22;0.0395)		BRCA - Breast invasive adenocarcinoma(366;0.13)														---	---	---	---
AOC3	8639	broad.mit.edu	37	17	41003976	41003976	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41003976C>T	uc002ibv.2	+	1	776	c.616C>T	c.(616-618)CGG>TGG	p.R206W		NM_003734	NP_003725	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3 precursor	206	Extracellular (Potential).				amine metabolic process|cell adhesion|inflammatory response	cell surface|integral to membrane|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|protein homodimerization activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			central_nervous_system(2)|ovary(1)|skin(1)	4		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)													---	---	---	---
MPP2	4355	broad.mit.edu	37	17	41959879	41959879	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41959879C>A	uc010wip.1	-	6	646	c.589G>T	c.(589-591)GGT>TGT	p.G197C	MPP2_uc002ien.1_Missense_Mutation_p.G169C|MPP2_uc010wim.1_Missense_Mutation_p.G141C|MPP2_uc002ieo.1_Missense_Mutation_p.G152C|MPP2_uc010win.1_Missense_Mutation_p.G13C|MPP2_uc010wio.1_Missense_Mutation_p.G141C|MPP2_uc010czm.1_Missense_Mutation_p.G135C	NM_005374	NP_005365	Q14168	MPP2_HUMAN	palmitoylated membrane protein 2	176					signal transduction	cell surface|integral to plasma membrane|membrane fraction	guanylate kinase activity				0		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)														---	---	---	---
MPP2	4355	broad.mit.edu	37	17	41975706	41975706	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41975706G>A	uc010wip.1	-	3	266	c.209C>T	c.(208-210)GCC>GTC	p.A70V	MPP2_uc002ien.1_Missense_Mutation_p.A42V|MPP2_uc010wim.1_Missense_Mutation_p.A14V|MPP2_uc002ieo.1_Missense_Mutation_p.A25V|MPP2_uc010win.1_Intron|MPP2_uc010wio.1_Missense_Mutation_p.A14V|MPP2_uc010czm.1_Missense_Mutation_p.A14V	NM_005374	NP_005365	Q14168	MPP2_HUMAN	palmitoylated membrane protein 2	25	L27 1.				signal transduction	cell surface|integral to plasma membrane|membrane fraction	guanylate kinase activity				0		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)														---	---	---	---
HDAC5	10014	broad.mit.edu	37	17	42170162	42170162	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42170162A>G	uc002ifd.1	-	7	865	c.654T>C	c.(652-654)CAT>CAC	p.H218H	HDAC5_uc002ife.1_Silent_p.H218H|HDAC5_uc002iff.1_Silent_p.H219H|HDAC5_uc010czp.1_Silent_p.H218H|HDAC5_uc002ifh.2_Silent_p.H218H	NM_005474	NP_005465	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5 isoform 1	218					B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)														---	---	---	---
GPATCH8	23131	broad.mit.edu	37	17	42475277	42475277	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42475277C>T	uc002igw.1	-	8	4232	c.4168G>A	c.(4168-4170)GCC>ACC	p.A1390T	GPATCH8_uc002igv.1_Missense_Mutation_p.A1312T|GPATCH8_uc010wiz.1_Missense_Mutation_p.A1312T	NM_001002909	NP_001002909	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1390	Poly-Ala.					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)														---	---	---	---
PLEKHM1	9842	broad.mit.edu	37	17	43531023	43531023	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43531023C>T	uc002ija.2	-	7	2365	c.2195G>A	c.(2194-2196)CGG>CAG	p.R732Q	PLEKHM1_uc010wjm.1_Missense_Mutation_p.R704Q|PLEKHM1_uc002ijb.2_Missense_Mutation_p.R207Q|PLEKHM1_uc010wjn.1_Missense_Mutation_p.R681Q|PLEKHM1_uc002ijc.2_Missense_Mutation_p.R186Q	NM_014798	NP_055613	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M	732	PH 2.				intracellular signal transduction	cytoplasm	metal ion binding				0	Renal(3;0.0405)																	---	---	---	---
NFE2L1	4779	broad.mit.edu	37	17	46136768	46136768	+	Missense_Mutation	SNP	G	A	A	rs144484468		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46136768G>A	uc002imz.3	+	6	2735	c.2084G>A	c.(2083-2085)CGG>CAG	p.R695Q	NFE2L1_uc002ina.3_Missense_Mutation_p.R665Q|NFE2L1_uc002inb.3_Missense_Mutation_p.R665Q|NFE2L1_uc010wle.1_Missense_Mutation_p.R507Q|NFE2L1_uc010wlf.1_Missense_Mutation_p.R539Q	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1	695	Leucine-zipper.				anatomical structure morphogenesis|heme biosynthetic process|inflammatory response|transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			skin(1)	1																		---	---	---	---
HOXB13	10481	broad.mit.edu	37	17	46805700	46805700	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46805700C>T	uc002ioa.2	-	1	412	c.256G>A	c.(256-258)GGG>AGG	p.G86R		NM_006361	NP_006352	Q92826	HXB13_HUMAN	homeobox B13	86					angiogenesis|epidermis development|response to wounding		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
NGFR	4804	broad.mit.edu	37	17	47583941	47583941	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47583941G>A	uc002ioz.3	+	3	614	c.489G>A	c.(487-489)CCG>CCA	p.P163P		NM_002507	NP_002498	P08138	TNR16_HUMAN	nerve growth factor receptor precursor	163	Extracellular (Potential).|TNFR-Cys 4.				anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|membrane protein intracellular domain proteolysis|negative regulation of axonogenesis|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis	cell surface|cytosol|endosome|extracellular region|integral to plasma membrane|nucleoplasm				ovary(1)|lung(1)	2	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)																	---	---	---	---
MYST2	11143	broad.mit.edu	37	17	47869286	47869286	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47869286C>T	uc002ipm.2	+	2	180	c.54C>T	c.(52-54)TCC>TCT	p.S18S	MYST2_uc002ipl.1_Silent_p.S18S|MYST2_uc010wma.1_Silent_p.S18S|MYST2_uc010wmb.1_Silent_p.S18S|MYST2_uc010wmc.1_Silent_p.S18S|MYST2_uc010wmd.1_5'UTR|MYST2_uc010wme.1_5'UTR	NM_007067	NP_008998	O95251	MYST2_HUMAN	MYST histone acetyltransferase 2	18	Ser-rich.				DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	histone acetyltransferase activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
ITGA3	3675	broad.mit.edu	37	17	48166496	48166496	+	3'UTR	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48166496G>A	uc010dbl.2	+	26					ITGA3_uc010dbm.2_Missense_Mutation_p.R1023H	NM_002204	NP_002195			integrin alpha 3 isoform a precursor						blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|leukocyte migration	cell surface|integrin complex	protein binding|receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48668860	48668860	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48668860C>T	uc002irk.1	+	11	2890	c.2518C>T	c.(2518-2520)CGT>TGT	p.R840C	CACNA1G_uc002iri.1_Missense_Mutation_p.R840C|CACNA1G_uc002irj.1_Missense_Mutation_p.R840C|CACNA1G_uc002irl.1_Missense_Mutation_p.R840C|CACNA1G_uc002irm.1_Missense_Mutation_p.R840C|CACNA1G_uc002irn.1_Missense_Mutation_p.R840C|CACNA1G_uc002iro.1_Missense_Mutation_p.R840C|CACNA1G_uc002irp.1_Missense_Mutation_p.R840C|CACNA1G_uc002irq.1_Missense_Mutation_p.R840C|CACNA1G_uc002irr.1_Missense_Mutation_p.R840C|CACNA1G_uc002irs.1_Missense_Mutation_p.R840C|CACNA1G_uc002irt.1_Missense_Mutation_p.R840C|CACNA1G_uc002irv.1_Missense_Mutation_p.R840C|CACNA1G_uc002irw.1_Missense_Mutation_p.R840C|CACNA1G_uc002iru.1_Missense_Mutation_p.R840C|CACNA1G_uc002irx.1_Missense_Mutation_p.R753C|CACNA1G_uc002iry.1_Missense_Mutation_p.R753C|CACNA1G_uc002irz.1_Missense_Mutation_p.R753C|CACNA1G_uc002isa.1_Missense_Mutation_p.R753C|CACNA1G_uc002isb.1_Missense_Mutation_p.R753C|CACNA1G_uc002isc.1_Missense_Mutation_p.R753C|CACNA1G_uc002isd.1_Missense_Mutation_p.R753C|CACNA1G_uc002ise.1_Missense_Mutation_p.R753C|CACNA1G_uc002isf.1_Missense_Mutation_p.R753C|CACNA1G_uc002isg.1_Missense_Mutation_p.R753C|CACNA1G_uc002ish.1_Missense_Mutation_p.R753C|CACNA1G_uc002isi.1_Missense_Mutation_p.R753C	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	840	Helical; Name=S4 of repeat II; (Potential).|II.				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
GDPD1	284161	broad.mit.edu	37	17	57351092	57351092	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57351092T>A	uc002ixk.1	+	10	1040	c.903T>A	c.(901-903)TAT>TAA	p.Y301*		NM_182569	NP_872375	Q8N9F7	GDPD1_HUMAN	glycerophosphodiester phosphodiesterase domain	301	GDPD.|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)																	---	---	---	---
KCNH6	81033	broad.mit.edu	37	17	61615460	61615460	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61615460C>T	uc002jay.2	+	7	1616	c.1536C>T	c.(1534-1536)TCC>TCT	p.S512S	KCNH6_uc010wpl.1_Silent_p.S389S|KCNH6_uc010wpm.1_Silent_p.S512S|KCNH6_uc002jaz.1_Silent_p.S459S	NM_030779	NP_110406	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H,	512	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent|signal transduction					skin(1)	1					Ibutilide(DB00308)													---	---	---	---
TACO1	51204	broad.mit.edu	37	17	61685281	61685281	+	Silent	SNP	C	T	T	rs151139810	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61685281C>T	uc002jbd.2	+	5	1013	c.813C>T	c.(811-813)CCC>CCT	p.P271P		NM_016360	NP_057444	Q9BSH4	TACO1_HUMAN	translational activator of mitochondrially	271					regulation of translation	mitochondrion					0																		---	---	---	---
FTSJ3	117246	broad.mit.edu	37	17	61897300	61897300	+	Silent	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61897300T>A	uc002jbz.2	-	20	2484	c.2406A>T	c.(2404-2406)GTA>GTT	p.V802V	FTSJ3_uc002jca.2_Silent_p.V802V	NM_017647	NP_060117	Q8IY81	RRMJ3_HUMAN	FtsJ homolog 3	802					RNA methylation|rRNA processing	nucleolus	methyltransferase activity|nucleic acid binding			ovary(1)	1																		---	---	---	---
CCDC45	90799	broad.mit.edu	37	17	62527046	62527046	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62527046G>A	uc002jem.2	+	13	1507	c.1449G>A	c.(1447-1449)GCG>GCA	p.A483A	CCDC45_uc002jen.2_RNA|CCDC45_uc010wqb.1_Silent_p.A319A|CCDC45_uc002jeo.1_5'Flank	NM_138363	NP_612372	Q96GE4	CEP95_HUMAN	coiled-coil domain containing 45	483						centrosome|spindle pole	protein binding				0	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)															---	---	---	---
CACNG4	27092	broad.mit.edu	37	17	65020985	65020985	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65020985G>A	uc002jft.1	+	3	329	c.314G>A	c.(313-315)CGA>CAA	p.R105Q		NM_014405	NP_055220	Q9UBN1	CCG4_HUMAN	voltage-dependent calcium channel gamma-4	105	Extracellular (Potential).				membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane	voltage-gated calcium channel activity			central_nervous_system(1)	1	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)															---	---	---	---
CACNG4	27092	broad.mit.edu	37	17	65027085	65027085	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65027085G>A	uc002jft.1	+	4	964	c.949G>A	c.(949-951)GTC>ATC	p.V317I		NM_014405	NP_055220	Q9UBN1	CCG4_HUMAN	voltage-dependent calcium channel gamma-4	317	Cytoplasmic (Potential).				membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane	voltage-gated calcium channel activity			central_nervous_system(1)	1	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)															---	---	---	---
ARSG	22901	broad.mit.edu	37	17	66391298	66391298	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66391298C>T	uc002jhc.2	+	10	1972	c.1176C>T	c.(1174-1176)TCC>TCT	p.S392S	ARSG_uc002jhb.1_Silent_p.S228S	NM_014960	NP_055775	Q96EG1	ARSG_HUMAN	Arylsulfatase G precursor	392					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)															---	---	---	---
CD300E	342510	broad.mit.edu	37	17	72613483	72613483	+	Silent	SNP	G	A	A	rs111412583	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72613483G>A	uc002jlb.1	-	2	203	c.162C>T	c.(160-162)TAC>TAT	p.Y54Y		NM_181449	NP_852114	Q496F6	CLM2_HUMAN	CD300e molecule precursor	54	Ig-like V-type.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
TMEM104	54868	broad.mit.edu	37	17	72832455	72832455	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72832455G>A	uc002jls.3	+	10	1282	c.1120G>A	c.(1120-1122)GTG>ATG	p.V374M	TMEM104_uc010wrf.1_Intron|TMEM104_uc010wrg.1_Intron|TMEM104_uc010dfx.2_Missense_Mutation_p.V374M	NM_017728	NP_060198	Q8NE00	TM104_HUMAN	transmembrane protein 104	374	Helical; (Potential).					integral to membrane					0	all_lung(278;0.23)																	---	---	---	---
GGA3	23163	broad.mit.edu	37	17	73239539	73239539	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73239539A>G	uc002jni.1	-	5	422	c.413T>C	c.(412-414)CTG>CCG	p.L138P	GGA3_uc002jnj.1_Missense_Mutation_p.L105P|GGA3_uc010wrw.1_Missense_Mutation_p.L16P|GGA3_uc002jnk.1_Missense_Mutation_p.L66P|GGA3_uc010wrx.1_Missense_Mutation_p.L16P|GGA3_uc010wry.1_Missense_Mutation_p.L66P|GGA3_uc010wrz.1_Missense_Mutation_p.L105P	NM_138619	NP_619525	Q9NZ52	GGA3_HUMAN	ADP-ribosylation factor binding protein 3	138	VHS.|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)															---	---	---	---
EVPL	2125	broad.mit.edu	37	17	74005351	74005351	+	Missense_Mutation	SNP	G	A	A	rs145535523		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74005351G>A	uc002jqi.2	-	22	4163	c.3935C>T	c.(3934-3936)ACG>ATG	p.T1312M	EVPL_uc010wss.1_Missense_Mutation_p.T1334M|EVPL_uc010wst.1_Missense_Mutation_p.T782M	NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	1312	Central fibrous rod domain.				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	74005498	74005498	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74005498C>T	uc002jqi.2	-	22	4016	c.3788G>A	c.(3787-3789)AGC>AAC	p.S1263N	EVPL_uc010wss.1_Missense_Mutation_p.S1285N|EVPL_uc010wst.1_Missense_Mutation_p.S733N	NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	1263	Central fibrous rod domain.				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	74020120	74020120	+	Silent	SNP	C	T	T	rs143599595	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74020120C>T	uc002jqi.2	-	2	408	c.180G>A	c.(178-180)ACG>ACA	p.T60T	EVPL_uc010wss.1_Silent_p.T60T|EVPL_uc010wst.1_5'UTR	NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	60	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																		---	---	---	---
EXOC7	23265	broad.mit.edu	37	17	74077354	74077354	+	3'UTR	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74077354C>A	uc002jqs.2	-	20					ZACN_uc002jqn.2_Intron|ZACN_uc002jqo.2_Intron|ZACN_uc010dgu.2_Intron|EXOC7_uc002jqp.1_3'UTR|EXOC7_uc010dgv.1_3'UTR|EXOC7_uc002jqq.2_3'UTR|EXOC7_uc010wsw.1_3'UTR|EXOC7_uc010wsx.1_3'UTR|EXOC7_uc002jqr.2_3'UTR|EXOC7_uc010wsv.1_3'UTR	NM_001145297	NP_001138769			exocyst complex component 7 isoform 4						exocytosis|protein transport	centriolar satellite|cytosol|exocyst|plasma membrane	protein binding				0			LUSC - Lung squamous cell carcinoma(166;0.187)															---	---	---	---
RNF213	57674	broad.mit.edu	37	17	78313974	78313974	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78313974A>G	uc002jyh.1	+	1	249	c.26A>G	c.(25-27)CAC>CGC	p.H9R		NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)															---	---	---	---
BAIAP2	10458	broad.mit.edu	37	17	79077502	79077502	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79077502C>T	uc002jzg.2	+	8	951	c.843C>T	c.(841-843)CCC>CCT	p.P281P	BAIAP2_uc002jyz.3_Silent_p.P281P|BAIAP2_uc002jza.2_Silent_p.P281P|BAIAP2_uc002jzc.2_Silent_p.P281P|BAIAP2_uc002jzb.2_Silent_p.P38P|BAIAP2_uc002jzd.2_Silent_p.P281P|BAIAP2_uc002jzf.2_Silent_p.P281P|BAIAP2_uc002jze.2_Silent_p.P314P|BAIAP2_uc010wuh.1_Silent_p.P203P|BAIAP2_uc002jzh.2_Silent_p.P282P|BAIAP2_uc010wui.1_Silent_p.P144P	NM_017451	NP_059345	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2 isoform 2	281					axonogenesis|filopodium assembly|insulin receptor signaling pathway|regulation of actin cytoskeleton organization|response to bacterium	cell junction|cytoskeleton|cytosol|filopodium|nucleus|ruffle	cytoskeletal adaptor activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding				0	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)															---	---	---	---
HEXDC	284004	broad.mit.edu	37	17	80397594	80397594	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80397594G>A	uc002kew.2	+						HEXDC_uc002kev.3_Intron|HEXDC_uc010diq.2_Intron|HEXDC_uc010wvm.1_RNA|HEXDC_uc010wvn.1_Missense_Mutation_p.M92I					SubName: Full=Hexosaminidase (Glycosyl hydrolase family 20, catalytic domain) containing, isoform CRA_c; SubName: Full=Hexosaminidase D;						carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)|skin(1)	2	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)															---	---	---	---
FOXK2	3607	broad.mit.edu	37	17	80521332	80521332	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80521332C>T	uc002kfn.2	+	2	693	c.522C>T	c.(520-522)GCC>GCT	p.A174A	FOXK2_uc002kfm.1_Silent_p.A174A|FOXK2_uc010diu.2_Silent_p.A174A	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2	174					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)															---	---	---	---
FN3K	64122	broad.mit.edu	37	17	80708606	80708606	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80708606G>A	uc010wvs.1	+	6	966	c.905G>A	c.(904-906)GGC>GAC	p.G302D	TBCD_uc002kfx.1_5'Flank|TBCD_uc002kfy.1_5'Flank|TBCD_uc002kfz.2_5'Flank	NM_022158	NP_071441	Q9H479	FN3K_HUMAN	fructosamine 3 kinase	302					fructoselysine metabolic process		fructosamine-3-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)															---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3879216	3879216	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									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)																---	---	---	---
TXNDC2	84203	broad.mit.edu	37	18	9887885	9887885	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9887885T>C	uc002koi.3	+	2	1858	c.1409T>C	c.(1408-1410)CTG>CCG	p.L470P	TXNDC2_uc010wzq.1_RNA|TXNDC2_uc002koh.3_Missense_Mutation_p.L403P	NM_001098529	NP_001091999	Q86VQ3	TXND2_HUMAN	thioredoxin domain-containing 2 isoform 2	470	Thioredoxin.				cell differentiation|cell redox homeostasis|glycerol ether metabolic process|multicellular organismal development|spermatogenesis	cytoplasm	electron carrier activity|nutrient reservoir activity|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity			ovary(1)|pancreas(1)	2																		---	---	---	---
NAPG	8774	broad.mit.edu	37	18	10532792	10532792	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10532792C>T	uc002kon.2	+	3	436	c.209C>T	c.(208-210)GCT>GTT	p.A70V	NAPG_uc010wzr.1_5'UTR|NAPG_uc002koo.2_Intron	NM_003826	NP_003817	Q99747	SNAG_HUMAN	N-ethylmaleimide-sensitive factor attachment	70					cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0																		---	---	---	---
IMPA2	3613	broad.mit.edu	37	18	12028085	12028085	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12028085T>C	uc002kqp.1	+	6	748	c.534T>C	c.(532-534)CGT>CGC	p.R178R	IMPA2_uc002kqo.1_5'UTR|IMPA2_uc002kqq.1_Silent_p.R58R	NM_014214	NP_055029	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2	178					inositol phosphate dephosphorylation|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(2)	2					Lithium(DB01356)													---	---	---	---
SNRPD1	6632	broad.mit.edu	37	18	19203788	19203788	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19203788G>A	uc002ktj.1	+	3	302	c.171G>A	c.(169-171)ACG>ACA	p.T57T		NM_006938	NP_008869	P62314	SMD1_HUMAN	small nuclear ribonucleoprotein D1 polypeptide	57					ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	catalytic step 2 spliceosome|cytosol|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	protein binding|RNA binding				0																		---	---	---	---
RBBP8	5932	broad.mit.edu	37	18	20529570	20529570	+	Intron	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20529570T>C	uc002ktw.2	+						RBBP8_uc002kty.2_Intron|RBBP8_uc002ktz.2_Intron|RBBP8_uc002kua.2_Intron|RBBP8_uc002ktx.1_Intron	NM_002894	NP_002885			retinoblastoma binding protein 8 isoform a						cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter	nucleus	damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)|lung(1)|skin(1)	3	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31323629	31323629	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31323629A>G	uc010dmg.1	+	12	3872	c.3817A>G	c.(3817-3819)ACA>GCA	p.T1273A	ASXL3_uc002kxq.2_Missense_Mutation_p.T980A	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1273	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31325578	31325578	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31325578C>T	uc010dmg.1	+	12	5821	c.5766C>T	c.(5764-5766)GAC>GAT	p.D1922D	ASXL3_uc002kxq.2_Silent_p.D1629D	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1922					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34174816	34174816	+	Missense_Mutation	SNP	G	A	A	rs144223411		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34174816G>A	uc002kzt.1	+	7	770	c.673G>A	c.(673-675)GCA>ACA	p.A225T	FHOD3_uc002kzr.1_Missense_Mutation_p.A225T|FHOD3_uc002kzs.1_Missense_Mutation_p.A225T|FHOD3_uc002kzu.1_Missense_Mutation_p.A50T|FHOD3_uc010dmz.1_5'UTR	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	225	GBD/FH3.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43446902	43446902	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43446902T>C	uc002lbm.2	-	38	6582	c.6482A>G	c.(6481-6483)TAC>TGC	p.Y2161C	KIAA1632_uc010xcq.1_Missense_Mutation_p.Y715C|KIAA1632_uc010xcr.1_RNA|KIAA1632_uc010xcs.1_RNA|KIAA1632_uc002lbn.2_Missense_Mutation_p.Y1036C	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	2161					autophagy						0																		---	---	---	---
ST8SIA5	29906	broad.mit.edu	37	18	44336460	44336460	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44336460C>T	uc002lcj.1	-	1	580	c.12G>A	c.(10-12)GCG>GCA	p.A4A	ST8SIA5_uc010xcy.1_Silent_p.A4A|ST8SIA5_uc010xcz.1_Silent_p.A4A|ST8SIA5_uc010dno.1_Silent_p.A4A	NM_013305	NP_037437	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide	4	Cytoplasmic (Potential).				glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3																		---	---	---	---
POLI	11201	broad.mit.edu	37	18	51820306	51820306	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51820306C>A	uc002lfj.3	+	10	1760	c.1692C>A	c.(1690-1692)GCC>GCA	p.A564A	POLI_uc010xds.1_Silent_p.A485A|POLI_uc002lfk.3_Silent_p.A461A|POLI_uc010dpg.2_Silent_p.A160A	NM_007195	NP_009126	Q9UNA4	POLI_HUMAN	DNA polymerase iota	564					DNA repair|DNA replication	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding|protein binding			ovary(2)|kidney(1)	3				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54339760	54339760	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54339760G>T	uc002lgk.1	+	2	225	c.14G>T	c.(13-15)AGC>ATC	p.S5I	WDR7_uc010dpk.1_RNA|WDR7_uc002lgl.1_Missense_Mutation_p.S5I	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	5										ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)														---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54358513	54358513	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54358513G>T	uc002lgk.1	+	8	995	c.784G>T	c.(784-786)GGG>TGG	p.G262W	WDR7_uc010dpk.1_RNA|WDR7_uc002lgl.1_Missense_Mutation_p.G262W	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	262										ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)														---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54424292	54424292	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54424292G>A	uc002lgk.1	+	15	2679	c.2468G>A	c.(2467-2469)CGC>CAC	p.R823H	WDR7_uc010dpk.1_RNA|WDR7_uc002lgl.1_Missense_Mutation_p.R823H	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	823										ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)														---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54424475	54424475	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54424475G>A	uc002lgk.1	+	15	2862	c.2651G>A	c.(2650-2652)CGT>CAT	p.R884H	WDR7_uc010dpk.1_RNA|WDR7_uc002lgl.1_Missense_Mutation_p.R884H	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	884										ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)														---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59221656	59221656	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59221656G>A	uc010dps.1	+	11	2146	c.2134G>A	c.(2134-2136)GTG>ATG	p.V712M	CDH20_uc002lif.2_Missense_Mutation_p.V706M	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	712	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)																---	---	---	---
RNF152	220441	broad.mit.edu	37	18	59483442	59483442	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59483442G>A	uc002lih.1	-	2	667	c.255C>T	c.(253-255)TCC>TCT	p.S85S		NM_173557	NP_775828	Q8N8N0	RN152_HUMAN	ring finger protein 152	85					apoptosis|protein K48-linked ubiquitination	integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding			breast(1)	1		Colorectal(73;0.186)																---	---	---	---
KIAA1468	57614	broad.mit.edu	37	18	59888742	59888742	+	Intron	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59888742T>A	uc002lil.2	+						KIAA1468_uc002lik.1_Intron|KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_Intron	NM_020854	NP_065905			hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)																---	---	---	---
PHLPP1	23239	broad.mit.edu	37	18	60645690	60645690	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60645690G>A	uc002lis.2	+	18	2822	c.2644G>A	c.(2644-2646)GAT>AAT	p.D882N		NM_194449	NP_919431	O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein	1394	PP2C-like.				apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0																		---	---	---	---
CCDC102B	79839	broad.mit.edu	37	18	66541894	66541894	+	Intron	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66541894T>G	uc002lkk.2	+						CCDC102B_uc002lki.2_Intron|CCDC102B_uc002lkj.1_Intron	NM_001093729	NP_001087198			coiled-coil domain containing 102B											ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)																---	---	---	---
TSHZ1	10194	broad.mit.edu	37	18	72999537	72999537	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72999537C>T	uc002lly.2	+	2	2603	c.2040C>T	c.(2038-2040)AAC>AAT	p.N680N		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	725						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)														---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	77104366	77104366	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77104366C>T	uc002lmx.2	+						ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmz.1_Intron|ATP9B_uc002lna.2_Intron|ATP9B_uc002lnb.1_5'Flank	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)														---	---	---	---
HCN2	610	broad.mit.edu	37	19	613971	613971	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:613971C>T	uc002lpe.2	+	7	1998	c.1945C>T	c.(1945-1947)CGG>TGG	p.R649W		NM_001194	NP_001185	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic	649	cAMP.|Cytoplasmic (Potential).				cell-cell signaling|muscle contraction	voltage-gated potassium channel complex	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
PTBP1	5725	broad.mit.edu	37	19	804843	804843	+	Silent	SNP	C	T	T	rs147803014		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:804843C>T	uc002lpr.2	+	7	727	c.621C>T	c.(619-621)TTC>TTT	p.F207F	PTBP1_uc002lpp.2_Silent_p.F207F|PTBP1_uc002lpq.2_Silent_p.F207F|PTBP1_uc002lps.2_Intron|PTBP1_uc002lpt.2_RNA|PTBP1_uc002lpu.1_Silent_p.F177F	NM_031991	NP_114368	P26599	PTBP1_HUMAN	polypyrimidine tract-binding protein 1 isoform	207	RRM 2.				negative regulation of muscle cell differentiation|nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome	heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	mRNA binding|nucleotide binding|poly-pyrimidine tract binding|protein binding			kidney(1)|skin(1)	2		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|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)														---	---	---	---
C19orf6	91304	broad.mit.edu	37	19	1010455	1010455	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1010455G>A	uc002lqr.1	-	11	1903	c.1757C>T	c.(1756-1758)CCG>CTG	p.P586L	uc002lqp.1_5'Flank|C19orf6_uc002lqq.1_RNA|C19orf6_uc002lqs.1_3'UTR	NM_001033026	NP_001028198	Q4ZIN3	MBRL_HUMAN	membralin isoform 1	586						cytoplasm|integral to membrane				pancreas(2)|breast(1)	3		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)|GBM - Glioblastoma multiforme(1328;0.0252)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
DAZAP1	26528	broad.mit.edu	37	19	1428885	1428885	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1428885G>A	uc002lsn.2	+	8	780	c.591G>A	c.(589-591)GCG>GCA	p.A197A	DAZAP1_uc002lsm.2_Silent_p.A197A|DAZAP1_uc002lso.2_Silent_p.A196A|DAZAP1_uc002lsl.1_Silent_p.A197A	NM_018959	NP_061832	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1 isoform b	197					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)														---	---	---	---
APC2	10297	broad.mit.edu	37	19	1466805	1466805	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1466805G>T	uc002lsr.1	+	15	3713	c.3505G>T	c.(3505-3507)GGC>TGC	p.G1169C	APC2_uc002lss.1_Missense_Mutation_p.G751C|APC2_uc002lst.1_Missense_Mutation_p.G1169C|APC2_uc002lsu.1_Missense_Mutation_p.G1168C|C19orf25_uc010xgn.1_Intron	NM_005883	NP_005874	O95996	APC2_HUMAN	adenomatosis polyposis coli 2	1169	Interaction with CTNNB1.|2.|Ser-rich.|5 X 20 AA approximate repeat of F-X-V-E- X-T-P-X-C-F-S-R-X-S-S-L-S-S-L-S.				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|Wnt receptor signaling pathway	actin filament|catenin complex|cytoplasmic microtubule|Golgi membrane|lamellipodium membrane|perinuclear region of cytoplasm	beta-catenin binding|microtubule binding			breast(3)|pancreas(1)	4		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)														---	---	---	---
MOBKL2A	126308	broad.mit.edu	37	19	2076887	2076887	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2076887C>T	uc002luu.2	-	2	706	c.547G>A	c.(547-549)GTG>ATG	p.V183M	MOBKL2A_uc002luv.2_Missense_Mutation_p.V183M	NM_130807	NP_570719	Q96BX8	MOL2A_HUMAN	MOB-LAK	183						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)														---	---	---	---
C19orf29	58509	broad.mit.edu	37	19	3612132	3612132	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3612132C>T	uc002lyh.2	-	10	2119	c.2066G>A	c.(2065-2067)CGC>CAC	p.R689H	C19orf29_uc010xho.1_Missense_Mutation_p.R148H|C19orf29_uc010dtn.2_Missense_Mutation_p.R537H|C19orf29_uc002lyi.3_Missense_Mutation_p.R689H|C19orf29_uc010dto.2_RNA	NM_001080543	NP_001074012	Q8WUQ7	CS029_HUMAN	chromosome 19 open reading frame 29	689						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)														---	---	---	---
PIP5K1C	23396	broad.mit.edu	37	19	3641788	3641788	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3641788C>T	uc002lyj.1	-	15	1759	c.1702G>A	c.(1702-1704)GCG>ACG	p.A568T	PIP5K1C_uc010xhq.1_Missense_Mutation_p.A568T|PIP5K1C_uc010xhr.1_Missense_Mutation_p.A568T	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type	568					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)														---	---	---	---
PIP5K1C	23396	broad.mit.edu	37	19	3653507	3653507	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3653507G>A	uc002lyj.1	-	7	759	c.702C>T	c.(700-702)CGC>CGT	p.R234R	PIP5K1C_uc010xhq.1_Silent_p.R234R|PIP5K1C_uc010xhr.1_Silent_p.R234R	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type	234	PIPK.				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)														---	---	---	---
TJP3	27134	broad.mit.edu	37	19	3736172	3736172	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3736172C>T	uc010xhv.1	+	10	1236	c.1236C>T	c.(1234-1236)CCC>CCT	p.P412P	TJP3_uc010xhs.1_Silent_p.P379P|TJP3_uc010xht.1_Silent_p.P343P|TJP3_uc010xhu.1_Silent_p.P388P|TJP3_uc010xhw.1_Silent_p.P398P	NM_014428	NP_055243	O95049	ZO3_HUMAN	tight junction protein 3	393						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)														---	---	---	---
ZFR2	23217	broad.mit.edu	37	19	3831668	3831668	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3831668G>A	uc002lyw.2	-	4	600	c.588C>T	c.(586-588)ACC>ACT	p.T196T	ZFR2_uc010xhx.1_RNA	NM_015174	NP_055989	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2 isoform 1	196	Pro-rich.					intracellular	nucleic acid binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)														---	---	---	---
PLIN4	729359	broad.mit.edu	37	19	4512339	4512339	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4512339C>T	uc002mar.1	-	3	1591	c.1591G>A	c.(1591-1593)GTG>ATG	p.V531M	PLIN4_uc010dub.1_5'Flank	NM_001080400	NP_001073869	Q96Q06	PLIN4_HUMAN	plasma membrane associated protein, S3-12	531	27 X 33 AA approximate tandem repeat.|14.					lipid particle|plasma membrane					0																		---	---	---	---
SEMA6B	10501	broad.mit.edu	37	19	4550844	4550844	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4550844G>A	uc010duc.1	-	10	1126	c.1088C>T	c.(1087-1089)ACG>ATG	p.T363M	SEMA6B_uc010dud.2_Missense_Mutation_p.T363M|SEMA6B_uc010xih.1_Missense_Mutation_p.T363M	NM_032108	NP_115484	Q9H3T3	SEM6B_HUMAN	semaphorin 6B precursor	363	Extracellular (Potential).|Sema.				cell differentiation|nervous system development	integral to membrane	receptor activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SEMA6B	10501	broad.mit.edu	37	19	4554436	4554436	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4554436G>T	uc010duc.1	-	8	773	c.735C>A	c.(733-735)TTC>TTA	p.F245L	SEMA6B_uc010dud.2_Missense_Mutation_p.F245L|SEMA6B_uc010xih.1_Missense_Mutation_p.F245L	NM_032108	NP_115484	Q9H3T3	SEM6B_HUMAN	semaphorin 6B precursor	245	Extracellular (Potential).|Sema.				cell differentiation|nervous system development	integral to membrane	receptor activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
PLIN3	10226	broad.mit.edu	37	19	4859941	4859941	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4859941C>T	uc002mbj.2	-	3	339	c.162G>A	c.(160-162)CCG>CCA	p.P54P	PLIN3_uc002mbk.2_Silent_p.P54P|PLIN3_uc002mbl.3_Silent_p.P54P	NM_005817	NP_005808	O60664	PLIN3_HUMAN	mannose 6 phosphate receptor binding protein 1	54					vesicle-mediated transport	endosome membrane|Golgi apparatus|lipid particle	protein binding				0					Galsulfase(DB01279)|Idursulfase(DB01271)													---	---	---	---
UHRF1	29128	broad.mit.edu	37	19	4954817	4954817	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4954817C>T	uc002mbo.2	+	17	2282	c.2114C>T	c.(2113-2115)CCG>CTG	p.P705L	UHRF1_uc010xik.1_RNA|UHRF1_uc010duf.2_RNA|UHRF1_uc002mbp.2_Missense_Mutation_p.P718L	NM_001048201	NP_001041666	Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains	705					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)														---	---	---	---
KDM4B	23030	broad.mit.edu	37	19	5119686	5119686	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5119686C>T	uc002mbq.3	+	11	1364	c.1138C>T	c.(1138-1140)CCC>TCC	p.P380S	KDM4B_uc010xim.1_Missense_Mutation_p.P414S|KDM4B_uc002mbr.3_Missense_Mutation_p.P138S	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B	380					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1																		---	---	---	---
RFX2	5990	broad.mit.edu	37	19	6004208	6004208	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6004208G>A	uc002meb.2	-						RFX2_uc002mec.2_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																		---	---	---	---
INSR	3643	broad.mit.edu	37	19	7122772	7122772	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7122772G>A	uc002mgd.1	-	19	3491	c.3382C>T	c.(3382-3384)CGC>TGC	p.R1128C	INSR_uc002mge.1_Missense_Mutation_p.R1116C	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)													---	---	---	---
ZNF358	140467	broad.mit.edu	37	19	7585781	7585781	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7585781C>T	uc002mgn.2	+	2	1823	c.1653C>T	c.(1651-1653)GGC>GGT	p.G551G	MCOLN1_uc010dvh.1_5'Flank|MCOLN1_uc002mgo.2_5'Flank|MCOLN1_uc002mgp.2_5'Flank	NM_018083	NP_060553	Q9NW07	ZN358_HUMAN	zinc finger protein 358	551					embryonic forelimb morphogenesis|neural tube development|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
KIAA1543	57662	broad.mit.edu	37	19	7682715	7682715	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7682715G>A	uc002mgv.3	+	17	3623	c.3522G>A	c.(3520-3522)ACG>ACA	p.T1174T	KIAA1543_uc002mgu.3_Silent_p.T1201T|KIAA1543_uc002mgw.2_Silent_p.T304T	NM_020902	NP_065953	Q9P1Y5	CAMP3_HUMAN	NEZHA isoform 2	1174	CKK.				epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1																		---	---	---	---
PCP2	126006	broad.mit.edu	37	19	7696566	7696566	+	3'UTR	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7696566C>A	uc002mgz.2	-	4					XAB2_uc002mgx.2_5'Flank	NM_174895	NP_777555			Purkinje cell protein 2						signal transduction		GTPase activator activity				0																		---	---	---	---
MAP2K7	5609	broad.mit.edu	37	19	7975196	7975196	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7975196G>A	uc002mit.2	+	4	450	c.385G>A	c.(385-387)GGC>AGC	p.G129S	MAP2K7_uc002miv.2_Missense_Mutation_p.G129S|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Missense_Mutation_p.G129S|MAP2K7_uc010dvv.2_Missense_Mutation_p.G4S	NM_145185	NP_660186	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	129	Protein kinase.|ATP (By similarity).				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)													---	---	---	---
MAP2K7	5609	broad.mit.edu	37	19	7975348	7975348	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7975348G>A	uc002mit.2	+	5	523	c.458G>A	c.(457-459)CGC>CAC	p.R153H	MAP2K7_uc002miv.2_Missense_Mutation_p.R153H|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Missense_Mutation_p.R153H|MAP2K7_uc010dvv.2_Missense_Mutation_p.R28H	NM_145185	NP_660186	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	153	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)													---	---	---	---
MAP2K7	5609	broad.mit.edu	37	19	7976201	7976201	+	Missense_Mutation	SNP	C	A	A	rs56278855		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7976201C>A	uc002mit.2	+	8	987	c.922C>A	c.(922-924)CTG>ATG	p.L308M	MAP2K7_uc002miv.2_Missense_Mutation_p.L308M|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Missense_Mutation_p.L308M|MAP2K7_uc010dvv.2_Missense_Mutation_p.L183M	NM_145185	NP_660186	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	308	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	8176641	8176641	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8176641G>A	uc002mjf.2	-	31	3996	c.3975C>T	c.(3973-3975)TGC>TGT	p.C1325C		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1325	EGF-like 20; calcium-binding.					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	8320601	8320601	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8320601T>C	uc002mjg.2	+	5	722	c.402T>C	c.(400-402)TGT>TGC	p.C134C	LASS4_uc002mjh.2_Silent_p.C83C|LASS4_uc002mji.2_5'UTR|LASS4_uc010dvz.2_Silent_p.C134C	NM_024552	NP_078828	Q9HA82	CERS4_HUMAN	LAG1 homolog, ceramide synthase 4	134	TLC.					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																		---	---	---	---
HNRNPM	4670	broad.mit.edu	37	19	8533719	8533719	+	Splice_Site	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8533719G>A	uc010dwe.2	+	9	975	c.895_splice	c.e9+1	p.H299_splice	HNRNPM_uc010dwc.1_Splice_Site_p.H299_splice|HNRNPM_uc010xke.1_Splice_Site_p.H260_splice|HNRNPM_uc010dwd.2_Splice_Site_p.H260_splice|HNRNPM_uc002mka.2_Splice_Site_p.H179_splice	NM_005968	NP_005959			heterogeneous nuclear ribonucleoprotein M						alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0																		---	---	---	---
MYO1F	4542	broad.mit.edu	37	19	8615033	8615033	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8615033G>A	uc002mkg.2	-						MYO1F_uc002mkh.2_Intron	NM_012335	NP_036467			myosin IF							unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(1)	3																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9069699	9069699	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9069699T>C	uc002mkp.2	-	3	17951	c.17747A>G	c.(17746-17748)CAA>CGA	p.Q5916R		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5918	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																		---	---	---	---
ZNF560	147741	broad.mit.edu	37	19	9578164	9578164	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9578164G>A	uc002mlp.1	-	10	1669	c.1459C>T	c.(1459-1461)CGC>TGC	p.R487C	ZNF560_uc010dwr.1_Missense_Mutation_p.R381C	NM_152476	NP_689689	Q96MR9	ZN560_HUMAN	zinc finger protein 560	487					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|pancreas(1)|liver(1)	6																		---	---	---	---
COL5A3	50509	broad.mit.edu	37	19	10114729	10114729	+	Silent	SNP	C	T	T	rs140294240	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10114729C>T	uc002mmq.1	-	5	773	c.687G>A	c.(685-687)CCG>CCA	p.P229P		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	229	Nonhelical region.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)															---	---	---	---
ILF3	3609	broad.mit.edu	37	19	10793819	10793819	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10793819C>T	uc002mpn.2	+	14	1872	c.1555C>T	c.(1555-1557)CCG>TCG	p.P519S	ILF3_uc002mpm.2_Missense_Mutation_p.P523S|ILF3_uc002mpl.2_Missense_Mutation_p.P519S|ILF3_uc002mpk.2_Missense_Mutation_p.P519S|ILF3_uc010xli.1_Missense_Mutation_p.P117S|ILF3_uc002mpo.2_Missense_Mutation_p.P523S|ILF3_uc002mpp.2_Missense_Mutation_p.P344S|ILF3_uc002mpq.2_5'Flank	NM_012218	NP_036350	Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3 isoform a	519					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)															---	---	---	---
TMED1	11018	broad.mit.edu	37	19	10943787	10943787	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10943787A>C	uc002mpy.2	-	4	684	c.568T>G	c.(568-570)TTG>GTG	p.L190V	DNM2_uc002mpx.1_3'UTR	NM_006858	NP_006849	Q13445	TMED1_HUMAN	interleukin 1 receptor-like 1 ligand precursor	190	Extracellular (Potential).				cell-cell signaling|signal transduction|transport	integral to membrane|plasma membrane	receptor binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
PRKCSH	5589	broad.mit.edu	37	19	11548691	11548691	+	Intron	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11548691T>C	uc002mrt.2	+						CCDC151_uc002mrs.2_5'Flank|CCDC151_uc010dxz.2_5'Flank|PRKCSH_uc002mru.2_Intron|PRKCSH_uc010xlz.1_Intron|PRKCSH_uc010dya.2_Intron|PRKCSH_uc002mrv.1_Intron|PRKCSH_uc010dyb.2_Intron	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																		---	---	---	---
ZNF440	126070	broad.mit.edu	37	19	11942182	11942182	+	Splice_Site	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11942182G>A	uc002msp.1	+	4	348	c.192_splice	c.e4-1	p.R64_splice		NM_152357	NP_689570			zinc finger protein 440						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF709	163051	broad.mit.edu	37	19	12574828	12574828	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12574828T>A	uc002mtv.3	-	4	2069	c.1908A>T	c.(1906-1908)AGA>AGT	p.R636S	ZNF709_uc002mtw.3_Missense_Mutation_p.R604S|ZNF709_uc002mtx.3_Missense_Mutation_p.R636S	NM_152601	NP_689814	Q8N972	ZN709_HUMAN	zinc finger protein 709 isoform a	636	C2H2-type 19.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
MAST1	22983	broad.mit.edu	37	19	12963047	12963047	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12963047G>A	uc002mvm.2	+	9	1123	c.995G>A	c.(994-996)CGT>CAT	p.R332H	MAST1_uc002mvk.2_Missense_Mutation_p.R328H	NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase	332					cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7																		---	---	---	---
NFIX	4784	broad.mit.edu	37	19	13192651	13192651	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13192651G>A	uc010xmx.1	+	8	1313	c.1260G>A	c.(1258-1260)TCG>TCA	p.S420S	NFIX_uc002mwd.2_Silent_p.S412S|NFIX_uc002mwe.2_Silent_p.S404S|NFIX_uc002mwf.2_Silent_p.S374S|NFIX_uc002mwg.1_Silent_p.S411S			Q14938	NFIX_HUMAN	RecName: Full=Nuclear factor 1;	412					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)													OREG0025286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TRMT1	55621	broad.mit.edu	37	19	13223783	13223783	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13223783G>A	uc002mwj.2	-	5	934	c.684C>T	c.(682-684)GAC>GAT	p.D228D	TRMT1_uc002mwk.2_Silent_p.D228D|TRMT1_uc002mwl.3_Silent_p.D228D|TRMT1_uc010xmz.1_Silent_p.D14D	NM_017722	NP_060192	Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 isoform 1	228							RNA binding|tRNA (guanine-N2-)-methyltransferase activity|zinc ion binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)														---	---	---	---
RFX1	5989	broad.mit.edu	37	19	14080802	14080802	+	Intron	SNP	C	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14080802C>G	uc002mxv.2	-						RFX1_uc010dzi.2_Nonstop_Mutation_p.*500Y	NM_002918	NP_002909			regulatory factor X1						immune response	nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			lung(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)															---	---	---	---
OR1I1	126370	broad.mit.edu	37	19	15198125	15198125	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15198125G>A	uc010xoe.1	+	1	249	c.249G>A	c.(247-249)GCG>GCA	p.A83A		NM_001004713	NP_001004713	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I,	83	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3																		---	---	---	---
AKAP8L	26993	broad.mit.edu	37	19	15511752	15511752	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15511752G>A	uc002naw.1	-						AKAP8L_uc002nax.1_Intron|AKAP8L_uc010xoh.1_Intron|AKAP8L_uc002nay.1_Intron|AKAP8L_uc002naz.2_Intron	NM_014371	NP_055186			A kinase (PRKA) anchor protein 8-like							cytoplasm|nuclear matrix	DEAD/H-box RNA helicase binding|DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CYP4F12	66002	broad.mit.edu	37	19	15806782	15806782	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15806782C>T	uc002nbl.2	+	10	1213	c.1152C>T	c.(1150-1152)TGC>TGT	p.C384C		NM_023944	NP_076433			cytochrome P450, family 4, subfamily F,									p.C384C(1)		skin(3)|ovary(2)|central_nervous_system(2)	7	Acute lymphoblastic leukemia(2;0.0367)																	---	---	---	---
EPS15L1	58513	broad.mit.edu	37	19	16535966	16535966	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16535966C>T	uc002ndz.1	-	9	726	c.720G>A	c.(718-720)CCG>CCA	p.P240P	EPS15L1_uc002ndx.2_Silent_p.P240P|EPS15L1_uc002ndy.2_RNA|EPS15L1_uc010xpe.1_Silent_p.P130P|EPS15L1_uc010xpf.1_Silent_p.P143P|EPS15L1_uc002nea.1_Silent_p.P240P|EPS15L1_uc010eah.1_Silent_p.P240P|EPS15L1_uc002neb.1_Silent_p.P86P|EPS15L1_uc002nec.1_Silent_p.P240P	NM_021235	NP_067058	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway	240					endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	coated pit|nucleus|plasma membrane	calcium ion binding			ovary(3)|skin(2)	5																		---	---	---	---
NWD1	284434	broad.mit.edu	37	19	16918583	16918583	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16918583G>A	uc002neu.3	+	18	4345	c.3923G>A	c.(3922-3924)AGC>AAC	p.S1308N	NWD1_uc002net.3_Missense_Mutation_p.S1173N|NWD1_uc002nev.3_Missense_Mutation_p.S1102N			Q149M9	NWD1_HUMAN	RecName: Full=NACHT and WD repeat domain-containing protein 1;	1308							ATP binding			skin(3)|ovary(2)|pancreas(2)	7																		---	---	---	---
FCHO1	23149	broad.mit.edu	37	19	17893892	17893892	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17893892C>T	uc010ebb.2	+	23	2193	c.2004C>T	c.(2002-2004)AGC>AGT	p.S668S	FCHO1_uc002nhg.3_Silent_p.S668S|FCHO1_uc002nhh.2_Silent_p.S668S|FCHO1_uc010xpw.1_Silent_p.S618S|FCHO1_uc002nhi.2_Silent_p.S124S|FCHO1_uc002nhj.2_Silent_p.S12S	NM_001161358	NP_001154830	O14526	FCHO1_HUMAN	FCH domain only 1 isoform b	668										breast(1)	1																		---	---	---	---
LSM4	25804	broad.mit.edu	37	19	18420588	18420588	+	Silent	SNP	G	A	A	rs138296949	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18420588G>A	uc002niq.2	-	4	399	c.228C>T	c.(226-228)ATC>ATT	p.I76I		NM_012321	NP_036453	Q9Y4Z0	LSM4_HUMAN	U6 snRNA-associated Sm-like protein 4	76					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|mRNA processing|RNA splicing	cytosol|U6 snRNP	protein binding|RNA binding				0																		---	---	---	---
SFRS14	10147	broad.mit.edu	37	19	19119122	19119122	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19119122G>A	uc002nkx.2	-						SFRS14_uc002nkz.1_Intron|SFRS14_uc002nla.1_Intron|SFRS14_uc002nlb.2_Intron|SFRS14_uc010xqk.1_Intron	NM_014884	NP_055699			splicing factor, arginine/serine-rich 14						mRNA processing|RNA splicing	nucleus	RNA binding				0			OV - Ovarian serous cystadenocarcinoma(5;3.05e-05)|Epithelial(12;0.00161)															---	---	---	---
TMEM161A	54929	broad.mit.edu	37	19	19240983	19240983	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19240983C>T	uc002nlg.2	-	6	607	c.577G>A	c.(577-579)GAG>AAG	p.E193K	TMEM161A_uc010eca.2_RNA|TMEM161A_uc002nlh.2_Missense_Mutation_p.E168K|TMEM161A_uc002nli.2_Intron|TMEM161A_uc002nlj.2_Missense_Mutation_p.E68K	NM_017814	NP_060284	Q9NX61	T161A_HUMAN	transmembrane protein 161A precursor	193	Cytoplasmic (Potential).				cellular response to oxidative stress|cellular response to UV|negative regulation of apoptosis|positive regulation of DNA repair|response to retinoic acid	integral to membrane				breast(2)	2			OV - Ovarian serous cystadenocarcinoma(5;1.19e-05)|Epithelial(12;0.0011)															---	---	---	---
SF4	57794	broad.mit.edu	37	19	19391027	19391027	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19391027G>A	uc002nmh.2	-	9	1319	c.1317C>T	c.(1315-1317)GAC>GAT	p.D439D	SF4_uc002nmf.2_Translation_Start_Site|SF4_uc002nmg.2_Translation_Start_Site|SF4_uc002nmi.2_Silent_p.D229D|SF4_uc002nmj.2_Silent_p.D229D|SF4_uc002nme.2_Translation_Start_Site	NM_172231	NP_757386	Q8IWZ8	SUGP1_HUMAN	splicing factor 4	439					nuclear mRNA splicing, via spliceosome	nucleoplasm|spliceosomal complex	RNA binding				0																		---	---	---	---
ZNF208	7757	broad.mit.edu	37	19	22154680	22154680	+	Silent	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22154680A>C	uc002nqp.2	-	6	2921	c.2772T>G	c.(2770-2772)GCT>GCG	p.A924A	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)																---	---	---	---
ZNF676	163223	broad.mit.edu	37	19	22363176	22363176	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22363176G>C	uc002nqs.1	-	3	1661	c.1343C>G	c.(1342-1344)CCC>CGC	p.P448R		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	448					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)																---	---	---	---
ZNF99	7652	broad.mit.edu	37	19	22940373	22940373	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22940373T>C	uc010xrh.1	-	5	2065	c.2065A>G	c.(2065-2067)AAG>GAG	p.K689E		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)																---	---	---	---
TSHZ3	57616	broad.mit.edu	37	19	31769550	31769550	+	Silent	SNP	C	T	T	rs148943651		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31769550C>T	uc002nsy.3	-	2	1214	c.1149G>A	c.(1147-1149)TCG>TCA	p.S383S		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	383					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)																	---	---	---	---
RHPN2	85415	broad.mit.edu	37	19	33482843	33482843	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33482843C>T	uc002nuf.2	-	13	1596	c.1530G>A	c.(1528-1530)CGG>CGA	p.R510R	RHPN2_uc010xro.1_Silent_p.R359R|RHPN2_uc002nue.2_Silent_p.R240R	NM_033103	NP_149094	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	510					signal transduction	perinuclear region of cytoplasm	protein binding			central_nervous_system(5)|ovary(1)	6	Esophageal squamous(110;0.137)																	---	---	---	---
PEPD	5184	broad.mit.edu	37	19	33968960	33968960	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33968960G>A	uc002nur.3	-	7	675	c.540C>T	c.(538-540)ATC>ATT	p.I180I	PEPD_uc010xrr.1_Silent_p.I180I|PEPD_uc010xrs.1_Silent_p.I116I	NM_000285	NP_000276	P12955	PEPD_HUMAN	prolidase isoform 1	180					cellular amino acid metabolic process|collagen catabolic process|proteolysis		aminopeptidase activity|dipeptidase activity|manganese ion binding|metallocarboxypeptidase activity			ovary(2)	2	Esophageal squamous(110;0.137)																	---	---	---	---
GPI	2821	broad.mit.edu	37	19	34890536	34890536	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34890536G>A	uc002nvg.1	+	16	1577	c.1474G>A	c.(1474-1476)GCC>ACC	p.A492T	GPI_uc002nvf.2_Missense_Mutation_p.A531T|GPI_uc010xrv.1_Missense_Mutation_p.A503T|GPI_uc010xrw.1_Missense_Mutation_p.A464T|GPI_uc010edl.1_Intron|GPI_uc002nvi.1_Missense_Mutation_p.A155T	NM_000175	NP_000166	P06744	G6PI_HUMAN	glucose phosphate isomerase	492					angiogenesis|gluconeogenesis|glycolysis|hemostasis|humoral immune response	cytosol|extracellular space|nucleus|plasma membrane	cytokine activity|glucose-6-phosphate isomerase activity|growth factor activity			ovary(1)|kidney(1)	2	Esophageal squamous(110;0.162)																	---	---	---	---
GRAMD1A	57655	broad.mit.edu	37	19	35514240	35514240	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35514240G>A	uc010xse.1	+	18	2091	c.1954G>A	c.(1954-1956)GCC>ACC	p.A652T	GRAMD1A_uc002nxk.2_Missense_Mutation_p.A641T|GRAMD1A_uc002nxl.2_Missense_Mutation_p.A414T|GRAMD1A_uc010xsf.1_Missense_Mutation_p.A653T|GRAMD1A_uc002nxm.1_RNA|GRAMD1A_uc002nxn.1_Missense_Mutation_p.A263T	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1	652						integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)															---	---	---	---
USF2	7392	broad.mit.edu	37	19	35761384	35761384	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35761384G>A	uc002nyq.1	+	5	573	c.464G>A	c.(463-465)AGT>AAT	p.S155N	USF2_uc010xss.1_Missense_Mutation_p.S155N|USF2_uc002nyr.1_Missense_Mutation_p.S88N|USF2_uc002nys.1_5'UTR|USF2_uc002nyt.1_Intron|USF2_uc002nyu.1_5'UTR|USF2_uc002nyv.1_5'UTR	NM_003367	NP_003358	Q15853	USF2_HUMAN	upstream stimulatory factor 2 isoform 1	155					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)															---	---	---	---
USF2	7392	broad.mit.edu	37	19	35761690	35761690	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35761690G>A	uc002nyq.1	+	6	759	c.650G>A	c.(649-651)CGG>CAG	p.R217Q	USF2_uc010xss.1_Missense_Mutation_p.R217Q|USF2_uc002nyr.1_Missense_Mutation_p.R150Q|USF2_uc002nys.1_Missense_Mutation_p.R19Q|USF2_uc002nyt.1_Missense_Mutation_p.R86Q|USF2_uc002nyu.1_Missense_Mutation_p.R19Q|USF2_uc002nyv.1_Missense_Mutation_p.R19Q	NM_003367	NP_003358	Q15853	USF2_HUMAN	upstream stimulatory factor 2 isoform 1	217					lipid homeostasis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter by glucose	nucleus	bHLH transcription factor binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity				0	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)															---	---	---	---
CD22	933	broad.mit.edu	37	19	35828791	35828791	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35828791C>A	uc010edt.2	+	5	929	c.852C>A	c.(850-852)ACC>ACA	p.T284T	CD22_uc010xst.1_Silent_p.T112T|CD22_uc010edu.2_Silent_p.T284T|CD22_uc010edv.2_Silent_p.T284T|CD22_uc002nzb.3_Intron|CD22_uc010edx.2_RNA	NM_001771	NP_001762	P20273	CD22_HUMAN	CD22 molecule precursor	284	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion		protein binding|sugar binding			ovary(5)|lung(3)|breast(1)	9	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		OspA lipoprotein(DB00045)													---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36223276	36223276	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36223276C>A	uc010eei.2	+	29	5826	c.5826C>A	c.(5824-5826)CCC>CCA	p.P1942P		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	1942					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)															---	---	---	---
NFKBID	84807	broad.mit.edu	37	19	36387021	36387021	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36387021G>A	uc002oci.1	-	9	1041	c.467C>T	c.(466-468)CCG>CTG	p.P156L	NFKBID_uc002och.1_5'UTR|NFKBID_uc002ocj.1_Missense_Mutation_p.P171L	NM_139239	NP_640332	Q8NI38	IKBD_HUMAN	nuclear factor of kappa light polypeptide gene	156	ANK 4.				inflammatory response	nucleus					0																		---	---	---	---
CLIP3	25999	broad.mit.edu	37	19	36508783	36508783	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36508783C>T	uc010eeq.1	-	9	1576	c.1294G>A	c.(1294-1296)GTG>ATG	p.V432M	uc002ocy.2_Intron|CLIP3_uc002ocz.1_Missense_Mutation_p.V432M	NM_015526	NP_056341	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	432					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)															---	---	---	---
ZNF568	374900	broad.mit.edu	37	19	37441545	37441545	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37441545C>T	uc002ofc.2	+	7	2005	c.1490C>T	c.(1489-1491)ACG>ATG	p.T497M	ZNF568_uc010efg.2_Intron|ZNF568_uc010xtn.1_Intron|ZNF568_uc002ofd.2_Missense_Mutation_p.T421M|ZNF568_uc010efe.2_Missense_Mutation_p.T421M|ZNF568_uc010eff.1_Intron	NM_198539	NP_940941	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	497					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF420	147923	broad.mit.edu	37	19	37618976	37618976	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37618976A>C	uc002ofl.2	+	5	1298	c.1083A>C	c.(1081-1083)AAA>AAC	p.K361N		NM_144689	NP_653290	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	361					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF527	84503	broad.mit.edu	37	19	37879380	37879380	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37879380G>A	uc010efk.1	+	5	540	c.429G>A	c.(427-429)GCG>GCA	p.A143A	ZNF527_uc002ogf.3_Silent_p.A111A|ZNF527_uc010xtq.1_RNA	NM_032453	NP_115829	Q8NB42	ZN527_HUMAN	zinc finger protein 527	143					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)															---	---	---	---
YIF1B	90522	broad.mit.edu	37	19	38798088	38798088	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38798088C>T	uc002ohz.2	-	7	818	c.769G>A	c.(769-771)GTA>ATA	p.V257I	YIF1B_uc002ohw.2_Missense_Mutation_p.V226I|YIF1B_uc002ohx.2_Missense_Mutation_p.V242I|YIF1B_uc010xtx.1_Missense_Mutation_p.V240I|YIF1B_uc010xty.1_Missense_Mutation_p.V226I|YIF1B_uc002oia.2_Missense_Mutation_p.V254I|YIF1B_uc002ohy.2_Missense_Mutation_p.V254I|YIF1B_uc002oib.2_Missense_Mutation_p.V254I	NM_001039672	NP_001034761	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B isoform 5	257	Helical; (Potential).					integral to membrane					0	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
PSMD8	5714	broad.mit.edu	37	19	38873894	38873894	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38873894G>A	uc002oii.3	+	7	969	c.917G>A	c.(916-918)CGA>CAA	p.R306Q		NM_002812	NP_002803	P48556	PSMD8_HUMAN	proteasome 26S non-ATPase subunit 8	306					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|proteasome regulatory particle	protein binding			central_nervous_system(1)	1	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39068584	39068584	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39068584C>T	uc002oit.2	+	98	14329	c.14199C>T	c.(14197-14199)TAC>TAT	p.Y4733Y	RYR1_uc002oiu.2_Silent_p.Y4728Y	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4733					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
MAP4K1	11184	broad.mit.edu	37	19	39103240	39103240	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39103240C>T	uc002oix.1	-						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)															---	---	---	---
PLEKHG2	64857	broad.mit.edu	37	19	39913533	39913533	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39913533C>T	uc010xuz.1	+	18	2164	c.1839C>T	c.(1837-1839)CAC>CAT	p.H613H	PLEKHG2_uc010xuy.1_Silent_p.H554H|PLEKHG2_uc002olj.2_Intron|PLEKHG2_uc010xva.1_Silent_p.H391H	NM_022835	NP_073746	Q9H7P9	PKHG2_HUMAN	common-site lymphoma/leukemia guanine nucleotide	613					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			skin(2)|pancreas(1)|breast(1)	4	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
PSMC4	5704	broad.mit.edu	37	19	40485741	40485741	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40485741G>A	uc002omq.2	+	7	728	c.691G>A	c.(691-693)GTG>ATG	p.V231M	PSMC4_uc002omr.2_Missense_Mutation_p.V200M	NM_006503	NP_006494	P43686	PRS6B_HUMAN	proteasome 26S ATPase subunit 4 isoform 1	231					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	mitochondrion|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding			ovary(1)	1	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)																	---	---	---	---
AKT2	208	broad.mit.edu	37	19	40747883	40747883	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40747883C>T	uc002onf.2	-	6	797	c.535G>A	c.(535-537)GCC>ACC	p.A179T	AKT2_uc010egs.2_Missense_Mutation_p.A179T|AKT2_uc010egt.2_Missense_Mutation_p.A117T|AKT2_uc010xvj.1_Missense_Mutation_p.A117T|AKT2_uc010egu.1_Missense_Mutation_p.A117T|AKT2_uc010xvk.1_Missense_Mutation_p.A179T|AKT2_uc002one.2_Missense_Mutation_p.A75T	NM_001626	NP_001617	P31751	AKT2_HUMAN	AKT2 kinase	179	Protein 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 								---	---	---	---
C19orf47	126526	broad.mit.edu	37	19	40834366	40834366	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40834366C>T	uc002oni.3	-	6	505	c.504G>A	c.(502-504)TCG>TCA	p.S168S	C19orf47_uc002ong.2_Silent_p.S27S|C19orf47_uc002onh.2_Silent_p.S101S	NM_178830	NP_849152	Q8N9M1	CS047_HUMAN	hypothetical protein LOC126526	168										ovary(1)|skin(1)	2			Lung(22;0.000636)															---	---	---	---
LTBP4	8425	broad.mit.edu	37	19	41135394	41135394	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41135394G>A	uc002ooh.1	+	34	4814	c.4814G>A	c.(4813-4815)CGC>CAC	p.R1605H	LTBP4_uc002oog.1_Missense_Mutation_p.R1568H|LTBP4_uc002ooi.1_Missense_Mutation_p.R1538H|LTBP4_uc002ooj.1_Missense_Mutation_p.R478H|LTBP4_uc002ool.1_Missense_Mutation_p.R617H|LTBP4_uc010xvp.1_Missense_Mutation_p.R365H	NM_001042544	NP_001036009	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding	1605	EGF-like 16.				growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
CYP2S1	29785	broad.mit.edu	37	19	41709424	41709424	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41709424G>A	uc002opw.2	+	7	1101	c.1046G>A	c.(1045-1047)CGC>CAC	p.R349H	CYP2F1_uc010xvw.1_Intron|CYP2S1_uc010xvx.1_Missense_Mutation_p.R74H	NM_030622	NP_085125	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S,	349					xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity			skin(1)	1																		---	---	---	---
CCDC97	90324	broad.mit.edu	37	19	41822537	41822537	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41822537C>T	uc002oqg.2	+	2	417	c.295C>T	c.(295-297)CTG>TTG	p.L99L	CYP2F1_uc010xvw.1_Intron	NM_052848	NP_443080	Q96F63	CCD97_HUMAN	coiled-coil domain containing 97	99											0																		---	---	---	---
ZNF574	64763	broad.mit.edu	37	19	42583781	42583781	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42583781C>T	uc002osm.3	+	2	1192	c.1023C>T	c.(1021-1023)TGC>TGT	p.C341C	ZNF574_uc002osk.3_Silent_p.C431C	NM_022752	NP_073589	Q6ZN55	ZN574_HUMAN	zinc finger protein 574	341	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.059)																---	---	---	---
ERF	2077	broad.mit.edu	37	19	42752741	42752741	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42752741C>A	uc002ote.3	-	4	1681	c.1523G>T	c.(1522-1524)GGT>GTT	p.G508V	ERF_uc002otd.3_Missense_Mutation_p.G239V	NM_006494	NP_006485	P50548	ERF_HUMAN	Ets2 repressor factor	508					cell proliferation|regulation of transcription from RNA polymerase II promoter	nucleus	ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			lung(1)|kidney(1)|central_nervous_system(1)|skin(1)	4		Prostate(69;0.00682)																---	---	---	---
PSG5	5673	broad.mit.edu	37	19	43680089	43680089	+	Silent	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43680089G>T	uc002ovu.2	-	3	773	c.642C>A	c.(640-642)CCC>CCA	p.P214P	PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_Intron|PSG5_uc002ovx.2_Silent_p.P214P|PSG5_uc002ovv.2_Silent_p.P307P|PSG5_uc002ovw.2_Intron	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	214	Ig-like C2-type 1.				female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)																---	---	---	---
XRCC1	7515	broad.mit.edu	37	19	44048331	44048331	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44048331C>T	uc002owt.2	-	15	1797	c.1677G>A	c.(1675-1677)CGG>CGA	p.R559R	XRCC1_uc010xwp.1_Silent_p.R528R	NM_006297	NP_006288	P18887	XRCC1_HUMAN	X-ray repair cross complementing protein 1	559	BRCT 2.				base-excision repair|single strand break repair	nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(2)|large_intestine(1)|prostate(1)|breast(1)	7		Prostate(69;0.0153)											Other_BER_factors					---	---	---	---
CADM4	199731	broad.mit.edu	37	19	44131398	44131398	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44131398C>T	uc002oxc.1	-	3	333	c.284G>A	c.(283-285)CGC>CAC	p.R95H		NM_145296	NP_660339	Q8NFZ8	CADM4_HUMAN	cell adhesion molecule 4 precursor	95	Ig-like V-type.|Extracellular (Potential).				cell adhesion	integral to membrane					0		Prostate(69;0.0199)																---	---	---	---
IRGC	56269	broad.mit.edu	37	19	44223276	44223276	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44223276C>T	uc002oxh.2	+	2	713	c.566C>T	c.(565-567)GCT>GTT	p.A189V		NM_019612	NP_062558	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	189						membrane	GTP binding|hydrolase activity, acting on acid anhydrides			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(69;0.0435)																---	---	---	---
ZNF226	7769	broad.mit.edu	37	19	44676240	44676240	+	Splice_Site	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44676240G>T	uc002oyp.2	+	4	160	c.16_splice	c.e4-1	p.E6_splice	ZNF226_uc002oyn.2_Splice_Site_p.E6_splice|ZNF226_uc002oyo.2_Splice_Site_p.E6_splice|ZNF226_uc002oyq.2_Splice_Site|ZNF226_uc002oyr.2_Splice_Site|ZNF226_uc010ejg.2_Splice_Site_p.E6_splice|ZNF226_uc002oys.2_Splice_Site_p.E6_splice|ZNF226_uc002oyt.2_Splice_Site_p.E6_splice	NM_001032373	NP_001027545			zinc finger protein 226 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)|all_neural(266;0.202)																---	---	---	---
CBLC	23624	broad.mit.edu	37	19	45293358	45293358	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45293358G>A	uc002ozs.2	+						CBLC_uc010ejt.2_Intron	NM_012116	NP_036248			Cas-Br-M (murine) ecotropic retroviral						cell surface receptor linked signaling pathway|negative regulation of epidermal growth factor receptor activity|negative regulation of MAP kinase activity|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	calcium ion binding|epidermal growth factor receptor binding|phosphotyrosine binding|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|skin(1)	6	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)						M		AML								---	---	---	---
CLPTM1	1209	broad.mit.edu	37	19	45490450	45490450	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45490450C>T	uc002pai.2	+	8	822	c.807C>T	c.(805-807)GAC>GAT	p.D269D	CLPTM1_uc010ejv.1_Silent_p.D167D|CLPTM1_uc010xxf.1_Silent_p.D167D|CLPTM1_uc010xxg.1_Silent_p.D255D	NM_001294	NP_001285	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane	269	Extracellular (Potential).				cell differentiation|multicellular organismal development|regulation of T cell differentiation in thymus	external side of plasma membrane|integral to plasma membrane				ovary(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)														---	---	---	---
ERCC2	2068	broad.mit.edu	37	19	45855905	45855905	+	Silent	SNP	C	T	T	rs145835916		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45855905C>T	uc002pbj.2	-	21	1952	c.1905G>A	c.(1903-1905)GCG>GCA	p.A635A	ERCC2_uc002pbh.2_Silent_p.A198A|ERCC2_uc002pbi.2_Silent_p.A328A|ERCC2_uc010ejz.2_Silent_p.A557A|ERCC2_uc002pbk.2_Silent_p.A611A	NM_000400	NP_000391	P18074	ERCC2_HUMAN	excision repair cross-complementing rodent	635	Mediates interaction with MMS19.				cell cycle checkpoint|chromosome segregation|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|UV protection|viral reproduction	cytoplasm|holo TFIIH complex|MMXD complex	5'-3' DNA helicase activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding|protein C-terminus binding|protein N-terminus binding			lung(2)|pancreas(1)	3		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)				Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
FOXA3	3171	broad.mit.edu	37	19	46376101	46376101	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46376101A>G	uc002pdr.2	+	2	1035	c.838A>G	c.(838-840)ACA>GCA	p.T280A		NM_004497	NP_004488	P55318	FOXA3_HUMAN	forkhead box A3	280					brain development|cellular glucose homeostasis|cellular response to starvation|chromatin modification|embryo development|endocrine pancreas development|negative regulation of cell proliferation|neural plate anterior/posterior regionalization|neuron fate specification|positive regulation of hepatocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|spermatogenesis	transcription factor complex	DNA bending activity|double-stranded DNA binding|protein domain specific 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|transcription regulatory region DNA binding			breast(1)	1		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00453)|GBM - Glioblastoma multiforme(486;0.0518)|Epithelial(262;0.236)														---	---	---	---
IGFL4	444882	broad.mit.edu	37	19	46543646	46543646	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46543646C>T	uc002pdy.1	-	3	153	c.99G>A	c.(97-99)GCG>GCA	p.A33A		NM_001002923	NP_001002923	Q6B9Z1	IGFL4_HUMAN	IGF-like family member 4 precursor	33						extracellular region					0		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.0036)|GBM - Glioblastoma multiforme(486;0.022)|Epithelial(262;0.208)														---	---	---	---
PPP5C	5536	broad.mit.edu	37	19	46857048	46857048	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46857048C>T	uc002pem.2	+	2	225	c.165C>T	c.(163-165)ATC>ATT	p.I55I	PPP5C_uc010xya.1_5'UTR|PPP5C_uc002pen.2_Silent_p.I55I	NM_006247	NP_006238	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	55	TPR 1.				mitosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein dephosphorylation|transcription, DNA-dependent	Golgi apparatus|nucleus	metal ion binding|protein binding|protein serine/threonine phosphatase activity|signal transducer activity			lung(1)|pancreas(1)	2		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)														---	---	---	---
PNMAL1	55228	broad.mit.edu	37	19	46973945	46973945	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46973945G>A	uc002peq.3	-	2	654	c.348C>T	c.(346-348)GCC>GCT	p.A116A	PNMAL1_uc002per.3_Silent_p.A116A	NM_018215	NP_060685	Q86V59	PNML1_HUMAN	PNMA-like 1 isoform a	116											0		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)														---	---	---	---
GRLF1	2909	broad.mit.edu	37	19	47422067	47422067	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47422067G>A	uc010ekv.2	+	1	135	c.135G>A	c.(133-135)CCG>CCA	p.P45P		NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1	45					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)														---	---	---	---
SLC8A2	6543	broad.mit.edu	37	19	47951332	47951332	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47951332G>A	uc002pgx.2	-	4	1775	c.1497C>T	c.(1495-1497)GGC>GGT	p.G499G	SLC8A2_uc010xyq.1_Silent_p.G255G|SLC8A2_uc010xyr.1_Intron|SLC8A2_uc010ele.2_Silent_p.G499G	NM_015063	NP_055878	Q9UPR5	NAC2_HUMAN	solute carrier family 8 member 2 precursor	499	Cytoplasmic (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(1)	4		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)														---	---	---	---
PLEKHA4	57664	broad.mit.edu	37	19	49362226	49362226	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49362226C>T	uc002pkx.2	-	8	1414	c.863G>A	c.(862-864)CGC>CAC	p.R288H	PLEKHA4_uc002pkw.1_Intron|PLEKHA4_uc010eml.2_Missense_Mutation_p.R288H	NM_020904	NP_065955	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing family A	288	Pro-rich.					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	49368837	49368837	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49368837C>T	uc002pkx.2	-	3	666	c.115G>A	c.(115-117)GCC>ACC	p.A39T	PLEKHA4_uc010eml.2_Missense_Mutation_p.A39T	NM_020904	NP_065955	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing family A	39						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)														---	---	---	---
RUVBL2	10856	broad.mit.edu	37	19	49510397	49510397	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49510397C>T	uc002plr.1	+	5	401	c.388C>T	c.(388-390)CGC>TGC	p.R130C	RUVBL2_uc002plq.1_Missense_Mutation_p.R85C|RUVBL2_uc010yab.1_Missense_Mutation_p.R130C|RUVBL2_uc002pls.1_RNA|RUVBL2_uc010emn.1_Missense_Mutation_p.R85C|RUVBL2_uc010yac.1_Missense_Mutation_p.R85C	NM_006666	NP_006657	Q9Y230	RUVB2_HUMAN	RuvB-like 2	130					cellular response to UV|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|protein folding|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex|membrane|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|ATP-dependent DNA helicase activity|damaged DNA binding|identical protein binding|unfolded protein binding				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)														---	---	---	---
KCNA7	3743	broad.mit.edu	37	19	49573446	49573446	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49573446A>G	uc002pmg.2	-	2	1601	c.1245T>C	c.(1243-1245)CAT>CAC	p.H415H		NM_031886	NP_114092	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related	415						voltage-gated potassium channel complex	voltage-gated potassium channel activity			central_nervous_system(1)	1		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)														---	---	---	---
PRMT1	3276	broad.mit.edu	37	19	50189896	50189896	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50189896G>A	uc010enf.1	+	10	987	c.945G>A	c.(943-945)ACG>ACA	p.T315T	PRMT1_uc002ppc.1_RNA|PRMT1_uc002ppd.2_Silent_p.T291T|PRMT1_uc002ppe.2_Silent_p.T297T|PRMT1_uc002ppf.2_RNA|PRMT1_uc002ppg.2_Silent_p.T262T|PRMT1_uc010ybb.1_5'Flank|C19orf76_uc002pph.2_5'Flank	NM_001536	NP_001527	Q8WUW5	Q8WUW5_HUMAN	HMT1 hnRNP methyltransferase-like 2 isoform 1	296						cytoplasm	protein methyltransferase activity			ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)														---	---	---	---
ZNF473	25888	broad.mit.edu	37	19	50542512	50542512	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50542512C>T	uc002prn.2	+	3	341	c.104C>T	c.(103-105)GCG>GTG	p.A35V	ZNF473_uc002prm.2_Missense_Mutation_p.A35V|ZNF473_uc010ybo.1_Missense_Mutation_p.A23V	NM_001006656	NP_001006657	Q8WTR7	ZN473_HUMAN	zinc finger protein 473	35	KRAB.				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)														---	---	---	---
ZNF473	25888	broad.mit.edu	37	19	50545072	50545072	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50545072C>T	uc002prn.2	+	4	459	c.222C>T	c.(220-222)AGC>AGT	p.S74S	ZNF473_uc002prm.2_Silent_p.S74S|ZNF473_uc010ybo.1_Silent_p.S62S	NM_001006656	NP_001006657	Q8WTR7	ZN473_HUMAN	zinc finger protein 473	74	KRAB.				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)														---	---	---	---
GPR32	2854	broad.mit.edu	37	19	51274765	51274765	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51274765C>T	uc010ycf.1	+	1	908	c.908C>T	c.(907-909)GCC>GTC	p.A303V		NM_001506	NP_001497	O75388	GPR32_HUMAN	G protein-coupled receptor 32	303	Helical; Name=7; (Potential).					integral to plasma membrane	N-formyl peptide receptor activity			upper_aerodigestive_tract(1)	1		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)														---	---	---	---
ZNF468	90333	broad.mit.edu	37	19	53343967	53343967	+	3'UTR	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53343967T>G	uc002qaf.2	-	4					ZNF468_uc002qae.2_3'UTR	NM_001008801	NP_001008801			zinc finger protein ZNF468 isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.0358)														---	---	---	---
MBOAT7	79143	broad.mit.edu	37	19	54682578	54682578	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54682578C>T	uc002qdq.2	-	8	1201	c.935G>A	c.(934-936)CGG>CAG	p.R312Q	MBOAT7_uc010erg.2_5'UTR|MBOAT7_uc010yem.1_Missense_Mutation_p.R294Q|MBOAT7_uc002qdr.2_Missense_Mutation_p.R312Q|MBOAT7_uc002qds.2_Missense_Mutation_p.R239Q|MBOAT7_uc010yen.1_Missense_Mutation_p.R239Q|MBOAT7_uc002qdt.3_Missense_Mutation_p.R312Q	NM_024298	NP_077274	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain	312					phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)																	---	---	---	---
LILRB3	11025	broad.mit.edu	37	19	54720983	54720983	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54720983G>A	uc002qef.1	-	13	1986	c.1875C>T	c.(1873-1875)TAC>TAT	p.Y625Y	LILRB3_uc002qee.1_Silent_p.Y626Y|LILRB3_uc002qeh.1_Silent_p.Y625Y|LILRB3_uc002qeg.1_RNA|LILRB3_uc002qei.1_Silent_p.Y625Y|LILRA6_uc002qek.1_Silent_p.Y626Y|LILRB3_uc010erh.1_Silent_p.Y642Y|LILRB3_uc002qej.1_RNA|LILRA6_uc002qel.1_Silent_p.Y625Y|LILRA6_uc002qem.1_RNA|LILRB3_uc002qen.1_RNA|LILRB3_uc002qeo.1_Silent_p.Y626Y|LILRB3_uc002qep.1_Silent_p.Y626Y|LILRB3_uc002qeq.1_Silent_p.Y625Y|LILRB3_uc002qer.1_RNA|LILRB3_uc002qes.1_Silent_p.Y626Y	NM_006864	NP_006855	O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor,	625	ITIM motif 3.|Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	transmembrane receptor activity			skin(2)|ovary(1)	3	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)														---	---	---	---
NCR1	9437	broad.mit.edu	37	19	55420752	55420752	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55420752C>T	uc002qib.2	+	4	542	c.504C>T	c.(502-504)TAC>TAT	p.Y168Y	NCR1_uc002qic.2_Silent_p.Y168Y|NCR1_uc002qie.2_Silent_p.Y168Y|NCR1_uc002qid.2_Silent_p.Y73Y|NCR1_uc002qif.2_Silent_p.Y73Y|NCR1_uc010esj.2_Silent_p.Y61Y	NM_004829	NP_004820	O76036	NCTR1_HUMAN	natural cytotoxicity triggering receptor 1	168	Extracellular (Potential).|Ig-like 2.				cellular defense response|natural killer cell activation|regulation of natural killer cell mediated cytotoxicity	integral to plasma membrane|SWI/SNF complex	receptor activity|receptor signaling protein activity			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(193;0.0449)														---	---	---	---
NLRP2	55655	broad.mit.edu	37	19	55494974	55494974	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55494974C>T	uc002qij.2	+	6	1994	c.1908C>T	c.(1906-1908)GAC>GAT	p.D636D	NLRP2_uc010yfp.1_Silent_p.D613D|NLRP2_uc010esn.2_Silent_p.D612D|NLRP2_uc010eso.2_Silent_p.D633D|NLRP2_uc010esp.2_Silent_p.D614D	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	636					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)														---	---	---	---
NLRP9	338321	broad.mit.edu	37	19	56243922	56243922	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56243922G>A	uc002qly.2	-	2	1303	c.1275C>T	c.(1273-1275)GGC>GGT	p.G425G		NM_176820	NP_789790	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	425	NACHT.		G -> D (in a breast cancer sample; somatic mutation).			cytoplasm	ATP binding	p.G425D(1)		skin(4)|ovary(2)|breast(1)	7		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)														---	---	---	---
PEG3	5178	broad.mit.edu	37	19	57333110	57333110	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57333110C>T	uc002qnu.2	-	4	929	c.578G>A	c.(577-579)CGG>CAG	p.R193Q	ZIM2_uc010ygq.1_5'UTR|ZIM2_uc010ygr.1_5'UTR|ZIM2_uc002qnr.2_Missense_Mutation_p.R68Q|ZIM2_uc002qnq.2_Missense_Mutation_p.R68Q|ZIM2_uc010etp.2_Missense_Mutation_p.R68Q|ZIM2_uc010ygs.1_Missense_Mutation_p.R68Q|PEG3_uc002qnt.2_Missense_Mutation_p.R194Q|PEG3_uc002qnv.2_Missense_Mutation_p.R193Q|PEG3_uc002qnw.2_Missense_Mutation_p.R68Q|PEG3_uc002qnx.2_Missense_Mutation_p.R67Q|PEG3_uc010etr.2_Missense_Mutation_p.R193Q	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	193					apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	p.R193W(1)		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)														---	---	---	---
ZNF543	125919	broad.mit.edu	37	19	57839932	57839932	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57839932G>A	uc002qoi.1	+	4	1447	c.1102G>A	c.(1102-1104)GAA>AAA	p.E368K		NM_213598	NP_998763	Q08ER8	ZN543_HUMAN	zinc finger protein 543	368	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)|pancreas(1)	2		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;0.0257)														---	---	---	---
ZNF17	7565	broad.mit.edu	37	19	57931842	57931842	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57931842C>T	uc002qoo.1	+	3	1213	c.982C>T	c.(982-984)CGG>TGG	p.R328W	ZNF547_uc002qpm.3_Intron|ZNF17_uc002qop.1_Missense_Mutation_p.R330W	NM_006959	NP_008890	P17021	ZNF17_HUMAN	zinc finger protein 17	328					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)														---	---	---	---
ZNF549	256051	broad.mit.edu	37	19	58048866	58048866	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58048866G>T	uc002qpb.1	+	4	743	c.494G>T	c.(493-495)AGC>ATC	p.S165I	ZNF547_uc002qpm.3_Intron|ZNF549_uc010eud.1_Intron|ZNF549_uc002qpa.1_Missense_Mutation_p.S152I	NM_153263	NP_694995	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	165					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)														---	---	---	---
ZNF416	55659	broad.mit.edu	37	19	58083691	58083691	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58083691G>A	uc002qpf.2	-	4	1752	c.1581C>T	c.(1579-1581)TGC>TGT	p.C527C	ZNF547_uc002qpm.3_Intron	NM_017879	NP_060349	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	527	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)														---	---	---	---
SLC27A5	10998	broad.mit.edu	37	19	59011792	59011792	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59011792A>G	uc002qtc.2	-	6	1492	c.1382T>C	c.(1381-1383)CTG>CCG	p.L461P	SLC27A5_uc002qtb.2_5'Flank	NM_012254	NP_036386	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid	461	Cytoplasmic (Probable).				bile acid and bile salt transport|bile acid biosynthetic process|very long-chain fatty acid metabolic process	endoplasmic reticulum membrane|integral to membrane	ATP binding|cholate-CoA ligase activity|long-chain fatty acid-CoA ligase activity				0		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)														---	---	---	---
PSMF1	9491	broad.mit.edu	37	20	1106263	1106263	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1106263C>T	uc002wel.3	+	3	420	c.252C>T	c.(250-252)ACC>ACT	p.T84T	PSMF1_uc010zpo.1_5'UTR|PSMF1_uc002wem.3_Silent_p.T84T|PSMF1_uc010zpp.1_Silent_p.T84T|PSMF1_uc002wen.3_Silent_p.T84T	NM_178578	NP_848693	Q92530	PSMF1_HUMAN	proteasome inhibitor subunit 1	84					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome core complex	endopeptidase inhibitor activity|protein binding				0																		---	---	---	---
VPS16	64601	broad.mit.edu	37	20	2840378	2840378	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2840378T>C	uc002whe.2	+	2	115	c.67T>C	c.(67-69)TAC>CAC	p.Y23H	VPS16_uc002whf.2_Missense_Mutation_p.Y23H|VPS16_uc002whd.2_RNA|VPS16_uc002whg.2_5'Flank	NM_022575	NP_072097	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 isoform 1	23					intracellular protein transport	early endosome|HOPS complex|late endosome membrane|lysosomal membrane|recycling endosome				ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
ProSAPiP1	9762	broad.mit.edu	37	20	3146842	3146842	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3146842T>C	uc002wia.1	-	2	2022	c.624A>G	c.(622-624)CCA>CCG	p.P208P	ProSAPiP1_uc002wib.1_Silent_p.P208P	NM_014731	NP_055546	O60299	PRIP1_HUMAN	ProSAPiP1 protein	208						cell junction|cytoplasm|postsynaptic density|postsynaptic membrane				pancreas(1)	1																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3565398	3565398	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3565398G>T	uc002wim.2	+	18	3145	c.3055G>T	c.(3055-3057)GGT>TGT	p.G1019C	ATRN_uc002wil.2_Missense_Mutation_p.G1019C	NM_139321	NP_647537	O75882	ATRN_HUMAN	attractin isoform 1	1019	Extracellular (Potential).|PSI 4.				inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
SMOX	54498	broad.mit.edu	37	20	4164164	4164164	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4164164C>T	uc002wkm.1	+	6	1594	c.1393C>T	c.(1393-1395)CGG>TGG	p.R465W	SMOX_uc002wkk.1_Missense_Mutation_p.R412W|SMOX_uc002wkl.1_Missense_Mutation_p.R412W|SMOX_uc002wkn.1_Intron|SMOX_uc002wkp.2_Missense_Mutation_p.R465W|SMOX_uc010zqo.1_Missense_Mutation_p.R389W|SMOX_uc002wko.1_Missense_Mutation_p.R465W	NM_175839	NP_787033	Q9NWM0	SMOX_HUMAN	spermine oxidase isoform 1	465					polyamine biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	polyamine oxidase activity			breast(1)	1					Spermine(DB00127)													---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8862464	8862464	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8862464A>G	uc002wnb.2	+	32	3622	c.3619A>G	c.(3619-3621)ATC>GTC	p.I1207V	PLCB1_uc002wna.2_3'UTR	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	1207					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																		---	---	---	---
SNAP25	6616	broad.mit.edu	37	20	10277684	10277684	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10277684C>T	uc002wnq.1	+	6	605	c.393C>T	c.(391-393)GGC>GGT	p.G131G	SNAP25_uc002wnr.1_Silent_p.G131G|SNAP25_uc002wns.1_Silent_p.G68G|SNAP25_uc010gca.1_Silent_p.G131G|SNAP25_uc010gcb.1_Silent_p.G68G|SNAP25_uc010gcc.1_Intron	NM_130811	NP_570824	P60880	SNP25_HUMAN	synaptosomal-associated protein 25 isoform	131					energy reserve metabolic process|glutamate secretion|neurotransmitter uptake|synaptic vesicle docking involved in exocytosis	cell junction|growth cone|perinuclear region of cytoplasm|synapse|synaptosome				skin(2)	2					Botulinum Toxin Type A(DB00083)													---	---	---	---
JAG1	182	broad.mit.edu	37	20	10622442	10622442	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10622442C>T	uc002wnw.2	-	22	3187	c.2671G>A	c.(2671-2673)GCC>ACC	p.A891T	JAG1_uc010gcd.1_Missense_Mutation_p.A449T	NM_000214	NP_000205	P78504	JAG1_HUMAN	jagged 1 precursor	891	Extracellular (Potential).				angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1)	9														Alagille_Syndrome				---	---	---	---
OTOR	56914	broad.mit.edu	37	20	16729527	16729527	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16729527C>T	uc002wpj.2	+	2	175	c.131C>T	c.(130-132)GCT>GTT	p.A44V	OTOR_uc002wpk.2_5'Flank	NM_020157	NP_064542	Q9NRC9	OTOR_HUMAN	otoraplin precursor	44	SH3.				sensory perception of sound	extracellular region				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PCSK2	5126	broad.mit.edu	37	20	17462676	17462676	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17462676C>T	uc002wpm.2	+	12	2198	c.1878C>T	c.(1876-1878)GCC>GCT	p.A626A	PCSK2_uc002wpl.2_Silent_p.A607A|PCSK2_uc010zrm.1_Silent_p.A591A|PCSK2_uc002wpn.2_Silent_p.A280A	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	626					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)													---	---	---	---
CSRP2BP	57325	broad.mit.edu	37	20	18143418	18143418	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18143418G>A	uc002wqj.2	+	7	2122	c.1500G>A	c.(1498-1500)GCG>GCA	p.A500A	CSRP2BP_uc002wqk.2_Silent_p.A372A|CSRP2BP_uc010zru.1_Silent_p.A371A	NM_020536	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	500					histone H3 acetylation	Ada2/Gcn5/Ada3 transcription activator complex|cytoplasm	LIM domain binding|N-acetyltransferase activity			lung(3)|ovary(2)|skin(1)	6																		---	---	---	---
ZNF133	7692	broad.mit.edu	37	20	18296783	18296783	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18296783C>T	uc010gcq.2	+	5	1593	c.1288C>T	c.(1288-1290)CGG>TGG	p.R430W	ZNF133_uc010zrv.1_Missense_Mutation_p.R433W|ZNF133_uc010zrw.1_Missense_Mutation_p.R367W|ZNF133_uc010gcr.2_Missense_Mutation_p.R430W|ZNF133_uc010zrx.1_Missense_Mutation_p.R335W|ZNF133_uc002wql.3_Missense_Mutation_p.R429W|ZNF133_uc010gcs.2_Missense_Mutation_p.R429W|ZNF133_uc010zry.1_Missense_Mutation_p.R335W|ZNF133_uc002wqm.2_Missense_Mutation_p.R430W	NM_003434	NP_003425	P52736	ZN133_HUMAN	zinc finger protein 133	430	C2H2-type 8.					nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20055909	20055909	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20055909C>T	uc002wru.2	+						C20orf26_uc010gcw.1_Intron|C20orf26_uc010zse.1_Intron|C20orf26_uc010zsf.1_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20257973	20257973	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20257973G>A	uc002wru.2	+	22	2743	c.2667G>A	c.(2665-2667)GCG>GCA	p.A889A	C20orf26_uc010zse.1_Silent_p.A869A|C20orf26_uc002wrw.2_RNA	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074	889										ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
PAX1	5075	broad.mit.edu	37	20	21687147	21687147	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21687147C>T	uc002wsj.2	+	2	412	c.358C>T	c.(358-360)CGC>TGC	p.R120C	PAX1_uc010zsl.1_Missense_Mutation_p.R120C|PAX1_uc010zsm.1_Missense_Mutation_p.R96C	NM_006192	NP_006183	P15863	PAX1_HUMAN	paired box 1	120	Paired.				regulation of transcription, DNA-dependent|skeletal system development|transcription from RNA polymerase II promoter	nucleus	DNA binding			upper_aerodigestive_tract(1)|kidney(1)	2																		---	---	---	---
PAX1	5075	broad.mit.edu	37	20	21687491	21687491	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21687491C>T	uc002wsj.2	+	2	756	c.702C>T	c.(700-702)TAC>TAT	p.Y234Y	PAX1_uc010zsl.1_Silent_p.Y234Y|PAX1_uc010zsm.1_Silent_p.Y210Y	NM_006192	NP_006183	P15863	PAX1_HUMAN	paired box 1	234					regulation of transcription, DNA-dependent|skeletal system development|transcription from RNA polymerase II promoter	nucleus	DNA binding			upper_aerodigestive_tract(1)|kidney(1)	2																		---	---	---	---
ACSS1	84532	broad.mit.edu	37	20	25011401	25011401	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25011401T>C	uc002wub.2	-	3	1503	c.625A>G	c.(625-627)AAT>GAT	p.N209D	ACSS1_uc002wuc.2_Missense_Mutation_p.N209D|ACSS1_uc010gdc.2_Missense_Mutation_p.N209D|ACSS1_uc002wua.2_Missense_Mutation_p.N126D	NM_032501	NP_115890	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	209					acetyl-CoA biosynthetic process|ethanol oxidation|xenobiotic metabolic process	mitochondrial matrix	acetate-CoA ligase activity|AMP binding|ATP binding|protein binding			ovary(1)|skin(1)	2					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
MAPRE1	22919	broad.mit.edu	37	20	31427543	31427543	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31427543C>T	uc002wyh.2	+	5	617	c.478C>T	c.(478-480)CCC>TCC	p.P160S		NM_012325	NP_036457	Q15691	MARE1_HUMAN	microtubule-associated protein, RP/EB family,	160	Interaction with MTUS2/TIP150.				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																		---	---	---	---
CDK5RAP1	51654	broad.mit.edu	37	20	31967484	31967484	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31967484A>G	uc010gek.2	-	9	1056	c.932T>C	c.(931-933)GTG>GCG	p.V311A	CDK5RAP1_uc002wyy.2_Missense_Mutation_p.V207A|CDK5RAP1_uc002wyz.2_Missense_Mutation_p.V297A|CDK5RAP1_uc002wza.2_Missense_Mutation_p.V297A|CDK5RAP1_uc010gel.2_Missense_Mutation_p.V206A|CDK5RAP1_uc010gem.2_Intron|CDK5RAP1_uc002wzc.1_Missense_Mutation_p.V297A	NM_016408	NP_057492	Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	311					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																		---	---	---	---
CEP250	11190	broad.mit.edu	37	20	34053898	34053898	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34053898C>T	uc002xcm.2	+	8	1032	c.361C>T	c.(361-363)CGA>TGA	p.R121*	CEP250_uc010zve.1_5'UTR|CEP250_uc010gfe.1_RNA|CEP250_uc010zvd.1_RNA|CEP250_uc002xco.2_5'Flank	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2	121	Potential.				centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)															---	---	---	---
RBM12	10137	broad.mit.edu	37	20	34241967	34241967	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34241967A>G	uc002xdq.2	-	3	1510	c.1278T>C	c.(1276-1278)CAT>CAC	p.H426H	CPNE1_uc010zvj.1_5'Flank|CPNE1_uc002xde.2_Intron|CPNE1_uc002xdf.2_Intron|CPNE1_uc002xdg.2_Intron|CPNE1_uc010gfi.2_Intron|CPNE1_uc010gfj.2_Intron|CPNE1_uc002xdh.2_Intron|CPNE1_uc002xdi.2_Intron|CPNE1_uc002xdj.2_Intron|CPNE1_uc002xdk.2_Intron|CPNE1_uc002xdl.2_Intron|CPNE1_uc002xdm.2_Intron|CPNE1_uc010gfk.1_Intron|CPNE1_uc002xdn.1_Intron|CPNE1_uc002xdo.1_Intron|CPNE1_uc002xdp.1_Intron|RBM12_uc002xdr.2_Silent_p.H426H|RBM12_uc002xds.2_Silent_p.H426H	NM_152838	NP_690051	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	426						nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)													OREG0004044	type=REGULATORY REGION|Gene=CPNE1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
NDRG3	57446	broad.mit.edu	37	20	35317088	35317088	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35317088G>T	uc002xfw.2	-	4	275	c.193C>A	c.(193-195)CTC>ATC	p.L65I	NDRG3_uc002xfx.2_Missense_Mutation_p.L53I|NDRG3_uc010zvq.1_Intron|NDRG3_uc010zvr.1_Intron	NM_032013	NP_114402	Q9UGV2	NDRG3_HUMAN	N-myc downstream regulated gene 3 isoform a	65					cell differentiation|negative regulation of cell growth|spermatogenesis	cytoplasm				ovary(1)	1		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35663858	35663858	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35663858C>T	uc002xgi.2	-	15	2036	c.1957G>A	c.(1957-1959)GCA>ACA	p.A653T	RBL1_uc010zvt.1_RNA|RBL1_uc002xgj.1_Missense_Mutation_p.A653T	NM_002895	NP_002886	P28749	RBL1_HUMAN	retinoblastoma-like protein 1 isoform a	653	Pocket; binds T and E1A.|Spacer.				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)																---	---	---	---
RPN2	6185	broad.mit.edu	37	20	35835788	35835788	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35835788A>G	uc002xgp.2	+	7	1107	c.803A>G	c.(802-804)CAC>CGC	p.H268R	RPN2_uc002xgo.3_Missense_Mutation_p.H268R|RPN2_uc010gfw.2_Missense_Mutation_p.H111R|RPN2_uc002xgq.2_Missense_Mutation_p.H236R	NM_002951	NP_002942	P04844	RPN2_HUMAN	ribophorin II isoform 1 precursor	268	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|nucleus|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
GHRH	2691	broad.mit.edu	37	20	35884908	35884908	+	Intron	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35884908G>A	uc002xgr.2	-						GHRH_uc002xgs.2_Intron|GHRH_uc002xgt.2_Intron	NM_021081	NP_066567			growth hormone releasing hormone preproprotein						activation of adenylate cyclase activity by G-protein signaling pathway|adenohypophysis development|growth hormone secretion|positive regulation of cAMP biosynthetic process|positive regulation of cell proliferation|positive regulation of circadian sleep/wake cycle, REM sleep|positive regulation of growth hormone secretion|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of multicellular organism growth|response to food	extracellular space|terminal button	growth hormone-releasing hormone activity|growth hormone-releasing hormone receptor binding			ovary(1)	1		Myeloproliferative disorder(115;0.00878)																---	---	---	---
SLC32A1	140679	broad.mit.edu	37	20	37357184	37357184	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37357184G>A	uc002xjc.2	+	2	1743	c.1480G>A	c.(1480-1482)GTC>ATC	p.V494I		NM_080552	NP_542119	Q9H598	VIAAT_HUMAN	solute carrier family 32, member 1	494	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)													---	---	---	---
DHX35	60625	broad.mit.edu	37	20	37662959	37662959	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37662959C>T	uc002xjh.2	+	21	2077	c.2066C>T	c.(2065-2067)ACG>ATG	p.T689M	DHX35_uc010zwa.1_Missense_Mutation_p.T534M|DHX35_uc010zwb.1_Missense_Mutation_p.T534M|DHX35_uc010zwc.1_Missense_Mutation_p.T658M	NM_021931	NP_068750	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	689						catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|nucleic acid binding			lung(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
HNF4A	3172	broad.mit.edu	37	20	43034816	43034816	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43034816C>T	uc002xma.2	+	2	323	c.234C>T	c.(232-234)GAC>GAT	p.D78D	HNF4A_uc010zwo.1_Missense_Mutation_p.T69M|HNF4A_uc002xlt.2_Silent_p.D56D|HNF4A_uc002xlu.2_Silent_p.D56D|HNF4A_uc002xlv.2_Silent_p.D56D|HNF4A_uc002xly.2_Silent_p.D78D|HNF4A_uc002xlz.2_Silent_p.D78D|HNF4A_uc010ggq.2_Silent_p.D71D	NM_000457	NP_000448	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4 alpha isoform b	78	Nuclear receptor.|NR C4-type.				blood coagulation|endocrine pancreas development|glucose homeostasis|negative regulation of cell growth|negative regulation of cell proliferation|ornithine metabolic process|phospholipid homeostasis|positive regulation of cholesterol homeostasis|regulation of growth hormone receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to glucose stimulus|triglyceride homeostasis|xenobiotic metabolic process	cytoplasm	activating transcription factor binding|protein homodimerization activity|receptor binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
WFDC8	90199	broad.mit.edu	37	20	44184357	44184357	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44184357G>A	uc002xow.2	-	4	507	c.428C>T	c.(427-429)ACG>ATG	p.T143M	WFDC8_uc002xox.2_Missense_Mutation_p.T143M	NM_181510	NP_852611	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8 precursor	143	BPTI/Kunitz inhibitor.					extracellular region	serine-type endopeptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
MMP9	4318	broad.mit.edu	37	20	44641107	44641107	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44641107G>A	uc002xqz.2	+	8	1235	c.1216G>A	c.(1216-1218)GCG>ACG	p.A406T		NM_004994	NP_004985	P14780	MMP9_HUMAN	matrix metalloproteinase 9 preproprotein	406					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	44685876	44685876	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44685876C>T	uc010zxl.1	+	25	3338	c.3262C>T	c.(3262-3264)CGG>TGG	p.R1088W	SLC12A5_uc002xrb.2_Missense_Mutation_p.R1065W	NM_001134771	NP_001128243	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride	1088	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)													---	---	---	---
CDH22	64405	broad.mit.edu	37	20	44815281	44815281	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44815281G>A	uc002xrm.2	-	9	2010	c.1609C>T	c.(1609-1611)CGC>TGC	p.R537C	CDH22_uc010ghk.1_Missense_Mutation_p.R537C	NM_021248	NP_067071	Q9UJ99	CAD22_HUMAN	cadherin 22 precursor	537	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ARFGEF2	10564	broad.mit.edu	37	20	47605849	47605849	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47605849T>G	uc002xtx.3	+	19	2713	c.2561T>G	c.(2560-2562)CTG>CGG	p.L854R	ARFGEF2_uc010zyf.1_Missense_Mutation_p.L147R	NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine	854					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)															---	---	---	---
ARFGEF2	10564	broad.mit.edu	37	20	47611069	47611069	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47611069C>T	uc002xtx.3	+	22	3207	c.3055C>T	c.(3055-3057)CGT>TGT	p.R1019C	ARFGEF2_uc010zyf.1_Missense_Mutation_p.R312C	NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine	1019					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)															---	---	---	---
SNAI1	6615	broad.mit.edu	37	20	48604589	48604589	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48604589G>A	uc002xuz.2	+	3	861	c.791G>A	c.(790-792)CGC>CAC	p.R264H		NM_005985	NP_005976	O95863	SNAI1_HUMAN	snail 1 homolog	264					epithelial to mesenchymal transition|mesoderm formation|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|zinc ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)															---	---	---	---
ADNP	23394	broad.mit.edu	37	20	49508895	49508895	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49508895T>G	uc002xvt.1	-	5	2701	c.2356A>C	c.(2356-2358)ATT>CTT	p.I786L	ADNP_uc002xvu.1_Missense_Mutation_p.I786L	NM_015339	NP_056154	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector	786	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2																		---	---	---	---
ZNF217	7764	broad.mit.edu	37	20	52193292	52193292	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52193292C>T	uc002xwq.3	-	3	2282	c.2011G>A	c.(2011-2013)GCA>ACA	p.A671T	ZNF217_uc010gij.1_Missense_Mutation_p.A663T	NM_006526	NP_006517	O75362	ZN217_HUMAN	zinc finger protein 217	671					negative regulation of transcription, DNA-dependent	histone deacetylase complex	protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1)	6	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	56064013	56064013	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56064013C>T	uc010zzl.1	-	1	71	c.71G>A	c.(70-72)CGG>CAG	p.R24Q	CTCFL_uc010giu.2_RNA|CTCFL_uc010giv.2_RNA	NM_001008735	NP_001008735			high-mobility group box 1-like 1																														---	---	---	---
NPEPL1	79716	broad.mit.edu	37	20	57269569	57269569	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57269569G>A	uc010zzs.1	+	3	523	c.428G>A	c.(427-429)CGC>CAC	p.R143H	NPEPL1_uc010zzr.1_Missense_Mutation_p.R95H|NPEPL1_uc002xzn.2_RNA|NPEPL1_uc010gjo.1_Missense_Mutation_p.R115H|NPEPL1_uc002xzp.2_Missense_Mutation_p.R31H	NM_024663	NP_078939	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	143					proteolysis	cytoplasm	aminopeptidase activity|manganese ion binding|metalloexopeptidase activity				0	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)															---	---	---	---
ZNF831	128611	broad.mit.edu	37	20	57768886	57768886	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57768886T>C	uc002yan.2	+	1	2812	c.2812T>C	c.(2812-2814)TCC>CCC	p.S938P		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	938						intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)																	---	---	---	---
CDH26	60437	broad.mit.edu	37	20	58563985	58563985	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58563985G>A	uc002ybe.2	+	9	1350	c.1050G>A	c.(1048-1050)GCG>GCA	p.A350A	CDH26_uc002ybf.1_5'UTR|CDH26_uc010zzy.1_RNA	NM_177980	NP_817089	Q8IXH8	CAD26_HUMAN	cadherin-like 26 isoform a	350	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)															---	---	---	---
NTSR1	4923	broad.mit.edu	37	20	61391505	61391505	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61391505C>G	uc002ydf.2	+	4	1514	c.1143C>G	c.(1141-1143)TGC>TGG	p.C381W		NM_002531	NP_002522	P30989	NTR1_HUMAN	neurotensin receptor 1	381	Cytoplasmic (Potential).					endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	neurotensin receptor activity, G-protein coupled			skin(2)|lung(1)|central_nervous_system(1)	4	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)															---	---	---	---
YTHDF1	54915	broad.mit.edu	37	20	61834535	61834535	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61834535C>T	uc002yeh.2	-	4	1051	c.757G>A	c.(757-759)GGG>AGG	p.G253R	YTHDF1_uc011aaq.1_Missense_Mutation_p.G203R	NM_017798	NP_060268	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	253	Gln/Pro-rich.									ovary(2)	2																		---	---	---	---
KCNQ2	3785	broad.mit.edu	37	20	62070960	62070960	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62070960C>T	uc002yey.1	-	6	1095	c.918G>A	c.(916-918)GCG>GCA	p.A306A	KCNQ2_uc002yez.1_Silent_p.A306A|KCNQ2_uc002yfa.1_Silent_p.A306A|KCNQ2_uc002yfb.1_Silent_p.A306A|KCNQ2_uc011aax.1_Silent_p.A306A|KCNQ2_uc002yfc.1_Silent_p.A306A	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein	306	Helical; Name=Segment S6; (Potential).		A -> T (in EBN1; 20%-40% reduction of wt heteromeric current. Ratio of 1:1:2).		axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)													---	---	---	---
SRMS	6725	broad.mit.edu	37	20	62178751	62178751	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62178751C>T	uc002yfi.1	-	1	107	c.66G>A	c.(64-66)GCG>GCA	p.A22A		NM_080823	NP_543013	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory	22							ATP binding|non-membrane spanning protein tyrosine kinase activity			stomach(1)|lung(1)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)															---	---	---	---
PRIC285	85441	broad.mit.edu	37	20	62196899	62196899	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62196899G>A	uc002yfm.2	-	9	4168	c.3276C>T	c.(3274-3276)GAC>GAT	p.D1092D	PRIC285_uc002yfl.1_Silent_p.D523D	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285	1092					cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)															---	---	---	---
UCKL1	54963	broad.mit.edu	37	20	62577179	62577179	+	Silent	SNP	C	T	T	rs61743506	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62577179C>T	uc010gkn.2	-	4	604	c.561G>A	c.(559-561)ACG>ACA	p.T187T	UCKL1_uc011abm.1_Silent_p.T172T|UCKL1_uc011abn.1_RNA|UCKL1_uc011abo.1_RNA	NM_017859	NP_060329	Q9NWZ5	UCKL1_HUMAN	uridine-cytidine kinase 1-like 1	187					interspecies interaction between organisms	endoplasmic reticulum|nucleus	ATP binding|phosphotransferase activity, alcohol group as acceptor|protein binding|uridine kinase activity				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)																	---	---	---	---
ZNF512B	57473	broad.mit.edu	37	20	62598745	62598745	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62598745G>A	uc002yhl.1	-	3	307	c.253C>T	c.(253-255)CGA>TGA	p.R85*		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	85					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)																	---	---	---	---
OPRL1	4987	broad.mit.edu	37	20	62729786	62729786	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62729786G>A	uc002yic.2	+	5	1149	c.747G>A	c.(745-747)TCG>TCA	p.S249S	OPRL1_uc002yid.2_Silent_p.S249S|OPRL1_uc002yif.3_Silent_p.S244S	NM_182647	NP_872588	P41146	OPRX_HUMAN	opiate receptor-like 1	249	Cytoplasmic (Potential).				elevation of cytosolic calcium ion concentration|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception	integral to plasma membrane	protein binding|X-opioid receptor activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)																	---	---	---	---
NRIP1	8204	broad.mit.edu	37	21	16338141	16338141	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16338141G>A	uc002yjx.2	-	4	2971	c.2373C>T	c.(2371-2373)AGC>AGT	p.S791S		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	791	Repression domain 3.				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)														---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	30949413	30949413	+	Silent	SNP	C	T	T	rs142518822	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30949413C>T	uc002yno.1	-	14	2465	c.2001G>A	c.(1999-2001)ACG>ACA	p.T667T	GRIK1_uc002ynn.2_Silent_p.T652T|GRIK1_uc011acs.1_Silent_p.T667T|GRIK1_uc011act.1_Silent_p.T528T	NM_000830	NP_000821	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	667	Helical; (Potential).				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)													---	---	---	---
KRTAP15-1	254950	broad.mit.edu	37	21	31812904	31812904	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31812904C>T	uc002yod.2	+	1	259	c.259C>T	c.(259-261)CGC>TGC	p.R87C		NM_181623	NP_853654	Q3LI76	KR151_HUMAN	keratin associated protein 15-1	87						intermediate filament					0																		---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32493037	32493037	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32493037G>A	uc002yow.1	-	29	4897	c.4425C>T	c.(4423-4425)CCC>CCT	p.P1475P	TIAM1_uc011adk.1_3'UTR|TIAM1_uc011adl.1_Silent_p.P1415P	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1475					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																		---	---	---	---
GART	2618	broad.mit.edu	37	21	34903066	34903066	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34903066T>C	uc002yrx.2	-	7	857	c.722A>G	c.(721-723)CAG>CGG	p.Q241R	GART_uc002yrz.2_Missense_Mutation_p.Q241R|GART_uc010gmd.2_5'UTR|GART_uc002yry.2_Missense_Mutation_p.Q241R|GART_uc002ysa.2_Missense_Mutation_p.Q241R	NM_000819	NP_000810	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase,	241	ATP-grasp.				'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)													---	---	---	---
SIM2	6493	broad.mit.edu	37	21	38115733	38115733	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38115733C>A	uc002yvr.2	+	9	1100	c.1044C>A	c.(1042-1044)TCC>TCA	p.S348S	SIM2_uc002yvq.2_Silent_p.S348S	NM_005069	NP_005060	Q14190	SIM2_HUMAN	single-minded homolog 2 long isoform	348	Single-minded C-terminal.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1																		---	---	---	---
TTC3	7267	broad.mit.edu	37	21	38498385	38498385	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38498385G>A	uc002yvz.2	+	15	1344	c.1239G>A	c.(1237-1239)GCG>GCA	p.A413A	TTC3_uc011aee.1_Silent_p.A103A|TTC3_uc002ywa.2_Silent_p.A413A|TTC3_uc002ywb.2_Silent_p.A413A|TTC3_uc010gnf.2_Silent_p.A178A|TTC3_uc002ywc.2_Silent_p.A103A|TTC3_uc011aed.1_Silent_p.A103A|TTC3_uc010gne.1_Silent_p.A413A	NM_001001894	NP_001001894	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	413					protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(3)|ovary(2)|lung(2)|breast(2)	9		Myeloproliferative disorder(46;0.0412)																---	---	---	---
DSCR3	10311	broad.mit.edu	37	21	38600102	38600102	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38600102C>T	uc002ywf.1	-	8	903	c.664G>A	c.(664-666)GCA>ACA	p.A222T	DSCR3_uc010gnm.1_RNA|DSCR3_uc010gnn.1_Missense_Mutation_p.A180T|DSCR3_uc010gnl.2_Missense_Mutation_p.A195T|DSCR3_uc011aeg.1_Missense_Mutation_p.A145T|DSCR3_uc011aeh.1_Missense_Mutation_p.A97T	NM_006052	NP_006043	O14972	DSCR3_HUMAN	Down syndrome critical region protein 3	222					vacuolar transport	nucleus|retromer complex					0																		---	---	---	---
RIPK4	54101	broad.mit.edu	37	21	43161498	43161498	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43161498C>T	uc002yzn.1	-	8	1903	c.1855G>A	c.(1855-1857)GTG>ATG	p.V619M		NM_020639	NP_065690	P57078	RIPK4_HUMAN	ankyrin repeat domain 3	619						cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7																		---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43531469	43531469	+	Intron	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43531469C>A	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Missense_Mutation_p.P641T|UMODL1_uc002zag.1_Missense_Mutation_p.P713T|C21orf128_uc002zak.2_5'Flank	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																		---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43531694	43531694	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43531694G>T	uc002zaf.1	+	12	1978	c.1978G>T	c.(1978-1980)GCC>TCC	p.A660S	UMODL1_uc002zad.1_Missense_Mutation_p.A588S|UMODL1_uc002zae.1_Missense_Mutation_p.A716S|UMODL1_uc002zag.1_Missense_Mutation_p.A788S	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor	660	Extracellular (Potential).					cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
CBS	875	broad.mit.edu	37	21	44480625	44480625	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44480625G>A	uc002zcu.2	-	12	1316	c.1071C>T	c.(1069-1071)GCC>GCT	p.A357A	CBS_uc002zcs.1_Silent_p.A252A|CBS_uc002zct.2_Silent_p.A357A|CBS_uc002zcw.3_Silent_p.A357A|CBS_uc002zcv.2_Silent_p.A357A|CBS_uc002zcx.2_5'UTR	NM_000071	NP_000062	P35520	CBS_HUMAN	cystathionine-beta-synthase	357					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)													---	---	---	---
RRP1	8568	broad.mit.edu	37	21	45219516	45219516	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45219516G>A	uc002zds.2	+	9	970	c.877G>A	c.(877-879)GGC>AGC	p.G293S	RRP1_uc011aez.1_Missense_Mutation_p.G293S|RRP1_uc010gpk.1_Missense_Mutation_p.G143S|RRP1_uc010gpl.1_Missense_Mutation_p.G191S|RRP1_uc010gpm.1_Missense_Mutation_p.G160S	NM_003683	NP_003674	P56182	RRP1_HUMAN	ribosomal RNA processing 1 homolog	293					rRNA processing	nucleolus|preribosome, small subunit precursor					0				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)														---	---	---	---
PWP2	5822	broad.mit.edu	37	21	45535691	45535691	+	Silent	SNP	A	G	G	rs145366296		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45535691A>G	uc002zeb.2	+	7	816	c.726A>G	c.(724-726)GAA>GAG	p.E242E		NM_005049	NP_005040	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog	242	Poly-Glu.					cytoplasm|nucleolus	signal transducer activity			pancreas(1)	1				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)														---	---	---	---
TRPM2	7226	broad.mit.edu	37	21	45798982	45798982	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45798982G>A	uc002zet.1	+	9	1330	c.1117G>A	c.(1117-1119)GAC>AAC	p.D373N	TRPM2_uc002zeu.1_Missense_Mutation_p.D373N|TRPM2_uc002zew.1_Missense_Mutation_p.D373N|TRPM2_uc010gpt.1_Missense_Mutation_p.D373N|TRPM2_uc002zex.1_Missense_Mutation_p.D159N	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	373	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																		---	---	---	---
TRPM2	7226	broad.mit.edu	37	21	45825802	45825802	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45825802C>T	uc002zet.1	+	19	2885	c.2672C>T	c.(2671-2673)ACG>ATG	p.T891M	TRPM2_uc002zeu.1_Missense_Mutation_p.T891M|TRPM2_uc002zew.1_Missense_Mutation_p.T891M|TRPM2_uc010gpt.1_Missense_Mutation_p.T891M|TRPM2_uc002zex.1_Missense_Mutation_p.T677M|TRPM2_uc002zey.1_Missense_Mutation_p.T404M	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	891	Helical; (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
LRRC3	81543	broad.mit.edu	37	21	45876853	45876853	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45876853C>T	uc002zfa.2	+	2	619	c.326C>T	c.(325-327)GCG>GTG	p.A109V		NM_030891	NP_112153	Q9BY71	LRRC3_HUMAN	leucine-rich repeat-containing 3 precursor	109	LRR 2.					integral to membrane	protein binding				0		Breast(209;0.00908)		COAD - Colon adenocarcinoma(84;0.148)|Lung(125;0.195)														---	---	---	---
ADARB1	104	broad.mit.edu	37	21	46596311	46596311	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46596311G>T	uc002zgy.2	+	4	1130	c.695G>T	c.(694-696)AGT>ATT	p.S232I	ADARB1_uc002zgr.2_Missense_Mutation_p.S232I|ADARB1_uc002zgs.2_RNA|ADARB1_uc002zgw.2_Missense_Mutation_p.S232I|ADARB1_uc002zgv.2_RNA|ADARB1_uc002zgt.2_Missense_Mutation_p.S232I|ADARB1_uc010gpx.2_Intron|ADARB1_uc002zgq.2_RNA|ADARB1_uc002zgu.2_RNA|ADARB1_uc011afo.1_Missense_Mutation_p.S281I	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2	232	DRBM 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)														---	---	---	---
PCBP3	54039	broad.mit.edu	37	21	47360075	47360075	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47360075G>A	uc002zhq.1	+	13	1166	c.1041G>A	c.(1039-1041)CCG>CCA	p.P347P	PCBP3_uc002zhp.1_Silent_p.P327P|PCBP3_uc002zhs.1_Silent_p.P321P|PCBP3_uc002zhr.1_Silent_p.P346P|PCBP3_uc002zht.1_Silent_p.P337P	NM_020528	NP_065389	P57721	PCBP3_HUMAN	poly(rC) binding protein 3 isoform 1	347	KH 3.				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)														---	---	---	---
CCT8L2	150160	broad.mit.edu	37	22	17072267	17072267	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17072267C>T	uc002zlp.1	-	1	1434	c.1174G>A	c.(1174-1176)GTC>ATC	p.V392I		NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1	392					cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)																---	---	---	---
CCT8L2	150160	broad.mit.edu	37	22	17072678	17072678	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17072678C>A	uc002zlp.1	-	1	1023	c.763G>T	c.(763-765)GCA>TCA	p.A255S		NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1	255					cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)																---	---	---	---
DGCR2	9993	broad.mit.edu	37	22	19055664	19055664	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19055664C>T	uc002zoq.1	-	3	525	c.277G>A	c.(277-279)GAC>AAC	p.D93N	DGCR2_uc002zor.1_5'UTR|DGCR2_uc011agr.1_Missense_Mutation_p.D52N	NM_005137	NP_005128	P98153	IDD_HUMAN	integral membrane protein DGCR2 precursor	93	Extracellular (Potential).				cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding			large_intestine(1)	1	Colorectal(54;0.0993)																	---	---	---	---
HIRA	7290	broad.mit.edu	37	22	19379688	19379688	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19379688G>A	uc002zpf.1	-	9	1092	c.872C>T	c.(871-873)GCG>GTG	p.A291V	HIRA_uc011agx.1_Missense_Mutation_p.A157V|HIRA_uc010grn.1_Missense_Mutation_p.A291V|HIRA_uc010gro.1_Missense_Mutation_p.A247V|HIRA_uc010grp.2_RNA	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective	291	WD 6.				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)																	---	---	---	---
TXNRD2	10587	broad.mit.edu	37	22	19882652	19882652	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19882652C>T	uc011ahc.1	-						TXNRD2_uc002zql.1_Intron|TXNRD2_uc002zqm.1_Intron|TXNRD2_uc002zqn.1_Intron|TXNRD2_uc002zqo.1_Intron|TXNRD2_uc002zqp.1_Intron|TXNRD2_uc002zqr.1_Intron|TXNRD2_uc010grv.1_3'UTR|TXNRD2_uc002zqj.1_Intron|TXNRD2_uc002zqs.2_3'UTR	NM_006440	NP_006431			thioredoxin reductase 2 precursor						cell redox homeostasis|response to oxygen radical	mitochondrion	flavin adenine dinucleotide binding|NADP binding|thioredoxin-disulfide reductase activity			ovary(2)	2	Colorectal(54;0.0993)																	---	---	---	---
KLHL22	84861	broad.mit.edu	37	22	20819360	20819360	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20819360G>A	uc002zsl.1	-	4	1006	c.897C>T	c.(895-897)TGC>TGT	p.C299C	KLHL22_uc011ahr.1_Silent_p.C156C|KLHL22_uc002zsm.1_Silent_p.C299C	NM_032775	NP_116164	Q53GT1	KLH22_HUMAN	kelch-like	299	Kelch 1.				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)															---	---	---	---
LZTR1	8216	broad.mit.edu	37	22	21351217	21351217	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21351217C>T	uc002zto.2	+	20	2471	c.2368C>T	c.(2368-2370)CGG>TGG	p.R790W	LZTR1_uc002ztn.2_Missense_Mutation_p.R749W|LZTR1_uc011ahy.1_Missense_Mutation_p.R771W|LZTR1_uc002ztp.2_Missense_Mutation_p.R96W	NM_006767	NP_006758	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	790					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)															---	---	---	---
GGTLC2	91227	broad.mit.edu	37	22	22989563	22989563	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22989563C>T	uc010gtt.2	+						LOC96610_uc011aim.1_Intron|POM121L1P_uc011ait.1_5'Flank|GGTLC2_uc010gts.2_Silent_p.L139L	NM_199127	NP_954578			gamma-glutamyltransferase-like 4 isoform 1						glutathione biosynthetic process		gamma-glutamyltransferase activity			ovary(1)	1	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)														---	---	---	---
PIWIL3	440822	broad.mit.edu	37	22	25145382	25145382	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25145382A>G	uc003abd.1	-	11	1740	c.1323T>C	c.(1321-1323)AAT>AAC	p.N441N	PIWIL3_uc011ajx.1_Silent_p.N332N|PIWIL3_uc011ajy.1_Silent_p.N332N|PIWIL3_uc010gut.1_Silent_p.N441N	NM_001008496	NP_001008496	Q7Z3Z3	PIWL3_HUMAN	piwi-like 3	441					cell differentiation|gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatogenesis	cytoplasm	RNA binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
HPS4	89781	broad.mit.edu	37	22	26861510	26861510	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26861510T>C	uc003acl.2	-	10	1373	c.714A>G	c.(712-714)GCA>GCG	p.A238A	HPS4_uc003aci.2_Silent_p.A233A|HPS4_uc003acj.2_Silent_p.A102A|HPS4_uc003ack.2_Silent_p.A29A|HPS4_uc003acn.2_Silent_p.A84A|HPS4_uc010gvd.1_Silent_p.A256A|HPS4_uc003ach.2_5'UTR	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	238					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0														Hermansky-Pudlak_syndrome				---	---	---	---
HPS4	89781	broad.mit.edu	37	22	26868359	26868359	+	Missense_Mutation	SNP	G	A	A	rs150403254	by1000genomes	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26868359G>A	uc003acl.2	-	6	1069	c.410C>T	c.(409-411)ACG>ATG	p.T137M	HPS4_uc003aci.2_Missense_Mutation_p.T132M|HPS4_uc003acj.2_Translation_Start_Site|HPS4_uc003ack.2_Translation_Start_Site|HPS4_uc003acn.2_Translation_Start_Site|HPS4_uc010gvd.1_Missense_Mutation_p.T137M|HPS4_uc003ach.2_Translation_Start_Site	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	137					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0														Hermansky-Pudlak_syndrome				---	---	---	---
CRYBB1	1414	broad.mit.edu	37	22	27012211	27012211	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27012211C>A	uc003acy.1	-	2	143	c.73G>T	c.(73-75)GGG>TGG	p.G25W		NM_001887	NP_001878	P53674	CRBB1_HUMAN	crystallin, beta B1	25	N-terminal arm.				visual perception		structural constituent of eye lens			ovary(1)	1																		---	---	---	---
AP1B1	162	broad.mit.edu	37	22	29755831	29755831	+	Silent	SNP	G	A	A	rs143484030	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29755831G>A	uc003afj.2	-	4	445	c.261C>T	c.(259-261)GCC>GCT	p.A87A	AP1B1_uc003afi.2_Silent_p.A87A|AP1B1_uc003afk.2_Silent_p.A87A|AP1B1_uc003afl.2_Silent_p.A87A	NM_001127	NP_001118	Q10567	AP1B1_HUMAN	adaptor-related protein complex 1 beta 1 subunit	87					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																OREG0026449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36702620	36702620	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36702620C>T	uc003apg.2	-	16	2108	c.1877G>A	c.(1876-1878)GGC>GAC	p.G626D	MYH9_uc003aph.1_Missense_Mutation_p.G490D	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	626	Myosin head-like.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36708256	36708256	+	Silent	SNP	C	T	T	rs145517108	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36708256C>T	uc003apg.2	-	14	1797	c.1566G>A	c.(1564-1566)CCG>CCA	p.P522P	MYH9_uc003aph.1_Silent_p.P386P	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	522	Myosin head-like.				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				---	---	---	---
PLA2G6	8398	broad.mit.edu	37	22	38525530	38525530	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38525530C>T	uc003auy.1	-	8	1253	c.1117G>A	c.(1117-1119)GGA>AGA	p.G373R	PLA2G6_uc003auz.1_Missense_Mutation_p.G373R|PLA2G6_uc003ava.1_Missense_Mutation_p.G373R|PLA2G6_uc003avb.2_Missense_Mutation_p.G373R|PLA2G6_uc010gxk.1_RNA|PLA2G6_uc011ano.1_Missense_Mutation_p.G338R	NM_003560	NP_003551	O60733	PA2G6_HUMAN	phospholipase A2, group VI isoform a	373	ANK 7.				cardiolipin biosynthetic process|cell death|lipid catabolic process	centrosome|membrane				ovary(1)	1	Melanoma(58;0.045)				Quinacrine(DB01103)													---	---	---	---
KCNJ4	3761	broad.mit.edu	37	22	38823343	38823343	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38823343G>A	uc003avs.1	-	2	892	c.795C>T	c.(793-795)ATC>ATT	p.I265I	KCNJ4_uc003avt.1_Silent_p.I265I	NM_004981	NP_004972	P48050	IRK4_HUMAN	potassium inwardly-rectifying channel J4	265	Cytoplasmic (By similarity).				synaptic transmission	basolateral plasma membrane|voltage-gated potassium channel complex	inward rectifier potassium channel activity|PDZ domain binding				0	Melanoma(58;0.0286)																	---	---	---	---
RPL3	6122	broad.mit.edu	37	22	39712858	39712858	+	Intron	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39712858G>T	uc003axi.2	-						RPL3_uc003axh.2_Intron|RPL3_uc003axj.2_Translation_Start_Site|RPL3_uc010gxx.2_Intron|RPL3_uc003axg.2_Intron|RPL3_uc003axk.1_Translation_Start_Site	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)															OREG0026575	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TAB1	10454	broad.mit.edu	37	22	39826041	39826041	+	Silent	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39826041G>T	uc003axt.2	+	11	1378	c.1329G>T	c.(1327-1329)CTG>CTT	p.L443L	TAB1_uc003axr.2_Silent_p.L519L|TAB1_uc011aok.1_Silent_p.L277L|TAB1_uc003axu.1_Intron	NM_006116	NP_006107	Q15750	TAB1_HUMAN	mitogen-activated protein kinase kinase kinase 7	443					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																		---	---	---	---
EP300	2033	broad.mit.edu	37	22	41564766	41564766	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41564766G>A	uc003azl.3	+	25	4462	c.4067G>A	c.(4066-4068)CGA>CAA	p.R1356Q		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	1356					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				---	---	---	---
RANGAP1	5905	broad.mit.edu	37	22	41652106	41652106	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41652106T>C	uc003azs.2	-	9	2462	c.992A>G	c.(991-993)AAC>AGC	p.N331S	RANGAP1_uc003azt.2_Missense_Mutation_p.N331S|RANGAP1_uc003azu.2_Missense_Mutation_p.N331S|RANGAP1_uc011aoz.1_Missense_Mutation_p.N276S	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	331	LRR 6.				mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0																		---	---	---	---
A4GALT	53947	broad.mit.edu	37	22	43089153	43089153	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43089153C>T	uc003bdb.2	-	3	1066	c.805G>A	c.(805-807)GAG>AAG	p.E269K	A4GALT_uc010gzd.2_Missense_Mutation_p.E269K	NM_017436	NP_059132	Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	269	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																		---	---	---	---
SCUBE1	80274	broad.mit.edu	37	22	43604220	43604220	+	Silent	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43604220C>A	uc003bdt.1	-	20	2680	c.2592G>T	c.(2590-2592)ACG>ACT	p.T864T		NM_173050	NP_766638	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	864	CUB.				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)																---	---	---	---
FBLN1	2192	broad.mit.edu	37	22	45972965	45972965	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45972965G>A	uc003bgj.1	+	16	2096	c.1949G>A	c.(1948-1950)CGT>CAT	p.R650H		NM_006486	NP_006477	P23142	FBLN1_HUMAN	fibulin 1 isoform D	650					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)														---	---	---	---
C22orf40	150383	broad.mit.edu	37	22	46643046	46643046	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46643046C>T	uc003bhe.2	-	3	227	c.186G>A	c.(184-186)TCG>TCA	p.S62S	C22orf40_uc003bhc.2_Silent_p.S62S|C22orf40_uc003bhd.2_Silent_p.S62S|C22orf40_uc003bhf.2_RNA	NM_207327	NP_997210	Q6NVV7	CV040_HUMAN	hypothetical protein LOC150383	62											0																		---	---	---	---
PKDREJ	10343	broad.mit.edu	37	22	46658051	46658051	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46658051C>T	uc003bhh.2	-	1	1169	c.1169G>A	c.(1168-1170)CGA>CAA	p.R390Q		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	390	Extracellular (Potential).|REJ.				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)														---	---	---	---
GRAMD4	23151	broad.mit.edu	37	22	47064782	47064782	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47064782A>T	uc003bhx.2	+	12	1100	c.1061A>T	c.(1060-1062)TAC>TTC	p.Y354F	GRAMD4_uc010had.2_Missense_Mutation_p.Y293F	NM_015124	NP_055939	Q6IC98	GRAM4_HUMAN	death-inducing-protein	354	Helical; (Potential).				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)														---	---	---	---
TUBGCP6	85378	broad.mit.edu	37	22	50663014	50663014	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50663014C>T	uc003bkb.1	-	11	2503	c.1991G>A	c.(1990-1992)CGT>CAT	p.R664H	TUBGCP6_uc003bka.1_5'Flank|TUBGCP6_uc010har.1_Missense_Mutation_p.R664H|TUBGCP6_uc010has.1_RNA|TUBGCP6_uc010hat.1_5'UTR|TUBGCP6_uc003bkd.1_Missense_Mutation_p.R18H	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	664					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
PLXNB2	23654	broad.mit.edu	37	22	50716155	50716155	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50716155C>T	uc003bkv.3	-	33	5167	c.5061G>A	c.(5059-5061)CGG>CGA	p.R1687R	PLXNB2_uc003bkt.1_Silent_p.R479R|PLXNB2_uc003bku.1_Silent_p.R672R	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor	1687	Cytoplasmic (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)|skin(1)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
PLXNB2	23654	broad.mit.edu	37	22	50728968	50728968	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50728968C>T	uc003bkv.3	-	3	152	c.46G>A	c.(46-48)GCA>ACA	p.A16T		NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor	16					regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)|skin(1)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
SCO2	9997	broad.mit.edu	37	22	50962178	50962178	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50962178G>A	uc003bma.2	-	2	839	c.663C>T	c.(661-663)ATC>ATT	p.I221I	SCO2_uc003blz.3_Silent_p.I221I	NM_005138	NP_005129	O43819	SCO2_HUMAN	cytochrome oxidase deficient homolog 2	221	Thioredoxin.				cell redox homeostasis|cellular copper ion homeostasis|copper ion transport|oxidation-reduction process|respiratory chain complex IV assembly	mitochondrial inner membrane	copper ion binding				0		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
SHANK3	85358	broad.mit.edu	37	22	51160465	51160465	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51160465G>A	uc003bne.1	+	22	4252	c.4252G>A	c.(4252-4254)GGA>AGA	p.G1418R	SHANK3_uc003bnf.1_Missense_Mutation_p.G865R|SHANK3_uc010hbg.1_Missense_Mutation_p.G600R	NM_001080420	NP_001073889	F2Z3L0	F2Z3L0_HUMAN	SH3 and multiple ankyrin repeat domains 3	1418										central_nervous_system(1)	1		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)														---	---	---	---
IL3RA	3563	broad.mit.edu	37	X	1471117	1471117	+	Silent	SNP	C	T	T	rs142385163	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1471117C>T	uc004cps.2	+	5	772	c.423C>T	c.(421-423)AAC>AAT	p.N141N	IL3RA_uc011mhd.1_Silent_p.N63N	NM_002183	NP_002174	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha precursor	141	Extracellular (Potential).					integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)													---	---	---	---
SFRS17A	8227	broad.mit.edu	37	X	1712726	1712726	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1712726G>A	uc004cqa.2	+	2	567	c.371G>A	c.(370-372)CGC>CAC	p.R124H	SFRS17A_uc010ncx.1_Missense_Mutation_p.R124H|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	124					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)																---	---	---	---
ARSD	414	broad.mit.edu	37	X	2825515	2825515	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2825515G>A	uc004cqy.2	-	10	1655	c.1579C>T	c.(1579-1581)CGG>TGG	p.R527W	ARSD_uc004cqz.1_RNA	NM_001669	NP_001660	P51689	ARSD_HUMAN	arylsulfatase D isoform a precursor	527						lysosome	arylsulfatase activity|metal ion 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)																---	---	---	---
MXRA5	25878	broad.mit.edu	37	X	3228450	3228450	+	Silent	SNP	G	A	A	rs147057004		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3228450G>A	uc004crg.3	-	7	7951	c.7794C>T	c.(7792-7794)GAC>GAT	p.D2598D		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	2598	Ig-like C2-type 10.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)																---	---	---	---
MXRA5	25878	broad.mit.edu	37	X	3240641	3240641	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3240641G>T	uc004crg.3	-	5	3242	c.3085C>A	c.(3085-3087)CCA>ACA	p.P1029T		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	1029						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)																---	---	---	---
SHROOM2	357	broad.mit.edu	37	X	9914758	9914758	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9914758C>T	uc004csu.1	+	10	4722	c.4632C>T	c.(4630-4632)GAC>GAT	p.D1544D	SHROOM2_uc004csv.2_Silent_p.D378D|SHROOM2_uc011mic.1_Silent_p.D379D|SHROOM2_uc004csw.1_Silent_p.D379D	NM_001649	NP_001640	Q13796	SHRM2_HUMAN	apical protein of Xenopus-like	1544	ASD2.				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)																---	---	---	---
FRMPD4	9758	broad.mit.edu	37	X	12722594	12722594	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12722594C>T	uc004cuz.1	+	11	1693	c.1187C>T	c.(1186-1188)CCG>CTG	p.P396L	FRMPD4_uc011mij.1_Missense_Mutation_p.P388L	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	396	FERM.				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																		---	---	---	---
TLR8	51311	broad.mit.edu	37	X	12939203	12939203	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12939203A>G	uc004cve.2	+	2	2112	c.2044A>G	c.(2044-2046)ACA>GCA	p.T682A	TLR8_uc004cvd.2_Missense_Mutation_p.T700A	NM_138636	NP_619542	Q9NR97	TLR8_HUMAN	toll-like receptor 8 precursor	682	Extracellular (Potential).|LRR 20.				cellular response to mechanical stimulus|defense response to virus|I-kappaB kinase/NF-kappaB cascade|immunoglobulin mediated immune response|inflammatory response|innate immune response|positive regulation of innate immune response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process	endosome membrane	DNA binding|double-stranded RNA binding|single-stranded RNA binding|transmembrane receptor activity			ovary(4)|lung(2)|large_intestine(1)	7																		---	---	---	---
FIGF	2277	broad.mit.edu	37	X	15381444	15381444	+	Intron	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15381444T>A	uc004cwt.1	-							NM_004469	NP_004460			vascular endothelial growth factor D						angiogenesis|cell differentiation|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of mast cell chemotaxis|vascular endothelial growth factor receptor signaling pathway	extracellular space|membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity|platelet-derived growth factor receptor binding			ovary(1)|breast(1)|central_nervous_system(1)	3	Hepatocellular(33;0.183)																	---	---	---	---
ACE2	59272	broad.mit.edu	37	X	15607507	15607507	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15607507C>T	uc004cxa.1	-	5	824	c.656G>A	c.(655-657)CGC>CAC	p.R219H	ACE2_uc004cxb.2_Missense_Mutation_p.R219H	NM_021804	NP_068576	Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2 precursor	219	Extracellular (Potential).			R->D: No effect on interaction with SARS- CoV spike glycoprotein.	angiotensin-mediated drinking behavior|proteolysis|receptor biosynthetic process|regulation of cell proliferation|virion attachment, binding of host cell surface receptor	cell surface|extracellular space|integral to membrane|membrane raft|plasma membrane	carboxypeptidase activity|glycoprotein binding|metallopeptidase activity|peptidyl-dipeptidase activity|viral receptor activity|zinc ion binding			ovary(3)	3	Hepatocellular(33;0.183)				Moexipril(DB00691)													---	---	---	---
CTPS2	56474	broad.mit.edu	37	X	16720886	16720886	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16720886G>A	uc004cxk.2	-	2	884	c.140C>T	c.(139-141)GCT>GTT	p.A47V	CTPS2_uc004cxl.2_Missense_Mutation_p.A47V|CTPS2_uc004cxm.2_Missense_Mutation_p.A47V	NM_001144002	NP_001137474	Q9NRF8	PYRG2_HUMAN	cytidine triphosphate synthase II	47					glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine nucleotide biosynthetic process	cytosol	ATP binding|CTP synthase activity			ovary(1)	1	Hepatocellular(33;0.0997)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18622107	18622107	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18622107C>T	uc004cym.2	+	12	1316	c.1063C>T	c.(1063-1065)CGG>TGG	p.R355W	CDKL5_uc004cyn.2_Missense_Mutation_p.R355W	NM_003159	NP_003150	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	355					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)																	---	---	---	---
MAP3K15	389840	broad.mit.edu	37	X	19475114	19475114	+	5'UTR	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19475114C>T	uc004czk.1	-	5					MAP3K15_uc004czj.1_5'UTR	NM_001001671	NP_001001671			mitogen-activated protein kinase kinase kinase								ATP binding|MAP kinase kinase kinase activity|metal ion binding			ovary(3)|lung(2)|stomach(1)|skin(1)	7	Hepatocellular(33;0.183)																	---	---	---	---
KLHL34	257240	broad.mit.edu	37	X	21674083	21674083	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21674083C>T	uc004czz.1	-	1	2366	c.1824G>A	c.(1822-1824)GCG>GCA	p.A608A		NM_153270	NP_695002	Q8N239	KLH34_HUMAN	kelch-like 34	608	Kelch 6.									ovary(1)	1																		---	---	---	---
MAGEB6	158809	broad.mit.edu	37	X	26212473	26212473	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26212473C>T	uc004dbr.2	+	2	659	c.510C>T	c.(508-510)GCC>GCT	p.A170A	MAGEB6_uc010ngc.1_5'UTR	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	170										ovary(3)	3																		---	---	---	---
FAM47A	158724	broad.mit.edu	37	X	34149285	34149285	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34149285G>A	uc004ddg.2	-	1	1144	c.1111C>T	c.(1111-1113)CGG>TGG	p.R371W		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	371										ovary(4)|central_nervous_system(1)	5																		---	---	---	---
FAM47B	170062	broad.mit.edu	37	X	34962859	34962859	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34962859C>T	uc004ddi.1	+	1	1929	c.1911C>T	c.(1909-1911)GAC>GAT	p.D637D		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	637										ovary(3)|breast(1)	4																		---	---	---	---
USP9X	8239	broad.mit.edu	37	X	40996215	40996215	+	Silent	SNP	A	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40996215A>G	uc004dfb.2	+	6	1227	c.594A>G	c.(592-594)TCA>TCG	p.S198S	USP9X_uc004dfc.2_Silent_p.S198S	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	198					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6																		---	---	---	---
RGN	9104	broad.mit.edu	37	X	46943850	46943850	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46943850C>T	uc004dgz.1	+	4	1166	c.197C>T	c.(196-198)TCG>TTG	p.S66L	RGN_uc004dha.1_Missense_Mutation_p.S66L|RGN_uc010nho.1_Missense_Mutation_p.S13L|RGN_uc010nhp.1_Missense_Mutation_p.S66L	NM_152869	NP_690608	Q15493	RGN_HUMAN	regucalcin	66					cellular calcium ion homeostasis|positive regulation of ATPase activity|regulation of calcium-mediated signaling	cytoplasm|nucleus	calcium ion binding|enzyme regulator activity|gluconolactonase activity|zinc ion binding				0																		---	---	---	---
RBM10	8241	broad.mit.edu	37	X	47030582	47030582	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47030582G>T	uc004dhf.2	+	4	736	c.357G>T	c.(355-357)GAG>GAT	p.E119D	RBM10_uc004dhe.1_Missense_Mutation_p.E109D|RBM10_uc004dhg.2_Intron|RBM10_uc004dhh.2_Missense_Mutation_p.E119D|RBM10_uc010nhq.2_Intron|RBM10_uc004dhi.2_Missense_Mutation_p.E184D	NM_005676	NP_005667	P98175	RBM10_HUMAN	RNA binding motif protein 10 isoform 1	119	Poly-Glu.				mRNA processing|RNA splicing	chromatin remodeling complex	nucleotide binding|RNA binding|zinc ion binding			ovary(1)|large_intestine(1)|prostate(1)|breast(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	47658289	47658289	+	IGR	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47658289C>T								LOC100133957 (138513 upstream) : ZNF81 (38012 downstream)																																			---	---	---	---
SSX6	280657	broad.mit.edu	37	X	47969428	47969428	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47969428G>T	uc004dix.1	+	2	187	c.65G>T	c.(64-66)AGC>ATC	p.S22I	SSX6_uc011mlv.1_Missense_Mutation_p.S22I	NM_173357	NP_775493			SubName: Full=Putative uncharacterized protein SSX1;												0																		---	---	---	---
SSX5	6758	broad.mit.edu	37	X	48053565	48053565	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48053565C>A	uc004dja.1	-	4	333	c.280G>T	c.(280-282)GTT>TTT	p.V94F	SSX5_uc004diz.1_Missense_Mutation_p.V135F	NM_175723	NP_783729	O60225	SSX5_HUMAN	synovial sarcoma, X breakpoint 5 isoform b	94					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0																		---	---	---	---
SSX1	6756	broad.mit.edu	37	X	48123279	48123279	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48123279C>T	uc004djb.1	+	6	484	c.393C>T	c.(391-393)GGC>GGT	p.G131G		NM_005635	NP_005626	Q16384	SSX1_HUMAN	synovial sarcoma, X breakpoint 1	131					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|transcription corepressor activity		SS18/SSX1(1169)	soft_tissue(1169)	1169																		---	---	---	---
TBC1D25	4943	broad.mit.edu	37	X	48399811	48399811	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48399811C>T	uc004dka.1	+	2	325	c.214C>T	c.(214-216)CGA>TGA	p.R72*	TBC1D25_uc011mly.1_5'UTR|TBC1D25_uc004dkb.1_5'UTR|TBC1D25_uc011mlz.1_Intron|TBC1D25_uc011mma.1_5'UTR|TBC1D25_uc004dkc.1_5'UTR|TBC1D25_uc011mmb.1_Nonsense_Mutation_p.R76*|TBC1D25_uc011mmc.1_5'UTR|TBC1D25_uc011mmd.1_5'UTR	NM_002536	NP_002527	Q3MII6	TBC25_HUMAN	TBC1 domain family, member 25	72						intracellular	Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
PQBP1	10084	broad.mit.edu	37	X	48759706	48759706	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48759706C>T	uc004dle.2	+	5	678	c.489C>T	c.(487-489)CGC>CGT	p.R163R	PQBP1_uc004dlf.2_Silent_p.R163R|PQBP1_uc004dlg.2_Silent_p.R163R|PQBP1_uc004dld.2_Intron|PQBP1_uc004dlh.2_Silent_p.R163R|PQBP1_uc004dli.2_Silent_p.R163R|PQBP1_uc004dlj.1_Silent_p.R163R|PQBP1_uc004dln.2_Silent_p.R163R|PQBP1_uc010nih.2_RNA|PQBP1_uc010nii.2_Silent_p.R121R|PQBP1_uc004dlk.2_Intron|PQBP1_uc004dll.2_Intron|PQBP1_uc004dlm.2_Silent_p.R121R|PQBP1_uc010nij.2_Intron	NM_001032382	NP_001027554	O60828	PQBP1_HUMAN	polyglutamine binding protein 1	163	Arg-rich.|3-7.|7 X 2 AA tandem repeats of [DE]-R.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|transcription coactivator activity			large_intestine(1)	1																		---	---	---	---
SYP	6855	broad.mit.edu	37	X	49049793	49049793	+	Missense_Mutation	SNP	C	T	T	rs150959416		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49049793C>T	uc004dmz.1	-	5	567	c.551G>A	c.(550-552)CGC>CAC	p.R184H	SYP_uc011mmz.1_Missense_Mutation_p.R66H|SYP_uc004dna.1_Missense_Mutation_p.R178H	NM_003179	NP_003170	P08247	SYPH_HUMAN	synaptophysin	184	Vesicular (Potential).|MARVEL.				regulation of long-term neuronal synaptic plasticity|regulation of short-term neuronal synaptic plasticity|synaptic vesicle maturation|synaptic vesicle membrane organization	cell junction|integral to synaptic vesicle membrane|synaptosome	calcium ion binding|cholesterol binding|transporter activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(315;0.00016)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	49920814	49920814	+	IGR	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49920814C>T								CLCN5 (56922 upstream) : AKAP4 (34597 downstream)																																			---	---	---	---
SHROOM4	57477	broad.mit.edu	37	X	50341254	50341254	+	Intron	SNP	C	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50341254C>A	uc004dpe.2	-						SHROOM4_uc004dpd.3_Intron	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)																	---	---	---	---
GPR173	54328	broad.mit.edu	37	X	53106173	53106173	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53106173G>A	uc004dru.2	+	2	628	c.370G>A	c.(370-372)GCC>ACC	p.A124T		NM_018969	NP_061842	Q9NS66	GP173_HUMAN	G protein-coupled receptor 173	124	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1																		---	---	---	---
HUWE1	10075	broad.mit.edu	37	X	53587313	53587313	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53587313G>A	uc004dsp.2	-	56	7974	c.7572C>T	c.(7570-7572)GAC>GAT	p.D2524D	HUWE1_uc004dsn.2_Silent_p.D1348D	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	2524					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	53589102	53589102	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53589102C>T	uc004dsp.2	-	54	7710	c.7308G>A	c.(7306-7308)GAG>GAA	p.E2436E	HUWE1_uc004dsn.2_Silent_p.E1260E	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	2436	Asp-rich.|Glu-rich.				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																		---	---	---	---
MAGED2	10916	broad.mit.edu	37	X	54841883	54841883	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54841883G>A	uc004dtk.1	+	12	1683	c.1589G>A	c.(1588-1590)CGG>CAG	p.R530Q	MAGED2_uc004dtl.1_Missense_Mutation_p.R530Q|MAGED2_uc004dtm.1_Missense_Mutation_p.R445Q|MAGED2_uc010nkc.1_Intron|MAGED2_uc004dtn.1_Missense_Mutation_p.R530Q|MAGED2_uc004dto.1_Missense_Mutation_p.R504Q	NM_177433	NP_803182	Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	530										ovary(2)|breast(1)	3																		---	---	---	---
TRO	7216	broad.mit.edu	37	X	54957360	54957360	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54957360C>T	uc004dtq.2	+	12	4310	c.4203C>T	c.(4201-4203)AAC>AAT	p.N1401N	TRO_uc004dts.2_Intron|TRO_uc004dtr.2_Intron|TRO_uc004dtt.2_RNA|TRO_uc004dtu.2_RNA|TRO_uc004dtv.2_Intron|TRO_uc011mok.1_Silent_p.N932N|TRO_uc004dtw.2_Silent_p.N1004N|TRO_uc004dtx.2_Silent_p.N784N	NM_001039705	NP_001034794	Q12816	TROP_HUMAN	trophinin isoform 5	1401	60; approximate.|62 X 10 AA approximate tandem repeats.				embryo implantation|homophilic cell adhesion	integral to plasma membrane				ovary(1)	1																		---	---	---	---
USP51	158880	broad.mit.edu	37	X	55514444	55514444	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55514444C>G	uc004dun.1	-	2	1008	c.929G>C	c.(928-930)AGA>ACA	p.R310T	USP51_uc011moo.1_Intron	NM_201286	NP_958443	Q70EK9	UBP51_HUMAN	ubiquitin specific protease 51	310					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3																		---	---	---	---
OPHN1	4983	broad.mit.edu	37	X	67293039	67293039	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67293039G>A	uc004dww.3	-	20	2083	c.1789C>T	c.(1789-1791)CGA>TGA	p.R597*	OPHN1_uc011mpg.1_Nonsense_Mutation_p.R597*	NM_002547	NP_002538	O60890	OPHN1_HUMAN	oligophrenin 1	597					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																		---	---	---	---
NLGN3	54413	broad.mit.edu	37	X	70389754	70389754	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70389754G>A	uc004dzb.2	+	7	2598	c.2294G>A	c.(2293-2295)CGC>CAC	p.R765H	NLGN3_uc004dzc.2_Missense_Mutation_p.R648H|NLGN3_uc011mps.1_Missense_Mutation_p.R745H|NLGN3_uc004dze.2_Missense_Mutation_p.R583H	NM_018977	NP_061850	Q9NZ94	NLGN3_HUMAN	neuroligin 3	785	Cytoplasmic (Potential).				neuron cell-cell adhesion|positive regulation of synaptogenesis|receptor-mediated endocytosis|social behavior|synapse assembly	cell surface|endocytic vesicle|integral to plasma membrane|synapse	neurexin binding|receptor activity			ovary(1)	1	Renal(35;0.156)																	---	---	---	---
ACRC	93953	broad.mit.edu	37	X	70823624	70823624	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70823624C>T	uc004eae.2	+	8	998	c.497C>T	c.(496-498)TCG>TTG	p.S166L	BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	166	Asp/Ser-rich.					nucleus				ovary(3)	3	Renal(35;0.156)																	---	---	---	---
HDAC8	55869	broad.mit.edu	37	X	71681927	71681927	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71681927G>A	uc004eau.2	-	9	974	c.932C>T	c.(931-933)ACG>ATG	p.T311M	HDAC8_uc011mqe.1_Missense_Mutation_p.T168M|HDAC8_uc011mqf.1_Missense_Mutation_p.T116M|HDAC8_uc011mqg.1_Missense_Mutation_p.T220M	NM_018486	NP_060956	Q9BY41	HDAC8_HUMAN	histone deacetylase 8	311	Histone deacetylase.				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)													---	---	---	---
XIST	7503	broad.mit.edu	37	X	73065310	73065310	+	RNA	SNP	A	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73065310A>T	uc004ebm.1	-	1		c.7279T>A				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0																		---	---	---	---
ZCCHC13	389874	broad.mit.edu	37	X	73524363	73524363	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73524363C>T	uc004ebs.3	+	1	339	c.262C>T	c.(262-264)CGC>TGC	p.R88C		NM_203303	NP_976048	Q8WW36	ZCH13_HUMAN	zinc finger, CCHC domain containing 13	88							nucleic acid binding|zinc ion binding				0																		---	---	---	---
KIAA2022	340533	broad.mit.edu	37	X	73961202	73961202	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73961202G>A	uc004eby.2	-	3	3807	c.3190C>T	c.(3190-3192)CGC>TGC	p.R1064C		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	1064					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15																		---	---	---	---
MAGEE1	57692	broad.mit.edu	37	X	75650737	75650737	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75650737T>G	uc004ecm.1	+	1	2621	c.2414T>G	c.(2413-2415)CTT>CGT	p.L805R		NM_020932	NP_065983	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	805	Interaction with DTNA (By similarity).|MAGE 2.					dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane				breast(3)|ovary(1)|pancreas(1)|skin(1)	6																		---	---	---	---
TBX22	50945	broad.mit.edu	37	X	79279656	79279656	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79279656C>T	uc010nmg.1	+	4	585	c.451C>T	c.(451-453)CGC>TGC	p.R151C	TBX22_uc004edi.1_Missense_Mutation_p.R31C|TBX22_uc004edj.1_Missense_Mutation_p.R151C	NM_001109878	NP_001103348	Q9Y458	TBX22_HUMAN	T-box 22 isoform 1	151	T-box.				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	79980463	79980463	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79980463C>T	uc004edt.2	-	15	1753	c.1490G>A	c.(1489-1491)CGG>CAG	p.R497Q	BRWD3_uc004edo.2_Missense_Mutation_p.R93Q|BRWD3_uc004edp.2_Missense_Mutation_p.R326Q|BRWD3_uc004edq.2_Missense_Mutation_p.R93Q|BRWD3_uc010nmj.1_Missense_Mutation_p.R93Q|BRWD3_uc004edr.2_Missense_Mutation_p.R167Q|BRWD3_uc004eds.2_Missense_Mutation_p.R93Q|BRWD3_uc004edu.2_Missense_Mutation_p.R167Q|BRWD3_uc004edv.2_Missense_Mutation_p.R93Q|BRWD3_uc004edw.2_Missense_Mutation_p.R93Q|BRWD3_uc004edx.2_Missense_Mutation_p.R93Q|BRWD3_uc004edy.2_Missense_Mutation_p.R93Q|BRWD3_uc004edz.2_Missense_Mutation_p.R167Q|BRWD3_uc004eea.2_Missense_Mutation_p.R167Q|BRWD3_uc004eeb.2_Missense_Mutation_p.R93Q	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	497	WD 8.									ovary(4)	4																		---	---	---	---
POU3F4	5456	broad.mit.edu	37	X	82764299	82764299	+	Missense_Mutation	SNP	C	T	T	rs104894924		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82764299C>T	uc004eeg.2	+	1	1031	c.967C>T	c.(967-969)CGT>TGT	p.R323C		NM_000307	NP_000298	P49335	PO3F4_HUMAN	POU domain, class 3, transcription factor 4	323	Homeobox.		R -> G (in DFNX2; somatic mosaicism in 50% of the peripheral blood lymphocytes).		sensory perception of sound	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
NAP1L3	4675	broad.mit.edu	37	X	92927271	92927271	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:92927271G>T	uc004efq.2	-	1	1338	c.1033C>A	c.(1033-1035)CTG>ATG	p.L345M	FAM133A_uc004efr.1_5'Flank	NM_004538	NP_004529	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	345					nucleosome assembly	chromatin assembly complex				ovary(1)|skin(1)	2																		---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96854260	96854260	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96854260C>T	uc004efu.3	+	27	3646	c.3250C>T	c.(3250-3252)CGA>TGA	p.R1084*		NM_006729	NP_006720	O60879	DIAP2_HUMAN	diaphanous 2 isoform 156	1084					cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4																		---	---	---	---
PCDH19	57526	broad.mit.edu	37	X	99551449	99551449	+	Silent	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99551449G>T	uc010nmz.2	-	6	4949	c.3273C>A	c.(3271-3273)GCC>GCA	p.A1091A	PCDH19_uc004efw.3_Silent_p.A1043A|PCDH19_uc004efx.3_Silent_p.A1044A	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b	1091	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7																		---	---	---	---
XKRX	402415	broad.mit.edu	37	X	100169452	100169452	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100169452G>A	uc004egn.2	-	3	1830	c.1225C>T	c.(1225-1227)CGC>TGC	p.R409C	XKRX_uc011mre.1_Missense_Mutation_p.R205C	NM_212559	NP_997724	Q6PP77	XKR2_HUMAN	XK, Kell blood group complex subunit-related,	409						integral to membrane|plasma membrane				breast(1)	1																		---	---	---	---
CENPI	2491	broad.mit.edu	37	X	100387216	100387216	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100387216G>A	uc004egx.2	+	13	1595	c.1325G>A	c.(1324-1326)AGC>AAC	p.S442N	CENPI_uc011mrg.1_Missense_Mutation_p.S442N|CENPI_uc004egy.2_Missense_Mutation_p.S442N	NM_006733	NP_006724	Q92674	CENPI_HUMAN	centromere protein I	442					CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			skin(1)	1																		---	---	---	---
HNRNPH2	3188	broad.mit.edu	37	X	100667790	100667790	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100667790T>G	uc004ehm.2	+	2	984	c.814T>G	c.(814-816)TCT>GCT	p.S272A	HNRNPH2_uc004ehn.2_Missense_Mutation_p.S272A	NM_019597	NP_062543	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2	272	2 X 16 AA Gly-rich approximate repeats.				nuclear mRNA splicing, via spliceosome	actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
NXF5	55998	broad.mit.edu	37	X	101095488	101095488	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101095488G>A	uc011mrk.1	-	10	1041	c.681C>T	c.(679-681)GAC>GAT	p.D227D	NXF5_uc004eih.1_RNA|NXF5_uc004eii.1_RNA|NXF5_uc004eij.1_RNA|NXF5_uc004eik.1_RNA|NXF5_uc004eil.1_RNA	NM_032946	NP_116564	Q9H1B4	NXF5_HUMAN	nuclear RNA export factor 5	227	LRR 3.				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	101138866	101138866	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101138866G>A	uc004eim.2	-	2	4518	c.1020C>T	c.(1018-1020)TAC>TAT	p.Y340Y	ZMAT1_uc011mrl.1_Silent_p.Y511Y|ZMAT1_uc004ein.2_Silent_p.Y340Y|ZMAT1_uc011mrm.1_Silent_p.Y340Y	NM_032441	NP_115817	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin type 1 isoform 3	340						nucleus	zinc ion binding			ovary(1)	1																		---	---	---	---
FAM199X	139231	broad.mit.edu	37	X	103434329	103434329	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103434329G>A	uc004elw.2	+	6	1203	c.1037G>A	c.(1036-1038)CGC>CAC	p.R346H	FAM199X_uc004elx.2_Missense_Mutation_p.R120H	NM_207318	NP_997201	Q6PEV8	F199X_HUMAN	hypothetical protein LOC139231	346										ovary(1)	1																		---	---	---	---
NRK	203447	broad.mit.edu	37	X	105153047	105153047	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105153047C>T	uc004emd.2	+	13	1717	c.1414C>T	c.(1414-1416)CGG>TGG	p.R472W	NRK_uc010npc.1_Missense_Mutation_p.R140W	NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase	472	Gln-rich.						ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14															HNSCC(51;0.14)			---	---	---	---
CXorf57	55086	broad.mit.edu	37	X	105865880	105865880	+	Splice_Site	SNP	G	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105865880G>C	uc004emi.3	+	2	795	c.644_splice	c.e2-1	p.D215_splice	CXorf57_uc004emj.3_Splice_Site_p.D215_splice|CXorf57_uc004emh.2_Splice_Site_p.D215_splice	NM_018015	NP_060485			hypothetical protein LOC55086											ovary(1)|lung(1)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	106844964	106844964	+	IGR	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106844964C>T								CXorf41 (357492 upstream) : PRPS1 (26690 downstream)																																			---	---	---	---
IRS4	8471	broad.mit.edu	37	X	107978724	107978724	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107978724C>T	uc004eoc.2	-	1	884	c.851G>A	c.(850-852)CGC>CAC	p.R284H		NM_003604	NP_003595	O14654	IRS4_HUMAN	insulin receptor substrate 4	284	IRS-type PTB.					plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			ovary(4)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	10																		---	---	---	---
CHRDL1	91851	broad.mit.edu	37	X	109964646	109964646	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109964646C>T	uc004eou.3	-	5	763	c.414G>A	c.(412-414)CGG>CGA	p.R138R	CHRDL1_uc004eov.2_Silent_p.R132R|CHRDL1_uc004eow.2_Silent_p.R137R|CHRDL1_uc010nps.2_Silent_p.R137R|CHRDL1_uc004eot.2_Intron|CHRDL1_uc011mss.1_Intron|CHRDL1_uc004eox.3_Silent_p.R131R	NM_001143981	NP_001137453	Q9BU40	CRDL1_HUMAN	chordin-like 1 isoform 1 precursor	131	VWFC 2.				BMP signaling pathway|cell differentiation|nervous system development|ossification	extracellular region					0																		---	---	---	---
ALG13	79868	broad.mit.edu	37	X	110954936	110954936	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110954936C>T	uc011msy.1	+	6	902	c.868C>T	c.(868-870)CGG>TGG	p.R290W	ALG13_uc011msw.1_Missense_Mutation_p.R212W|ALG13_uc011msx.1_Missense_Mutation_p.R186W|ALG13_uc011msz.1_Missense_Mutation_p.R212W|ALG13_uc011mta.1_Missense_Mutation_p.R186W|ALG13_uc011mtb.1_Missense_Mutation_p.R186W			Q9NP73	ALG13_HUMAN	SubName: Full=Asparagine-linked glycosylation 13 homolog (S. cerevisiae);	290	OTU.				dolichol-linked oligosaccharide biosynthetic process|lipid glycosylation|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane	carbohydrate binding|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity			lung(1)	1																		---	---	---	---
TRPC5	7224	broad.mit.edu	37	X	111090440	111090440	+	Silent	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111090440T>C	uc004epl.1	-	6	2521	c.1602A>G	c.(1600-1602)GGA>GGG	p.G534G	TRPC5_uc004epm.1_Silent_p.G534G	NM_012471	NP_036603	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel,	534	Extracellular (Potential).				axon guidance	calcium channel complex|integral to plasma membrane	protein binding|store-operated calcium channel activity			urinary_tract(1)	1																		---	---	---	---
HTR2C	3358	broad.mit.edu	37	X	113965896	113965896	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113965896G>T	uc004epu.1	+	4	957	c.229G>T	c.(229-231)GCA>TCA	p.A77S	HTR2C_uc010nqc.1_Missense_Mutation_p.A77S|HTR2C_uc004epv.1_Missense_Mutation_p.A77S	NM_000868	NP_000859	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C	77	Helical; Name=1; (By similarity).				cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)													---	---	---	---
LRCH2	57631	broad.mit.edu	37	X	114419019	114419019	+	Silent	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114419019T>A	uc010nqe.2	-	3	607	c.576A>T	c.(574-576)GTA>GTT	p.V192V	LRCH2_uc004epz.2_Silent_p.V192V	NM_020871	NP_065922	Q5VUJ6	LRCH2_HUMAN	leucine-rich repeats and calponin homology (CH)	192	LRR 5.									ovary(1)	1																		---	---	---	---
LRCH2	57631	broad.mit.edu	37	X	114422934	114422934	+	Splice_Site	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114422934C>T	uc010nqe.2	-	2	381	c.350_splice	c.e2-1	p.D117_splice	LRCH2_uc004epz.2_Splice_Site_p.D117_splice|RBMXL3_uc011mte.1_5'Flank	NM_020871	NP_065922			leucine-rich repeats and calponin homology (CH)											ovary(1)	1																		---	---	---	---
FAM70A	55026	broad.mit.edu	37	X	119419025	119419025	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119419025G>A	uc004eso.3	-	7	768	c.541C>T	c.(541-543)CGG>TGG	p.R181W	FAM70A_uc004esp.3_Missense_Mutation_p.R157W|FAM70A_uc010nqo.2_Intron	NM_017938	NP_060408	Q5JRV8	FA70A_HUMAN	hypothetical protein LOC55026 isoform 1	181						integral to membrane				lung(1)|breast(1)	2																		---	---	---	---
SASH3	54440	broad.mit.edu	37	X	128924995	128924995	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128924995C>T	uc011mun.1	+	4	562	c.380C>T	c.(379-381)GCG>GTG	p.A127V	SASH3_uc004euu.2_Missense_Mutation_p.A127V|SASH3_uc011muo.1_Missense_Mutation_p.A44V	NM_018990	NP_061863	O75995	SASH3_HUMAN	SAM and SH3 domain containing 3	127										ovary(2)|pancreas(1)	3																		---	---	---	---
ARHGAP36	158763	broad.mit.edu	37	X	130222706	130222706	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130222706C>T	uc004evz.2	+	12	1936	c.1591C>T	c.(1591-1593)CGT>TGT	p.R531C	ARHGAP36_uc004ewa.2_Missense_Mutation_p.R519C|ARHGAP36_uc004ewb.2_Missense_Mutation_p.R500C|ARHGAP36_uc004ewc.2_Missense_Mutation_p.R395C	NM_144967	NP_659404	Q6ZRI8	RHG36_HUMAN	hypothetical protein LOC158763 precursor	531					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3																		---	---	---	---
GPC4	2239	broad.mit.edu	37	X	132445391	132445391	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132445391G>A	uc004exc.1	-	4	984	c.772C>T	c.(772-774)CGG>TGG	p.R258W	GPC4_uc011mvg.1_Missense_Mutation_p.R188W	NM_001448	NP_001439	O75487	GPC4_HUMAN	glypican 4 precursor	258					anatomical structure morphogenesis|cell proliferation	anchored to membrane|external side of plasma membrane|extracellular space|insoluble fraction|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MIR450B	100126302	broad.mit.edu	37	X	133674535	133674535	+	5'Flank	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133674535T>C	hsa-mir-450b|MI0005531	-						MIR450A1_hsa-mir-450a-1|MI0001652_5'Flank|uc011mvl.1_5'Flank																	0																		---	---	---	---
MIR542	664617	broad.mit.edu	37	X	133675434	133675434	+	RNA	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133675434G>A	hsa-mir-542|MI0003686	-			c.34G>A			MIR450B_hsa-mir-450b|MI0005531_5'Flank|MIR450A1_hsa-mir-450a-1|MI0001652_5'Flank|uc011mvl.1_5'Flank|MIR450A2_hsa-mir-450a-2|MI0003187_5'Flank																	0																		---	---	---	---
FAM127A	8933	broad.mit.edu	37	X	134166473	134166473	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134166473G>A	uc004eyd.2	+	1	141	c.60G>A	c.(58-60)ACG>ACA	p.T20T	uc004eye.1_RNA	NM_001078171	NP_001071639	A6ZKI3	F127A_HUMAN	family with sequence similarity 127, member A	20											0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
FAM127B	26071	broad.mit.edu	37	X	134185793	134185793	+	3'UTR	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134185793C>T	uc004eyf.2	-	1					FAM127B_uc004eyg.3_Intron	NM_001078172	NP_001071640			family with sequence similarity 127, member B												0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
SAGE1	55511	broad.mit.edu	37	X	134989148	134989148	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134989148A>C	uc004ezh.2	+	8	967	c.800A>C	c.(799-801)AAC>ACC	p.N267T	SAGE1_uc010nry.1_Missense_Mutation_p.N236T|SAGE1_uc011mvv.1_Intron	NM_018666	NP_061136	Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	267										ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MMGT1	93380	broad.mit.edu	37	X	135047268	135047268	+	Missense_Mutation	SNP	G	A	A	rs150859420		TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135047268G>A	uc004ezi.1	-	4	611	c.311C>T	c.(310-312)TCG>TTG	p.S104L	MMGT1_uc011mvw.1_Missense_Mutation_p.S169L	NM_173470	NP_775741	Q8N4V1	MMGT1_HUMAN	membrane magnesium transporter 1 precursor	104	Cytoplasmic (Potential).					early endosome membrane|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	magnesium ion transmembrane transporter activity				0																		---	---	---	---
GPR112	139378	broad.mit.edu	37	X	135469892	135469892	+	Intron	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135469892T>G	uc004ezu.1	+						GPR112_uc010nsb.1_Intron	NM_153834	NP_722576			G-protein coupled receptor 112						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)																	---	---	---	---
ARHGEF6	9459	broad.mit.edu	37	X	135751673	135751673	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135751673C>T	uc004fab.2	-	21	2620	c.2158G>A	c.(2158-2160)GCC>ACC	p.A720T	ARHGEF6_uc011mwd.1_Missense_Mutation_p.A593T|ARHGEF6_uc011mwe.1_Missense_Mutation_p.A566T	NM_004840	NP_004831	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor 6	720					apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
FGF13	2258	broad.mit.edu	37	X	137793063	137793063	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137793063T>C	uc004fam.2	-	1	765	c.103A>G	c.(103-105)AAG>GAG	p.K35E	FGF13_uc004fan.2_Intron|FGF13_uc011mwi.1_Intron|FGF13_uc004faq.2_Intron|FGF13_uc004far.2_Intron|FGF13_uc011mwj.1_Intron|FGF13_uc011mwk.1_Intron|uc004fao.2_5'Flank	NM_004114	NP_004105	Q92913	FGF13_HUMAN	fibroblast growth factor 13 isoform 1	35					cell-cell signaling|MAPKKK cascade|nervous system development	cytoplasm|nucleus	growth factor activity|protein kinase activator activity			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
SPANXC	64663	broad.mit.edu	37	X	140335784	140335784	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140335784G>A	uc004fbk.2	-	2	216	c.160C>T	c.(160-162)CGC>TGC	p.R54C	SPANXC_uc004fbl.2_RNA	NM_022661	NP_073152	Q9NY87	SPNXC_HUMAN	sperm protein associated with the nucleus, X	54						cytoplasm|nucleus					0	Acute lymphoblastic leukemia(192;7.65e-05)																	---	---	---	---
MAGEC1	9947	broad.mit.edu	37	X	140994946	140994946	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140994946G>T	uc004fbt.2	+	4	2042	c.1756G>T	c.(1756-1758)GGG>TGG	p.G586W	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	586							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)														HNSCC(15;0.026)			---	---	---	---
SPANXN3	139067	broad.mit.edu	37	X	142605183	142605183	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142605183T>A	uc004fbw.2	-	1	125	c.37A>T	c.(37-39)ACG>TCG	p.T13S		NM_001009609	NP_001009609	Q5MJ09	SPXN3_HUMAN	SPANX-N3 protein	13										ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
CXorf1	9142	broad.mit.edu	37	X	144909328	144909328	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144909328T>G	uc004fch.2	+	1	401	c.133T>G	c.(133-135)TTA>GTA	p.L45V		NM_004709	NP_004700	O96002	CX001_HUMAN	hypothetical protein LOC9142	45											0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
ZNF275	10838	broad.mit.edu	37	X	152613196	152613196	+	Intron	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152613196C>T	uc004fhg.1	+						ZNF275_uc011mym.1_Silent_p.C351C|ZNF275_uc011myn.1_Silent_p.C288C					SubName: Full=cDNA FLJ16723 fis, clone UTERU3004418, highly similar to Zinc finger protein 275; SubName: Full=Putative uncharacterized protein ZNF275;							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
ATP2B3	492	broad.mit.edu	37	X	152813442	152813442	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152813442C>T	uc004fht.1	+	7	1234	c.1108C>T	c.(1108-1110)CAG>TAG	p.Q370*	ATP2B3_uc004fhs.1_Nonsense_Mutation_p.Q370*	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	370	Helical; (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
FAM58A	92002	broad.mit.edu	37	X	152860096	152860096	+	Missense_Mutation	SNP	C	T	T	rs150562029	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152860096C>T	uc010nug.2	-	2	255	c.152G>A	c.(151-153)CGC>CAC	p.R51H				Q8N1B3	FA58A_HUMAN	RecName: Full=Cyclin-related protein FAM58B;	113					regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent		protein kinase binding				0	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
SRPK3	26576	broad.mit.edu	37	X	153047269	153047269	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153047269T>A	uc004fil.2	+	4	403	c.371T>A	c.(370-372)ATC>AAC	p.I124N	SRPK3_uc004fik.2_Missense_Mutation_p.I190N|SRPK3_uc010nul.2_Missense_Mutation_p.I82N|SRPK3_uc004fin.2_Missense_Mutation_p.I124N|SRPK3_uc004fim.2_Missense_Mutation_p.I124N	NM_014370	NP_055185	Q9UPE1	SRPK3_HUMAN	serine arginine rich protein-specific kinase 3	124	Protein kinase.				cell differentiation|muscle organ development|muscle tissue development		ATP binding|protein serine/threonine kinase activity			pancreas(2)|lung(1)	3	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
L1CAM	3897	broad.mit.edu	37	X	153128277	153128277	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153128277G>A	uc004fjb.2	-	28	3723	c.3615C>T	c.(3613-3615)GAC>GAT	p.D1205D	L1CAM_uc004fjc.2_Silent_p.D1201D|L1CAM_uc010nuo.2_Silent_p.D1196D	NM_000425	NP_000416	P32004	L1CAM_HUMAN	L1 cell adhesion molecule isoform 1 precursor	1205	Cytoplasmic (Potential).				axon guidance|blood coagulation|cell death|leukocyte migration	integral to membrane				ovary(8)|central_nervous_system(1)	9	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
RENBP	5973	broad.mit.edu	37	X	153207102	153207102	+	Silent	SNP	G	A	A			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153207102G>A	uc004fjo.1	-	8	944	c.774C>T	c.(772-774)CAC>CAT	p.H258H	RENBP_uc011mzh.1_Missense_Mutation_p.T231I	NM_002910	NP_002901	P51606	RENBP_HUMAN	renin binding protein	258					mannose metabolic process|regulation of blood pressure		endopeptidase inhibitor activity|mannose-6-phosphate isomerase activity|N-acylglucosamine 2-epimerase activity			ovary(1)|pancreas(1)	2	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
FLNA	2316	broad.mit.edu	37	X	153581719	153581719	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153581719C>T	uc004fkk.2	-	37	6216	c.5967G>A	c.(5965-5967)CCG>CCA	p.P1989P	FLNA_uc004fki.2_Silent_p.P32P|FLNA_uc011mzn.1_Silent_p.P122P|FLNA_uc010nuu.1_Silent_p.P1981P	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1989	Filamin 18.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
GDI1	2664	broad.mit.edu	37	X	153669509	153669509	+	Silent	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153669509C>T	uc004fli.3	+	7	1128	c.786C>T	c.(784-786)AAC>AAT	p.N262N	GDI1_uc011mzo.1_3'UTR|GDI1_uc004flj.2_5'Flank|FAM50A_uc004fll.3_5'Flank	NM_001493	NP_001484	P31150	GDIA_HUMAN	GDP dissociation inhibitor 1	262					protein transport|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|midbody	GTPase activator activity|protein binding				0	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
FAM50A	9130	broad.mit.edu	37	X	153678623	153678623	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153678623C>T	uc004fll.3	+	12	1065	c.967C>T	c.(967-969)CGC>TGC	p.R323C		NM_004699	NP_004690	Q14320	FA50A_HUMAN	XAP-5 protein	323					spermatogenesis	nucleus				ovary(1)	1	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
PLXNA3	55558	broad.mit.edu	37	X	153689602	153689602	+	Missense_Mutation	SNP	C	T	T	rs147390702	byFrequency	TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153689602C>T	uc004flm.2	+	3	931	c.758C>T	c.(757-759)GCG>GTG	p.A253V		NM_017514	NP_059984	P51805	PLXA3_HUMAN	plexin A3 precursor	253	Sema.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
LAGE3	8270	broad.mit.edu	37	X	153706395	153706395	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153706395C>T	uc004fln.1	-	3	662	c.320G>A	c.(319-321)CGC>CAC	p.R107H		NM_006014	NP_006005	Q14657	LAGE3_HUMAN	L antigen family, member 3	107							protein binding				0	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
RAB39B	116442	broad.mit.edu	37	X	154490449	154490449	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4292-01	TCGA-BR-4292-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154490449C>T	uc004fne.2	-	2	560	c.281G>A	c.(280-282)CGC>CAC	p.R94H		NM_171998	NP_741995	Q96DA2	RB39B_HUMAN	RAB39B, member RAS oncogene family	94					protein transport|small GTPase mediated signal transduction|synapse organization|vesicle-mediated transport	Golgi apparatus|plasma membrane	GTP 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)																	---	---	---	---
